---
_id: '12672'
abstract:
- lang: eng
text: Cytosine methylation within CG dinucleotides (mCG) can be epigenetically inherited
over many generations. Such inheritance is thought to be mediated by a semiconservative
mechanism that produces binary present/absent methylation patterns. However, we
show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic
mCG is stably inherited across many generations and is quantitatively associated
with transposon expression. We develop a mathematical model that estimates the
rates of semiconservative maintenance failure and de novo methylation at each
transposon, demonstrating that mCG can be stably inherited at any level via a
dynamic balance of these activities. We find that DRM2 – the core methyltransferase
of the RNA-directed DNA methylation pathway – catalyzes most of the heterochromatic
de novo mCG, with de novo rates orders of magnitude higher than previously thought,
whereas chromomethylases make smaller contributions. Our results demonstrate that
stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive
de novo methylation.
acknowledgement: The authors would like to thank Jasper Rine for advice and mentorship
to D.B.L., Lesley Philips, Timothy Wells, Sophie Able, and Christina Wistrom for
support with plant growth, and Bhagyshree Jamge and Frédéric Berger for help with
analysis of ddm1 × WT RNA-sequencing data. This work was supported by BBSRC Institute
Strategic Program GEN (BB/P013511/1) to X.F., M.H., and D.Z., a European Research
Council grant MaintainMeth (725746) to D.Z., and a postdoctoral fellowship from
the Helen Hay Whitney Foundation to D.B.L.
article_number: '112132'
article_processing_charge: Yes
article_type: original
author:
- first_name: David B.
full_name: Lyons, David B.
last_name: Lyons
- first_name: Amy
full_name: Briffa, Amy
last_name: Briffa
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Jaemyung
full_name: Choi, Jaemyung
last_name: Choi
- first_name: Elizabeth
full_name: Hollwey, Elizabeth
id: b8c4f54b-e484-11eb-8fdc-a54df64ef6dd
last_name: Hollwey
- first_name: Jack
full_name: Colicchio, Jack
last_name: Colicchio
- first_name: Ian
full_name: Anderson, Ian
last_name: Anderson
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Martin
full_name: Howard, Martin
last_name: Howard
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Lyons DB, Briffa A, He S, et al. Extensive de novo activity stabilizes epigenetic
inheritance of CG methylation in Arabidopsis transposons. Cell Reports.
2023;42(3). doi:10.1016/j.celrep.2023.112132
apa: Lyons, D. B., Briffa, A., He, S., Choi, J., Hollwey, E., Colicchio, J., … Zilberman,
D. (2023). Extensive de novo activity stabilizes epigenetic inheritance of CG
methylation in Arabidopsis transposons. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.112132
chicago: Lyons, David B., Amy Briffa, Shengbo He, Jaemyung Choi, Elizabeth Hollwey,
Jack Colicchio, Ian Anderson, Xiaoqi Feng, Martin Howard, and Daniel Zilberman.
“Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation
in Arabidopsis Transposons.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.112132.
ieee: D. B. Lyons et al., “Extensive de novo activity stabilizes epigenetic
inheritance of CG methylation in Arabidopsis transposons,” Cell Reports,
vol. 42, no. 3. Elsevier, 2023.
ista: Lyons DB, Briffa A, He S, Choi J, Hollwey E, Colicchio J, Anderson I, Feng
X, Howard M, Zilberman D. 2023. Extensive de novo activity stabilizes epigenetic
inheritance of CG methylation in Arabidopsis transposons. Cell Reports. 42(3),
112132.
mla: Lyons, David B., et al. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance
of CG Methylation in Arabidopsis Transposons.” Cell Reports, vol. 42, no.
3, 112132, Elsevier, 2023, doi:10.1016/j.celrep.2023.112132.
short: D.B. Lyons, A. Briffa, S. He, J. Choi, E. Hollwey, J. Colicchio, I. Anderson,
X. Feng, M. Howard, D. Zilberman, Cell Reports 42 (2023).
date_created: 2023-02-23T09:17:44Z
date_published: 2023-03-28T00:00:00Z
date_updated: 2023-11-02T12:23:45Z
day: '28'
ddc:
- '580'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1016/j.celrep.2023.112132
ec_funded: 1
external_id:
isi:
- '000944921600001'
file:
- access_level: open_access
checksum: 6cbc44fdb18bf18834c9e2a5b9c67123
content_type: application/pdf
creator: kschuh
date_created: 2023-05-11T10:41:42Z
date_updated: 2023-05-11T10:41:42Z
file_id: '12941'
file_name: 2023_CellReports_Lyons.pdf
file_size: 8401261
relation: main_file
success: 1
file_date_updated: 2023-05-11T10:41:42Z
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 62935a00-2b32-11ec-9570-eff30fa39068
call_identifier: H2020
grant_number: '725746'
name: Quantitative analysis of DNA methylation maintenance with chromatin
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extensive de novo activity stabilizes epigenetic inheritance of CG methylation
in Arabidopsis transposons
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2023'
...
---
_id: '14551'
abstract:
- lang: eng
text: Methylation of CG dinucleotides (mCGs), which regulates eukaryotic genome
functions, is epigenetically propagated by Dnmt1/MET1 methyltransferases. How
mCG is established and transmitted across generations despite imperfect enzyme
fidelity is unclear. Whether mCG variation in natural populations is governed
by genetic or epigenetic inheritance also remains mysterious. Here, we show that
MET1 de novo activity, which is enhanced by existing proximate methylation, seeds
and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is restricted
by active demethylation and suppressed by histone variant H2A.Z, producing localized
mCG patterns. Based on these observations, we develop a stochastic mathematical
model that precisely recapitulates mCG inheritance dynamics and predicts intragenic
mCG patterns and their population-scale variation given only CG site spacing.
Our results demonstrate that intragenic mCG establishment, inheritance, and variance
constitute a unified epigenetic process, revealing that intragenic mCG undergoes
large, millennia-long epigenetic fluctuations and can therefore mediate evolution
on this timescale.
acknowledgement: We would like to thank Xiaoqi Feng, Ander Movilla Miangolarra, and
Suzanne de Bruijn for discussions. This work was supported by BBSRC Institute Strategic
Programme GEN (BB/P013511/1) to M.H. and D.Z. and by a European Research Council
grant MaintainMeth (725746) to D.Z.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Amy
full_name: Briffa, Amy
last_name: Briffa
- first_name: Elizabeth
full_name: Hollwey, Elizabeth
id: b8c4f54b-e484-11eb-8fdc-a54df64ef6dd
last_name: Hollwey
- first_name: Zaigham
full_name: Shahzad, Zaigham
last_name: Shahzad
- first_name: Jonathan D.
full_name: Moore, Jonathan D.
last_name: Moore
- first_name: David B.
full_name: Lyons, David B.
last_name: Lyons
- first_name: Martin
full_name: Howard, Martin
last_name: Howard
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Briffa A, Hollwey E, Shahzad Z, et al. Millennia-long epigenetic fluctuations
generate intragenic DNA methylation variance in Arabidopsis populations. Cell
Systems. 2023;14(11):953-967. doi:10.1016/j.cels.2023.10.007
apa: Briffa, A., Hollwey, E., Shahzad, Z., Moore, J. D., Lyons, D. B., Howard, M.,
& Zilberman, D. (2023). Millennia-long epigenetic fluctuations generate intragenic
DNA methylation variance in Arabidopsis populations. Cell Systems. Elsevier.
https://doi.org/10.1016/j.cels.2023.10.007
chicago: Briffa, Amy, Elizabeth Hollwey, Zaigham Shahzad, Jonathan D. Moore, David
B. Lyons, Martin Howard, and Daniel Zilberman. “Millennia-Long Epigenetic Fluctuations
Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.” Cell
Systems. Elsevier, 2023. https://doi.org/10.1016/j.cels.2023.10.007.
ieee: A. Briffa et al., “Millennia-long epigenetic fluctuations generate
intragenic DNA methylation variance in Arabidopsis populations,” Cell Systems,
vol. 14, no. 11. Elsevier, pp. 953–967, 2023.
ista: Briffa A, Hollwey E, Shahzad Z, Moore JD, Lyons DB, Howard M, Zilberman D.
2023. Millennia-long epigenetic fluctuations generate intragenic DNA methylation
variance in Arabidopsis populations. Cell Systems. 14(11), 953–967.
mla: Briffa, Amy, et al. “Millennia-Long Epigenetic Fluctuations Generate Intragenic
DNA Methylation Variance in Arabidopsis Populations.” Cell Systems, vol.
14, no. 11, Elsevier, 2023, pp. 953–67, doi:10.1016/j.cels.2023.10.007.
short: A. Briffa, E. Hollwey, Z. Shahzad, J.D. Moore, D.B. Lyons, M. Howard, D.
Zilberman, Cell Systems 14 (2023) 953–967.
date_created: 2023-11-19T23:00:54Z
date_published: 2023-11-15T00:00:00Z
date_updated: 2023-11-20T11:24:34Z
day: '15'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1016/j.cels.2023.10.007
ec_funded: 1
external_id:
pmid:
- '37944515'
file:
- access_level: open_access
checksum: 101fdac59e6f1102d68ef91f2b5bd51a
content_type: application/pdf
creator: dernst
date_created: 2023-11-20T11:22:52Z
date_updated: 2023-11-20T11:22:52Z
file_id: '14580'
file_name: 2023_CellSystems_Briffa.pdf
file_size: 5587897
relation: main_file
success: 1
file_date_updated: 2023-11-20T11:22:52Z
has_accepted_license: '1'
intvolume: ' 14'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 953-967
pmid: 1
project:
- _id: 62935a00-2b32-11ec-9570-eff30fa39068
call_identifier: H2020
grant_number: '725746'
name: Quantitative analysis of DNA methylation maintenance with chromatin
publication: Cell Systems
publication_identifier:
eissn:
- 2405-4720
issn:
- 2405-4712
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Millennia-long epigenetic fluctuations generate intragenic DNA methylation
variance in Arabidopsis populations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '13965'
abstract:
- lang: eng
text: Many modes and mechanisms of epigenetic inheritance have been elucidated in
eukaryotes. Most of them are relatively short-term, generally not exceeding one
or a few organismal generations. However, emerging evidence indicates that one
mechanism, cytosine DNA methylation, can mediate epigenetic inheritance over much
longer timescales, which are mostly or completely inaccessible in the laboratory.
Here we discuss the evidence for, and mechanisms and implications of, such long-term
epigenetic inheritance. We argue that compelling evidence supports the long-term
epigenetic inheritance of gene body methylation, at least in the model angiosperm
Arabidopsis thaliana, and that variation in such methylation can therefore serve
as an epigenetic basis for phenotypic variation in natural populations.
article_number: '102087'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Elizabeth
full_name: Hollwey, Elizabeth
id: b8c4f54b-e484-11eb-8fdc-a54df64ef6dd
last_name: Hollwey
- first_name: Amy
full_name: Briffa, Amy
last_name: Briffa
- first_name: Martin
full_name: Howard, Martin
last_name: Howard
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Hollwey E, Briffa A, Howard M, Zilberman D. Concepts, mechanisms and implications
of long-term epigenetic inheritance. Current Opinion in Genetics and Development.
2023;81(8). doi:10.1016/j.gde.2023.102087
apa: Hollwey, E., Briffa, A., Howard, M., & Zilberman, D. (2023). Concepts,
mechanisms and implications of long-term epigenetic inheritance. Current Opinion
in Genetics and Development. Elsevier. https://doi.org/10.1016/j.gde.2023.102087
chicago: Hollwey, Elizabeth, Amy Briffa, Martin Howard, and Daniel Zilberman. “Concepts,
Mechanisms and Implications of Long-Term Epigenetic Inheritance.” Current Opinion
in Genetics and Development. Elsevier, 2023. https://doi.org/10.1016/j.gde.2023.102087.
ieee: E. Hollwey, A. Briffa, M. Howard, and D. Zilberman, “Concepts, mechanisms
and implications of long-term epigenetic inheritance,” Current Opinion in Genetics
and Development, vol. 81, no. 8. Elsevier, 2023.
ista: Hollwey E, Briffa A, Howard M, Zilberman D. 2023. Concepts, mechanisms and
implications of long-term epigenetic inheritance. Current Opinion in Genetics
and Development. 81(8), 102087.
mla: Hollwey, Elizabeth, et al. “Concepts, Mechanisms and Implications of Long-Term
Epigenetic Inheritance.” Current Opinion in Genetics and Development, vol.
81, no. 8, 102087, Elsevier, 2023, doi:10.1016/j.gde.2023.102087.
short: E. Hollwey, A. Briffa, M. Howard, D. Zilberman, Current Opinion in Genetics
and Development 81 (2023).
date_created: 2023-08-06T22:01:10Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2023-12-13T12:05:31Z
day: '01'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1016/j.gde.2023.102087
external_id:
isi:
- '001047020200001'
pmid:
- '37441873'
file:
- access_level: open_access
checksum: a294cd9506b80ed6ef218ef44ed32765
content_type: application/pdf
creator: dernst
date_created: 2023-08-07T08:32:26Z
date_updated: 2023-08-07T08:32:26Z
file_id: '13980'
file_name: 2023_CurrentOpinionGenetics_Hollwey.pdf
file_size: 2568632
relation: main_file
success: 1
file_date_updated: 2023-08-07T08:32:26Z
has_accepted_license: '1'
intvolume: ' 81'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Current Opinion in Genetics and Development
publication_identifier:
eissn:
- 1879-0380
issn:
- 0959-437X
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Concepts, mechanisms and implications of long-term epigenetic inheritance
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 81
year: '2023'
...
---
_id: '9877'
abstract:
- lang: eng
text: 'Parent-of-origin–dependent gene expression in mammals and flowering plants
results from differing chromatin imprints (genomic imprinting) between maternally
and paternally inherited alleles. Imprinted gene expression in the endosperm of
seeds is associated with localized hypomethylation of maternally but not paternally
inherited DNA, with certain small RNAs also displaying parent-of-origin–specific
expression. To understand the evolution of imprinting mechanisms in Oryza sativa
(rice), we analyzed imprinting divergence among four cultivars that span both
japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted
genes are imprinted across cultivars and enriched for functions in chromatin and
transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted
genes display divergent imprinting. Analyses of DNA methylation and small RNAs
revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed
DNA methylation, frequently overlap genes, and are imprinted four times more often
than genes. However, imprinting divergence most often correlated with local DNA
methylation epimutations (9 of 17 assessable loci), which were largely stable
within subspecies. Small insertion/deletion events and transposable element insertions
accompanied 4 of the 9 locally epimutated loci and associated with imprinting
divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic
variation occurred at key regulatory regions—the promoter and transcription start
site of maternally biased genes, and the promoter and gene body of paternally
biased genes. Our results reinforce models for the role of maternal-specific DNA
hypomethylation in imprinting of both maternally and paternally biased genes,
and highlight the role of transposition and epimutation in rice imprinting evolution.'
acknowledgement: We thank W. Schackwitz, M. Joel, and the Joint Genome Institute sequencing
team for generating the IR64 genome sequence and initial analysis; L. Bartley and
E. Marvinney for genomic DNA preparation for IR64 resequencing; and the University
of California (UC), Berkeley Sanger sequencing team for technical advice and service.
This work was partially funded by NSF Grant IOS-1025890 (to R.L.F. and D.Z.), NIH
Grant GM69415 (to R.L.F. and D.Z.), NIH Grant GM122968 (to P.C.R.), a Young Investigator
Grant from the Arnold and Mabel Beckman Foundation (to D.Z.), an International Fulbright
Science and Technology Award (to J.A.R.), and a Taiwan Ministry of Education Studying
Abroad Scholarship (to P.-H.H.). This work used the Vincent J. Coates Genomics Sequencing
Laboratory at UC Berkeley, supported by NIH Instrumentation Grant S10 OD018174.
article_number: e2104445118
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Deling
full_name: Ruan, Deling
last_name: Ruan
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Manoj K.
full_name: Sharma, Manoj K.
last_name: Sharma
- first_name: Rita
full_name: Sharma, Rita
last_name: Sharma
- first_name: XinYi
full_name: Ye, XinYi
last_name: Ye
- first_name: Nicholas D.
full_name: Nguyen, Nicholas D.
last_name: Nguyen
- first_name: Sukhranjan
full_name: Nijjar, Sukhranjan
last_name: Nijjar
- first_name: Pamela C.
full_name: Ronald, Pamela C.
last_name: Ronald
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Rodrigues JA, Hsieh P-H, Ruan D, et al. Divergence among rice cultivars reveals
roles for transposition and epimutation in ongoing evolution of genomic imprinting.
Proceedings of the National Academy of Sciences. 2021;118(29). doi:10.1073/pnas.2104445118
apa: Rodrigues, J. A., Hsieh, P.-H., Ruan, D., Nishimura, T., Sharma, M. K., Sharma,
R., … Zilberman, D. (2021). Divergence among rice cultivars reveals roles for
transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings
of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2104445118
chicago: Rodrigues, Jessica A., Ping-Hung Hsieh, Deling Ruan, Toshiro Nishimura,
Manoj K. Sharma, Rita Sharma, XinYi Ye, et al. “Divergence among Rice Cultivars
Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic
Imprinting.” Proceedings of the National Academy of Sciences. National
Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2104445118.
ieee: J. A. Rodrigues et al., “Divergence among rice cultivars reveals roles
for transposition and epimutation in ongoing evolution of genomic imprinting,”
Proceedings of the National Academy of Sciences, vol. 118, no. 29. National
Academy of Sciences, 2021.
ista: Rodrigues JA, Hsieh P-H, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen
ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. 2021. Divergence among rice
cultivars reveals roles for transposition and epimutation in ongoing evolution
of genomic imprinting. Proceedings of the National Academy of Sciences. 118(29),
e2104445118.
mla: Rodrigues, Jessica A., et al. “Divergence among Rice Cultivars Reveals Roles
for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.”
Proceedings of the National Academy of Sciences, vol. 118, no. 29, e2104445118,
National Academy of Sciences, 2021, doi:10.1073/pnas.2104445118.
short: J.A. Rodrigues, P.-H. Hsieh, D. Ruan, T. Nishimura, M.K. Sharma, R. Sharma,
X. Ye, N.D. Nguyen, S. Nijjar, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings
of the National Academy of Sciences 118 (2021).
date_created: 2021-08-10T19:30:41Z
date_published: 2021-07-16T00:00:00Z
date_updated: 2023-08-11T10:28:10Z
day: '16'
ddc:
- '580'
- '570'
department:
- _id: DaZi
doi: 10.1073/pnas.2104445118
external_id:
isi:
- '000685037700012'
pmid:
- '34272287'
file:
- access_level: open_access
checksum: 19e84ad8c03c60222744ee8e16cd6998
content_type: application/pdf
creator: asandaue
date_created: 2021-08-11T09:31:41Z
date_updated: 2021-08-11T09:31:41Z
file_id: '9879'
file_name: 2021_ProceedingsOfTheNationalAcademyOfSciences_Rodrigues.pdf
file_size: 1898360
relation: main_file
success: 1
file_date_updated: 2021-08-11T09:31:41Z
has_accepted_license: '1'
intvolume: ' 118'
isi: 1
issue: '29'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Divergence among rice cultivars reveals roles for transposition and epimutation
in ongoing evolution of genomic imprinting
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 118
year: '2021'
...
---
_id: '10533'
abstract:
- lang: eng
text: Flowering plants utilize small RNA molecules to guide DNA methyltransferases
to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially
targets euchromatic transposable elements. However, RdDM is thought to be recruited
by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin.
How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear.
Here we show that loss of histone H1 enhances heterochromatic RdDM, preferentially
at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component
that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation.
Instead, we find that non-CG methylation is specifically associated with small
RNA biogenesis, and without H1 small RNA production quantitatively expands to
non-CG methylated loci. Our results demonstrate that H1 enforces the separation
of euchromatic and heterochromatic DNA methylation pathways by excluding the small
RNA-generating branch of RdDM from non-CG methylated heterochromatin.
acknowledgement: We thank X Feng for helpful comments on the manuscript. This work
was supported by a European Research Council grant MaintainMeth (725746) to DZ.
article_number: e72676
article_processing_charge: No
article_type: original
author:
- first_name: Jaemyung
full_name: Choi, Jaemyung
last_name: Choi
- first_name: David B
full_name: Lyons, David B
last_name: Lyons
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Choi J, Lyons DB, Zilberman D. Histone H1 prevents non-CG methylation-mediated
small RNA biogenesis in Arabidopsis heterochromatin. eLife. 2021;10. doi:10.7554/elife.72676
apa: Choi, J., Lyons, D. B., & Zilberman, D. (2021). Histone H1 prevents non-CG
methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. ELife.
eLife Sciences Publications. https://doi.org/10.7554/elife.72676
chicago: Choi, Jaemyung, David B Lyons, and Daniel Zilberman. “Histone H1 Prevents
Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.”
ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.72676.
ieee: J. Choi, D. B. Lyons, and D. Zilberman, “Histone H1 prevents non-CG methylation-mediated
small RNA biogenesis in Arabidopsis heterochromatin,” eLife, vol. 10. eLife
Sciences Publications, 2021.
ista: Choi J, Lyons DB, Zilberman D. 2021. Histone H1 prevents non-CG methylation-mediated
small RNA biogenesis in Arabidopsis heterochromatin. eLife. 10, e72676.
mla: Choi, Jaemyung, et al. “Histone H1 Prevents Non-CG Methylation-Mediated Small
RNA Biogenesis in Arabidopsis Heterochromatin.” ELife, vol. 10, e72676,
eLife Sciences Publications, 2021, doi:10.7554/elife.72676.
short: J. Choi, D.B. Lyons, D. Zilberman, ELife 10 (2021).
date_created: 2021-12-10T13:12:08Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2023-08-17T06:21:08Z
day: '01'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.7554/elife.72676
ec_funded: 1
external_id:
isi:
- '000754832000001'
pmid:
- '34850679'
file:
- access_level: open_access
checksum: 22ed4c55fb550f6da02ae55c359be651
content_type: application/pdf
creator: dernst
date_created: 2022-05-16T10:42:22Z
date_updated: 2022-05-16T10:42:22Z
file_id: '11384'
file_name: 2021_eLife_Choi.pdf
file_size: 2715200
relation: main_file
success: 1
file_date_updated: 2022-05-16T10:42:22Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
keyword:
- genetics and molecular biology
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 62935a00-2b32-11ec-9570-eff30fa39068
call_identifier: H2020
grant_number: '725746'
name: Quantitative analysis of DNA methylation maintenance with chromatin
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis
heterochromatin
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2021'
...
---
_id: '9526'
abstract:
- lang: eng
text: DNA methylation and histone H1 mediate transcriptional silencing of genes
and transposable elements, but how they interact is unclear. In plants and animals
with mosaic genomic methylation, functionally mysterious methylation is also common
within constitutively active housekeeping genes. Here, we show that H1 is enriched
in methylated sequences, including genes, of Arabidopsis thaliana, yet this enrichment
is independent of DNA methylation. Loss of H1 disperses heterochromatin, globally
alters nucleosome organization, and activates H1-bound genes, but only weakly
de-represses transposable elements. However, H1 loss strongly activates transposable
elements hypomethylated through mutation of DNA methyltransferase MET1. Hypomethylation
of genes also activates antisense transcription, which is modestly enhanced by
H1 loss. Our results demonstrate that H1 and DNA methylation jointly maintain
transcriptional homeostasis by silencing transposable elements and aberrant intragenic
transcripts. Such functionality plausibly explains why DNA methylation, a well-known
mutagen, has been maintained within coding sequences of crucial plant and animal
genes.
article_processing_charge: No
article_type: original
author:
- first_name: Jaemyung
full_name: Choi, Jaemyung
last_name: Choi
- first_name: David B.
full_name: Lyons, David B.
last_name: Lyons
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Jonathan D.
full_name: Moore, Jonathan D.
last_name: Moore
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Choi J, Lyons DB, Kim MY, Moore JD, Zilberman D. DNA methylation and histone
H1 jointly repress transposable elements and aberrant intragenic transcripts.
Molecular Cell. 2020;77(2):310-323.e7. doi:10.1016/j.molcel.2019.10.011
apa: Choi, J., Lyons, D. B., Kim, M. Y., Moore, J. D., & Zilberman, D. (2020).
DNA methylation and histone H1 jointly repress transposable elements and aberrant
intragenic transcripts. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2019.10.011
chicago: Choi, Jaemyung, David B. Lyons, M. Yvonne Kim, Jonathan D. Moore, and Daniel
Zilberman. “DNA Methylation and Histone H1 Jointly Repress Transposable Elements
and Aberrant Intragenic Transcripts.” Molecular Cell. Elsevier, 2020. https://doi.org/10.1016/j.molcel.2019.10.011.
ieee: J. Choi, D. B. Lyons, M. Y. Kim, J. D. Moore, and D. Zilberman, “DNA methylation
and histone H1 jointly repress transposable elements and aberrant intragenic transcripts,”
Molecular Cell, vol. 77, no. 2. Elsevier, p. 310–323.e7, 2020.
ista: Choi J, Lyons DB, Kim MY, Moore JD, Zilberman D. 2020. DNA methylation and
histone H1 jointly repress transposable elements and aberrant intragenic transcripts.
Molecular Cell. 77(2), 310–323.e7.
mla: Choi, Jaemyung, et al. “DNA Methylation and Histone H1 Jointly Repress Transposable
Elements and Aberrant Intragenic Transcripts.” Molecular Cell, vol. 77,
no. 2, Elsevier, 2020, p. 310–323.e7, doi:10.1016/j.molcel.2019.10.011.
short: J. Choi, D.B. Lyons, M.Y. Kim, J.D. Moore, D. Zilberman, Molecular Cell 77
(2020) 310–323.e7.
date_created: 2021-06-08T06:37:09Z
date_published: 2020-01-16T00:00:00Z
date_updated: 2021-12-14T07:51:15Z
day: '16'
department:
- _id: DaZi
doi: 10.1016/j.molcel.2019.10.011
extern: '1'
external_id:
pmid:
- '31732458'
intvolume: ' 77'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.molcel.2019.10.011
month: '01'
oa: 1
oa_version: Published Version
page: 310-323.e7
pmid: 1
publication: Molecular Cell
publication_identifier:
eissn:
- 1097-4164
issn:
- 1097-2765
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation and histone H1 jointly repress transposable elements and aberrant
intragenic transcripts
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 77
year: '2020'
...
---
_id: '9460'
abstract:
- lang: eng
text: Epigenetic reprogramming is required for proper regulation of gene expression
in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for
seed viability, pollen function, and successful reproduction. The DEMETER (DME)
DNA glycosylase initiates localized DNA demethylation in vegetative and central
cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively.
In rice, the central cell genome displays local DNA hypomethylation, suggesting
that active DNA demethylation also occurs in rice; however, the enzyme responsible
for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING
1a (ROS1a) gene, which is related to DME and is essential for rice seed viability
and pollen function. Here, we report genome-wide analyses of DNA methylation in
wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative
cell genome is locally hypomethylated compared with sperm by a process that requires
ROS1a activity. We show that many ROS1a target sequences in the vegetative cell
are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates
the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation
is indirectly promoted by DNA demethylation in the vegetative cell. These results
reveal that DNA glycosylase-mediated DNA demethylation processes are conserved
in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally,
although global non-CG methylation levels of sperm and egg differ, the maternal
and paternal embryo genomes show similar non-CG methylation levels, suggesting
that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell
fusion.
article_processing_charge: No
article_type: original
author:
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Akemi
full_name: Ono, Akemi
last_name: Ono
- first_name: Stefan
full_name: Scholten, Stefan
last_name: Scholten
- first_name: Tetsu
full_name: Kinoshita, Tetsu
last_name: Kinoshita
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Takashi
full_name: Okamoto, Takashi
last_name: Okamoto
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
citation:
ama: Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative
cells promotes methylation in sperm. Proceedings of the National Academy of
Sciences. 2019;116(19):9652-9657. doi:10.1073/pnas.1821435116
apa: Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T.,
& Fischer, R. L. (2019). DNA demethylation by ROS1a in rice vegetative cells
promotes methylation in sperm. Proceedings of the National Academy of Sciences.
National Academy of Sciences. https://doi.org/10.1073/pnas.1821435116
chicago: Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman,
Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROS1a in Rice Vegetative
Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of
Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1821435116.
ieee: M. Y. Kim et al., “DNA demethylation by ROS1a in rice vegetative cells
promotes methylation in sperm,” Proceedings of the National Academy of Sciences,
vol. 116, no. 19. National Academy of Sciences, pp. 9652–9657, 2019.
ista: Kim MY, Ono A, Scholten S, Kinoshita T, Zilberman D, Okamoto T, Fischer RL.
2019. DNA demethylation by ROS1a in rice vegetative cells promotes methylation
in sperm. Proceedings of the National Academy of Sciences. 116(19), 9652–9657.
mla: Kim, M. Yvonne, et al. “DNA Demethylation by ROS1a in Rice Vegetative Cells
Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences,
vol. 116, no. 19, National Academy of Sciences, 2019, pp. 9652–57, doi:10.1073/pnas.1821435116.
short: M.Y. Kim, A. Ono, S. Scholten, T. Kinoshita, D. Zilberman, T. Okamoto, R.L.
Fischer, Proceedings of the National Academy of Sciences 116 (2019) 9652–9657.
date_created: 2021-06-04T12:38:20Z
date_published: 2019-05-07T00:00:00Z
date_updated: 2021-12-14T07:52:30Z
day: '07'
ddc:
- '580'
department:
- _id: DaZi
doi: 10.1073/pnas.1821435116
extern: '1'
external_id:
pmid:
- '31000601'
file:
- access_level: open_access
checksum: 5b0ae3779b8b21b5223bd2d3cceede3a
content_type: application/pdf
creator: asandaue
date_created: 2021-06-04T12:50:47Z
date_updated: 2021-06-04T12:50:47Z
file_id: '9461'
file_name: 2019_PNAS_Kim.pdf
file_size: 1142540
relation: main_file
success: 1
file_date_updated: 2021-06-04T12:50:47Z
has_accepted_license: '1'
intvolume: ' 116'
issue: '19'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 9652-9657
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA demethylation by ROS1a in rice vegetative cells promotes methylation in
sperm
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 116
year: '2019'
...
---
_id: '9530'
abstract:
- lang: eng
text: "Background\r\nDNA methylation of active genes, also known as gene body methylation,
is found in many animal and plant genomes. Despite this, the transcriptional and
developmental role of such methylation remains poorly understood. Here, we explore
the dynamic range of DNA methylation in honey bee, a model organism for gene body
methylation.\r\n\r\nResults\r\nOur data show that CG methylation in gene bodies
globally fluctuates during honey bee development. However, these changes cause
no gene expression alterations. Intriguingly, despite the global alterations,
tissue-specific CG methylation patterns of complete genes or exons are rare, implying
robust maintenance of genic methylation during development. Additionally, we show
that CG methylation maintenance fluctuates in somatic cells, while reaching maximum
fidelity in sperm cells. Finally, unlike universally present CG methylation, we
discovered non-CG methylation specifically in bee heads that resembles such methylation
in mammalian brain tissue.\r\n\r\nConclusions\r\nBased on these results, we propose
that gene body CG methylation can oscillate during development if it is kept to
a level adequate to preserve function. Additionally, our data suggest that heightened
non-CG methylation is a conserved regulator of animal nervous systems."
article_number: '62'
article_processing_charge: No
article_type: original
author:
- first_name: Keith D.
full_name: Harris, Keith D.
last_name: Harris
- first_name: James P. B.
full_name: Lloyd, James P. B.
last_name: Lloyd
- first_name: Katherine
full_name: Domb, Katherine
last_name: Domb
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
citation:
ama: Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. DNA methylation is maintained
with high fidelity in the honey bee germline and exhibits global non-functional
fluctuations during somatic development. Epigenetics and Chromatin. 2019;12.
doi:10.1186/s13072-019-0307-4
apa: Harris, K. D., Lloyd, J. P. B., Domb, K., Zilberman, D., & Zemach, A. (2019).
DNA methylation is maintained with high fidelity in the honey bee germline and
exhibits global non-functional fluctuations during somatic development. Epigenetics
and Chromatin. Springer Nature. https://doi.org/10.1186/s13072-019-0307-4
chicago: Harris, Keith D., James P. B. Lloyd, Katherine Domb, Daniel Zilberman,
and Assaf Zemach. “DNA Methylation Is Maintained with High Fidelity in the Honey
Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.”
Epigenetics and Chromatin. Springer Nature, 2019. https://doi.org/10.1186/s13072-019-0307-4.
ieee: K. D. Harris, J. P. B. Lloyd, K. Domb, D. Zilberman, and A. Zemach, “DNA methylation
is maintained with high fidelity in the honey bee germline and exhibits global
non-functional fluctuations during somatic development,” Epigenetics and Chromatin,
vol. 12. Springer Nature, 2019.
ista: Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. 2019. DNA methylation
is maintained with high fidelity in the honey bee germline and exhibits global
non-functional fluctuations during somatic development. Epigenetics and Chromatin.
12, 62.
mla: Harris, Keith D., et al. “DNA Methylation Is Maintained with High Fidelity
in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during
Somatic Development.” Epigenetics and Chromatin, vol. 12, 62, Springer
Nature, 2019, doi:10.1186/s13072-019-0307-4.
short: K.D. Harris, J.P.B. Lloyd, K. Domb, D. Zilberman, A. Zemach, Epigenetics
and Chromatin 12 (2019).
date_created: 2021-06-08T09:21:51Z
date_published: 2019-10-10T00:00:00Z
date_updated: 2021-12-14T07:53:00Z
day: '10'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1186/s13072-019-0307-4
extern: '1'
external_id:
pmid:
- '31601251'
file:
- access_level: open_access
checksum: 86ff50a7517891511af2733c76c81b67
content_type: application/pdf
creator: asandaue
date_created: 2021-06-08T09:29:19Z
date_updated: 2021-06-08T09:29:19Z
file_id: '9531'
file_name: 2019_EpigeneticsAndChromatin_Harris.pdf
file_size: 3221067
relation: main_file
success: 1
file_date_updated: 2021-06-08T09:29:19Z
has_accepted_license: '1'
intvolume: ' 12'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Epigenetics and Chromatin
publication_identifier:
eissn:
- 1756-8935
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation is maintained with high fidelity in the honey bee germline
and exhibits global non-functional fluctuations during somatic development
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 12
year: '2019'
...
---
_id: '9471'
abstract:
- lang: eng
text: The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation
and is required for endosperm genomic imprinting and embryo viability. Targets
of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons
and at the boundaries of large transposons, but how DME interacts with these diverse
chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1)
subunit of the chromatin remodeler FACT (facilitates chromatin transactions),
was previously shown to be involved in the DME-dependent regulation of genomic
imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction
between DME and chromatin, we focused on the activity of the two FACT subunits,
SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found
that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of
target sites, the first being euchromatic and accessible to DME, but the second,
representing over half of DME targets, requiring the action of FACT for DME-mediated
DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets
are GC-rich heterochromatin domains with high nucleosome occupancy enriched with
H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated
linker histone H1 specifically mediates the requirement for FACT at a subset of
DME-target loci. Overall, our results demonstrate that FACT is required for DME
targeting by facilitating its access to heterochromatin.
article_processing_charge: No
article_type: original
author:
- first_name: Jennifer M.
full_name: Frost, Jennifer M.
last_name: Frost
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Guen Tae
full_name: Park, Guen Tae
last_name: Park
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Miyuki
full_name: Nakamura, Miyuki
last_name: Nakamura
- first_name: Samuel J. H.
full_name: Lin, Samuel J. H.
last_name: Lin
- first_name: Hyunjin
full_name: Yoo, Hyunjin
last_name: Yoo
- first_name: Jaemyung
full_name: Choi, Jaemyung
last_name: Choi
- first_name: Yoko
full_name: Ikeda, Yoko
last_name: Ikeda
- first_name: Tetsu
full_name: Kinoshita, Tetsu
last_name: Kinoshita
- first_name: Yeonhee
full_name: Choi, Yeonhee
last_name: Choi
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
citation:
ama: Frost JM, Kim MY, Park GT, et al. FACT complex is required for DNA demethylation
at heterochromatin during reproduction in Arabidopsis. Proceedings of the National
Academy of Sciences. 2018;115(20):E4720-E4729. doi:10.1073/pnas.1713333115
apa: Frost, J. M., Kim, M. Y., Park, G. T., Hsieh, P.-H., Nakamura, M., Lin, S.
J. H., … Fischer, R. L. (2018). FACT complex is required for DNA demethylation
at heterochromatin during reproduction in Arabidopsis. Proceedings of the National
Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1713333115
chicago: Frost, Jennifer M., M. Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki
Nakamura, Samuel J. H. Lin, Hyunjin Yoo, et al. “FACT Complex Is Required for
DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1713333115.
ieee: J. M. Frost et al., “FACT complex is required for DNA demethylation
at heterochromatin during reproduction in Arabidopsis,” Proceedings of the
National Academy of Sciences, vol. 115, no. 20. National Academy of Sciences,
pp. E4720–E4729, 2018.
ista: Frost JM, Kim MY, Park GT, Hsieh P-H, Nakamura M, Lin SJH, Yoo H, Choi J,
Ikeda Y, Kinoshita T, Choi Y, Zilberman D, Fischer RL. 2018. FACT complex is required
for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings
of the National Academy of Sciences. 115(20), E4720–E4729.
mla: Frost, Jennifer M., et al. “FACT Complex Is Required for DNA Demethylation
at Heterochromatin during Reproduction in Arabidopsis.” Proceedings of the
National Academy of Sciences, vol. 115, no. 20, National Academy of Sciences,
2018, pp. E4720–29, doi:10.1073/pnas.1713333115.
short: J.M. Frost, M.Y. Kim, G.T. Park, P.-H. Hsieh, M. Nakamura, S.J.H. Lin, H.
Yoo, J. Choi, Y. Ikeda, T. Kinoshita, Y. Choi, D. Zilberman, R.L. Fischer, Proceedings
of the National Academy of Sciences 115 (2018) E4720–E4729.
date_created: 2021-06-07T06:11:28Z
date_published: 2018-05-15T00:00:00Z
date_updated: 2021-12-14T07:53:40Z
day: '15'
ddc:
- '580'
department:
- _id: DaZi
doi: 10.1073/pnas.1713333115
extern: '1'
external_id:
pmid:
- '29712855'
file:
- access_level: open_access
checksum: 810260dc0e3cc3033e15c19ad0dc123e
content_type: application/pdf
creator: asandaue
date_created: 2021-06-07T06:16:38Z
date_updated: 2021-06-07T06:16:38Z
file_id: '9472'
file_name: 2018_PNAS_Frost.pdf
file_size: 3045260
relation: main_file
success: 1
file_date_updated: 2021-06-07T06:16:38Z
has_accepted_license: '1'
intvolume: ' 115'
issue: '20'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: E4720-E4729
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: earlier_version
url: 'https://doi.org/10.1101/187674 '
scopus_import: '1'
status: public
title: FACT complex is required for DNA demethylation at heterochromatin during reproduction
in Arabidopsis
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 115
year: '2018'
...
---
_id: '9445'
abstract:
- lang: eng
text: Cytosine methylation regulates essential genome functions across eukaryotes,
but the fundamental question of whether nucleosomal or naked DNA is the preferred
substrate of plant and animal methyltransferases remains unresolved. Here, we
show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler
biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana
and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome,
suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases
in vivo. Furthermore, we show that simultaneous mutation of DDM1 and linker histone
H1 in Arabidopsis reproduces the strong linker-specific methylation patterns of
species that diverged from flowering plants and animals over a billion years ago.
Our results indicate that in the absence of remodeling, nucleosomes are strong
barriers to DNA methyltransferases. Linker-specific methylation can evolve simply
by breaking the connection between nucleosome remodeling and DNA methylation.
article_number: e30674
article_processing_charge: No
article_type: original
author:
- first_name: David B
full_name: Lyons, David B
last_name: Lyons
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped
in nucleosomes. eLife. 2017;6. doi:10.7554/elife.30674
apa: Lyons, D. B., & Zilberman, D. (2017). DDM1 and Lsh remodelers allow methylation
of DNA wrapped in nucleosomes. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.30674
chicago: Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation
of DNA Wrapped in Nucleosomes.” ELife. eLife Sciences Publications, 2017.
https://doi.org/10.7554/elife.30674.
ieee: D. B. Lyons and D. Zilberman, “DDM1 and Lsh remodelers allow methylation of
DNA wrapped in nucleosomes,” eLife, vol. 6. eLife Sciences Publications,
2017.
ista: Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of
DNA wrapped in nucleosomes. eLife. 6, e30674.
mla: Lyons, David B., and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation
of DNA Wrapped in Nucleosomes.” ELife, vol. 6, e30674, eLife Sciences Publications,
2017, doi:10.7554/elife.30674.
short: D.B. Lyons, D. Zilberman, ELife 6 (2017).
date_created: 2021-06-02T14:28:58Z
date_published: 2017-11-15T00:00:00Z
date_updated: 2021-12-14T07:54:36Z
day: '15'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.7554/elife.30674
extern: '1'
external_id:
pmid:
- '29140247'
file:
- access_level: open_access
checksum: 4cfcdd67511ae4aed3d993550e46e146
content_type: application/pdf
creator: cziletti
date_created: 2021-06-02T14:33:36Z
date_updated: 2021-06-02T14:33:36Z
file_id: '9446'
file_name: 2017_eLife_Lyons.pdf
file_size: 1603102
relation: main_file
success: 1
file_date_updated: 2021-06-02T14:33:36Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 6
year: '2017'
...
---
_id: '9506'
abstract:
- lang: eng
text: Methylation in the bodies of active genes is common in animals and vascular
plants. Evolutionary patterns indicate homeostatic functions for this type of
methylation.
article_number: '87'
article_processing_charge: No
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zilberman D. An evolutionary case for functional gene body methylation in plants
and animals. Genome Biology. 2017;18(1). doi:10.1186/s13059-017-1230-2
apa: Zilberman, D. (2017). An evolutionary case for functional gene body methylation
in plants and animals. Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-017-1230-2
chicago: Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation
in Plants and Animals.” Genome Biology. Springer Nature, 2017. https://doi.org/10.1186/s13059-017-1230-2.
ieee: D. Zilberman, “An evolutionary case for functional gene body methylation in
plants and animals,” Genome Biology, vol. 18, no. 1. Springer Nature, 2017.
ista: Zilberman D. 2017. An evolutionary case for functional gene body methylation
in plants and animals. Genome Biology. 18(1), 87.
mla: Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation
in Plants and Animals.” Genome Biology, vol. 18, no. 1, 87, Springer Nature,
2017, doi:10.1186/s13059-017-1230-2.
short: D. Zilberman, Genome Biology 18 (2017).
date_created: 2021-06-07T12:27:39Z
date_published: 2017-05-09T00:00:00Z
date_updated: 2021-12-14T07:55:02Z
day: '09'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1186/s13059-017-1230-2
extern: '1'
external_id:
pmid:
- '28486944'
file:
- access_level: open_access
checksum: 5a455ad914e7d225b1baa4ab07fd925e
content_type: application/pdf
creator: asandaue
date_created: 2021-06-07T12:31:36Z
date_updated: 2021-06-07T12:31:36Z
file_id: '9507'
file_name: 2017_GenomeBiology_Zilberman.pdf
file_size: 278183
relation: main_file
success: 1
file_date_updated: 2021-06-07T12:31:36Z
has_accepted_license: '1'
intvolume: ' 18'
issue: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
eissn:
- 1465-6906
issn:
- 1474-760X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: An evolutionary case for functional gene body methylation in plants and animals
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 18
year: '2017'
...
---
_id: '9456'
abstract:
- lang: eng
text: The discovery of introns four decades ago was one of the most unexpected findings
in molecular biology. Introns are sequences interrupting genes that must be removed
as part of messenger RNA production. Genome sequencing projects have shown that
most eukaryotic genes contain at least one intron, and frequently many. Comparison
of these genomes reveals a history of long evolutionary periods during which few
introns were gained, punctuated by episodes of rapid, extensive gain. However,
although several detailed mechanisms for such episodic intron generation have
been proposed, none has been empirically supported on a genomic scale. Here we
show how short, non-autonomous DNA transposons independently generated hundreds
to thousands of introns in the prasinophyte Micromonas pusilla and the pelagophyte
Aureococcus anophagefferens. Each transposon carries one splice site. The other
splice site is co-opted from the gene sequence that is duplicated upon transposon
insertion, allowing perfect splicing out of the RNA. The distributions of sequences
that can be co-opted are biased with respect to codons, and phasing of transposon-generated
introns is similarly biased. These transposons insert between pre-existing nucleosomes,
so that multiple nearby insertions generate nucleosome-sized intervening segments.
Thus, transposon insertion and sequence co-option may explain the intron phase
biases and prevalence of nucleosome-sized exons observed in eukaryotes. Overall,
the two independent examples of proliferating elements illustrate a general DNA
transposon mechanism that can plausibly account for episodes of rapid, extensive
intron gain during eukaryotic evolution.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Jason T.
full_name: Huff, Jason T.
last_name: Huff
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Scott W.
full_name: Roy, Scott W.
last_name: Roy
citation:
ama: Huff JT, Zilberman D, Roy SW. Mechanism for DNA transposons to generate introns
on genomic scales. Nature. 2016;538(7626):533-536. doi:10.1038/nature20110
apa: Huff, J. T., Zilberman, D., & Roy, S. W. (2016). Mechanism for DNA transposons
to generate introns on genomic scales. Nature. Springer Nature . https://doi.org/10.1038/nature20110
chicago: Huff, Jason T., Daniel Zilberman, and Scott W. Roy. “Mechanism for DNA
Transposons to Generate Introns on Genomic Scales.” Nature. Springer Nature
, 2016. https://doi.org/10.1038/nature20110.
ieee: J. T. Huff, D. Zilberman, and S. W. Roy, “Mechanism for DNA transposons to
generate introns on genomic scales,” Nature, vol. 538, no. 7626. Springer
Nature , pp. 533–536, 2016.
ista: Huff JT, Zilberman D, Roy SW. 2016. Mechanism for DNA transposons to generate
introns on genomic scales. Nature. 538(7626), 533–536.
mla: Huff, Jason T., et al. “Mechanism for DNA Transposons to Generate Introns on
Genomic Scales.” Nature, vol. 538, no. 7626, Springer Nature , 2016, pp.
533–36, doi:10.1038/nature20110.
short: J.T. Huff, D. Zilberman, S.W. Roy, Nature 538 (2016) 533–536.
date_created: 2021-06-04T11:34:55Z
date_published: 2016-10-27T00:00:00Z
date_updated: 2021-12-14T07:55:30Z
day: '27'
department:
- _id: DaZi
doi: 10.1038/nature20110
extern: '1'
external_id:
pmid:
- '27760113'
intvolume: ' 538'
issue: '7626'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5684705/
month: '10'
oa: 1
oa_version: Submitted Version
page: 533-536
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: 'Springer Nature '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanism for DNA transposons to generate introns on genomic scales
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 538
year: '2016'
...
---
_id: '9477'
abstract:
- lang: eng
text: Cytosine methylation is a DNA modification with important regulatory functions
in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive
DNA demethylation, which is required for proper gene expression in the endosperm,
a nutritive extraembryonic seed tissue. Endosperm arises from a fusion of a sperm
cell carried in the pollen and a female central cell. Endosperm DNA demethylation
is observed specifically on the chromosomes inherited from the central cell in
Arabidopsis thaliana, rice, and maize, and requires the DEMETER DNA demethylase
in Arabidopsis. DEMETER is expressed in the central cell before fertilization,
suggesting that endosperm demethylation patterns are inherited from the central
cell. Down-regulation of the MET1 DNA methyltransferase has also been proposed
to contribute to central cell demethylation. However, with the exception of three
maize genes, central cell DNA methylation has not been directly measured, leaving
the origin and mechanism of endosperm demethylation uncertain. Here, we report
genome-wide analysis of DNA methylation in the central cells of Arabidopsis and
rice—species that diverged 150 million years ago—as well as in rice egg cells.
We find that DNA demethylation in both species is initiated in central cells,
which requires DEMETER in Arabidopsis. However, we do not observe a global reduction
of CG methylation that would be indicative of lowered MET1 activity; on the contrary,
CG methylation efficiency is elevated in female gametes compared with nonsexual
tissues. Our results demonstrate that locus-specific, active DNA demethylation
in the central cell is the origin of maternal chromosome hypomethylation in the
endosperm.
article_processing_charge: No
article_type: original
author:
- first_name: Kyunghyuk
full_name: Park, Kyunghyuk
last_name: Park
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: Jin-Sup
full_name: Park, Jin-Sup
last_name: Park
- first_name: Youbong
full_name: Hyun, Youbong
last_name: Hyun
- first_name: Takashi
full_name: Okamoto, Takashi
last_name: Okamoto
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Yeonhee
full_name: Choi, Yeonhee
last_name: Choi
- first_name: Stefan
full_name: Scholten, Stefan
last_name: Scholten
citation:
ama: Park K, Kim MY, Vickers M, et al. DNA demethylation is initiated in the central
cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences.
2016;113(52):15138-15143. doi:10.1073/pnas.1619047114
apa: Park, K., Kim, M. Y., Vickers, M., Park, J.-S., Hyun, Y., Okamoto, T., … Scholten,
S. (2016). DNA demethylation is initiated in the central cells of Arabidopsis
and rice. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1619047114
chicago: Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun,
Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the
Central Cells of Arabidopsis and Rice.” Proceedings of the National Academy
of Sciences. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1619047114.
ieee: K. Park et al., “DNA demethylation is initiated in the central cells
of Arabidopsis and rice,” Proceedings of the National Academy of Sciences,
vol. 113, no. 52. National Academy of Sciences, pp. 15138–15143, 2016.
ista: Park K, Kim MY, Vickers M, Park J-S, Hyun Y, Okamoto T, Zilberman D, Fischer
RL, Feng X, Choi Y, Scholten S. 2016. DNA demethylation is initiated in the central
cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences.
113(52), 15138–15143.
mla: Park, Kyunghyuk, et al. “DNA Demethylation Is Initiated in the Central Cells
of Arabidopsis and Rice.” Proceedings of the National Academy of Sciences,
vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15138–43, doi:10.1073/pnas.1619047114.
short: K. Park, M.Y. Kim, M. Vickers, J.-S. Park, Y. Hyun, T. Okamoto, D. Zilberman,
R.L. Fischer, X. Feng, Y. Choi, S. Scholten, Proceedings of the National Academy
of Sciences 113 (2016) 15138–15143.
date_created: 2021-06-07T07:10:59Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2023-05-08T11:00:07Z
day: '27'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1073/pnas.1619047114
extern: '1'
external_id:
pmid:
- '27956642'
intvolume: ' 113'
issue: '52'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1619047114
month: '12'
oa: 1
oa_version: Published Version
page: 15138-15143
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA demethylation is initiated in the central cells of Arabidopsis and rice
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '9473'
abstract:
- lang: eng
text: Cytosine DNA methylation regulates the expression of eukaryotic genes and
transposons. Methylation is copied by methyltransferases after DNA replication,
which results in faithful transmission of methylation patterns during cell division
and, at least in flowering plants, across generations. Transgenerational inheritance
is mediated by a small group of cells that includes gametes and their progenitors.
However, methylation is usually analyzed in somatic tissues that do not contribute
to the next generation, and the mechanisms of transgenerational inheritance are
inferred from such studies. To gain a better understanding of how DNA methylation
is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cells-the
cell types that comprise pollen-with mutations in the DRM, CMT2, and CMT3 methyltransferases.
We find that DNA methylation dependency on these enzymes is similar in sperm,
vegetative cells, and somatic tissues, although DRM activity extends into heterochromatin
in vegetative cells, likely reflecting transcription of heterochromatic transposons
in this cell type. We also show that lack of histone H1, which elevates heterochromatic
DNA methylation in somatic tissues, does not have this effect in pollen. Instead,
levels of CG methylation in wild-type sperm and vegetative cells, as well as in
wild-type microspores from which both pollen cell types originate, are substantially
higher than in wild-type somatic tissues and similar to those of H1-depleted roots.
Our results demonstrate that the mechanisms of methylation maintenance are similar
between pollen and somatic cells, but the efficiency of CG methylation is higher
in pollen, allowing methylation patterns to be accurately inherited across generations.
article_processing_charge: No
article_type: original
author:
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Toby
full_name: Buttress, Toby
last_name: Buttress
- first_name: Hongbo
full_name: Gao, Hongbo
last_name: Gao
- first_name: Matthew
full_name: Couchman, Matthew
last_name: Couchman
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: Hsieh P-H, He S, Buttress T, et al. Arabidopsis male sexual lineage exhibits
more robust maintenance of CG methylation than somatic tissues. Proceedings
of the National Academy of Sciences. 2016;113(52):15132-15137. doi:10.1073/pnas.1619074114
apa: Hsieh, P.-H., He, S., Buttress, T., Gao, H., Couchman, M., Fischer, R. L.,
… Feng, X. (2016). Arabidopsis male sexual lineage exhibits more robust maintenance
of CG methylation than somatic tissues. Proceedings of the National Academy
of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1619074114
chicago: Hsieh, Ping-Hung, Shengbo He, Toby Buttress, Hongbo Gao, Matthew Couchman,
Robert L. Fischer, Daniel Zilberman, and Xiaoqi Feng. “Arabidopsis Male Sexual
Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.”
Proceedings of the National Academy of Sciences. National Academy of Sciences,
2016. https://doi.org/10.1073/pnas.1619074114.
ieee: P.-H. Hsieh et al., “Arabidopsis male sexual lineage exhibits more
robust maintenance of CG methylation than somatic tissues,” Proceedings of
the National Academy of Sciences, vol. 113, no. 52. National Academy of Sciences,
pp. 15132–15137, 2016.
ista: Hsieh P-H, He S, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng
X. 2016. Arabidopsis male sexual lineage exhibits more robust maintenance of CG
methylation than somatic tissues. Proceedings of the National Academy of Sciences.
113(52), 15132–15137.
mla: Hsieh, Ping-Hung, et al. “Arabidopsis Male Sexual Lineage Exhibits More Robust
Maintenance of CG Methylation than Somatic Tissues.” Proceedings of the National
Academy of Sciences, vol. 113, no. 52, National Academy of Sciences, 2016,
pp. 15132–37, doi:10.1073/pnas.1619074114.
short: P.-H. Hsieh, S. He, T. Buttress, H. Gao, M. Couchman, R.L. Fischer, D. Zilberman,
X. Feng, Proceedings of the National Academy of Sciences 113 (2016) 15132–15137.
date_created: 2021-06-07T06:21:39Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2023-05-08T11:00:40Z
day: '27'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1073/pnas.1619074114
extern: '1'
external_id:
pmid:
- '27956643'
intvolume: ' 113'
issue: '52'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1619074114
month: '12'
oa: 1
oa_version: Published Version
page: 15132-15137
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation
than somatic tissues
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '9532'
abstract:
- lang: eng
text: Genomic imprinting, an inherently epigenetic phenomenon defined by parent
of origin-dependent gene expression, is observed in mammals and flowering plants.
Genome-scale surveys of imprinted expression and the underlying differential epigenetic
marks have led to the discovery of hundreds of imprinted plant genes and confirmed
DNA and histone methylation as key regulators of plant imprinting. However, the
biological roles of the vast majority of imprinted plant genes are unknown, and
the evolutionary forces shaping plant imprinting remain rather opaque. Here, we
review the mechanisms of plant genomic imprinting and discuss theories of imprinting
evolution and biological significance in light of recent findings.
article_processing_charge: No
article_type: review
author:
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in
plants. Genes and Development. 2015;29(24):2517–2531. doi:10.1101/gad.269902.115
apa: Rodrigues, J. A., & Zilberman, D. (2015). Evolution and function of genomic
imprinting in plants. Genes and Development. Cold Spring Harbor Laboratory
Press. https://doi.org/10.1101/gad.269902.115
chicago: Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of
Genomic Imprinting in Plants.” Genes and Development. Cold Spring Harbor
Laboratory Press, 2015. https://doi.org/10.1101/gad.269902.115.
ieee: J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting
in plants,” Genes and Development, vol. 29, no. 24. Cold Spring Harbor
Laboratory Press, pp. 2517–2531, 2015.
ista: Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting
in plants. Genes and Development. 29(24), 2517–2531.
mla: Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic
Imprinting in Plants.” Genes and Development, vol. 29, no. 24, Cold Spring
Harbor Laboratory Press, 2015, pp. 2517–2531, doi:10.1101/gad.269902.115.
short: J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531.
date_created: 2021-06-08T09:56:24Z
date_published: 2015-12-15T00:00:00Z
date_updated: 2021-12-14T07:58:15Z
day: '15'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1101/gad.269902.115
extern: '1'
external_id:
pmid:
- '26680300'
file:
- access_level: open_access
checksum: 086a88cfca4677646da26ed960cb02e9
content_type: application/pdf
creator: asandaue
date_created: 2021-06-08T09:55:10Z
date_updated: 2021-06-08T09:55:10Z
file_id: '9533'
file_name: 2015_GenesAndDevelopment_Rodrigues.pdf
file_size: 1116846
relation: main_file
success: 1
file_date_updated: 2021-06-08T09:55:10Z
has_accepted_license: '1'
intvolume: ' 29'
issue: '24'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '12'
oa: 1
oa_version: Published Version
page: 2517–2531
pmid: 1
publication: Genes and Development
publication_identifier:
eissn:
- 1549-5477
issn:
- 0890-9369
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolution and function of genomic imprinting in plants
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 29
year: '2015'
...
---
_id: '9519'
abstract:
- lang: eng
text: Transposons are selfish genetic sequences that can increase their copy number
and inflict substantial damage on their hosts. To combat these genomic parasites,
plants have evolved multiple pathways to identify and silence transposons by methylating
their DNA. Plants have also evolved mechanisms to limit the collateral damage
from the antitransposon machinery. In this review, we examine recent developments
that have elucidated many of the molecular workings of these pathways. We also
highlight the evidence that the methylation and demethylation pathways interact,
indicating that plants have a highly sophisticated, integrated system of transposon
defense that has an important role in the regulation of gene expression.
article_processing_charge: No
article_type: review
author:
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity.
Trends in Plant Science. 2014;19(5):320-326. doi:10.1016/j.tplants.2014.01.014
apa: Kim, M. Y., & Zilberman, D. (2014). DNA methylation as a system of plant
genomic immunity. Trends in Plant Science. Elsevier. https://doi.org/10.1016/j.tplants.2014.01.014
chicago: Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant
Genomic Immunity.” Trends in Plant Science. Elsevier, 2014. https://doi.org/10.1016/j.tplants.2014.01.014.
ieee: M. Y. Kim and D. Zilberman, “DNA methylation as a system of plant genomic
immunity,” Trends in Plant Science, vol. 19, no. 5. Elsevier, pp. 320–326,
2014.
ista: Kim MY, Zilberman D. 2014. DNA methylation as a system of plant genomic immunity.
Trends in Plant Science. 19(5), 320–326.
mla: Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant
Genomic Immunity.” Trends in Plant Science, vol. 19, no. 5, Elsevier, 2014,
pp. 320–26, doi:10.1016/j.tplants.2014.01.014.
short: M.Y. Kim, D. Zilberman, Trends in Plant Science 19 (2014) 320–326.
date_created: 2021-06-07T14:38:09Z
date_published: 2014-05-04T00:00:00Z
date_updated: 2021-12-14T08:24:48Z
day: '04'
department:
- _id: DaZi
doi: 10.1016/j.tplants.2014.01.014
extern: '1'
external_id:
pmid:
- '24618094 '
intvolume: ' 19'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 320-326
pmid: 1
publication: Trends in Plant Science
publication_identifier:
eissn:
- 1878-4372
issn:
- 1360-1385
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation as a system of plant genomic immunity
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 19
year: '2014'
...
---
_id: '9458'
abstract:
- lang: eng
text: Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes.
Their genomes are typically depleted of CG dinucleotides because of imperfect
repair of deaminated methylcytosines. Here, we extensively survey diverse species
lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless
frequently present and catalyzed by a different DNA methyltransferase family,
Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years
ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered
methylation occurs at unprecedented densities and directly disfavors nucleosomes,
contributing to nucleosome positioning between clusters. Dense methylation is
enabled by a regime of genomic sequence evolution that enriches CG dinucleotides
and drives the highest CG frequencies known. Species with linker methylation have
small, transcriptionally active nuclei that approach the physical limits of chromatin
compaction. These features constitute a previously unappreciated genome architecture,
in which dense methylation influences nucleosome positions, likely facilitating
nuclear processes under extreme spatial constraints.
article_processing_charge: No
article_type: original
author:
- first_name: Jason T.
full_name: Huff, Jason T.
last_name: Huff
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome
positioning in diverse eukaryotes. Cell. 2014;156(6):1286-1297. doi:10.1016/j.cell.2014.01.029
apa: Huff, J. T., & Zilberman, D. (2014). Dnmt1-independent CG methylation contributes
to nucleosome positioning in diverse eukaryotes. Cell. Elsevier. https://doi.org/10.1016/j.cell.2014.01.029
chicago: Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation
Contributes to Nucleosome Positioning in Diverse Eukaryotes.” Cell. Elsevier,
2014. https://doi.org/10.1016/j.cell.2014.01.029.
ieee: J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes
to nucleosome positioning in diverse eukaryotes,” Cell, vol. 156, no. 6.
Elsevier, pp. 1286–1297, 2014.
ista: Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to
nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297.
mla: Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes
to Nucleosome Positioning in Diverse Eukaryotes.” Cell, vol. 156, no. 6,
Elsevier, 2014, pp. 1286–97, doi:10.1016/j.cell.2014.01.029.
short: J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297.
date_created: 2021-06-04T12:00:16Z
date_published: 2014-03-13T00:00:00Z
date_updated: 2021-12-14T08:22:36Z
day: '13'
department:
- _id: DaZi
doi: 10.1016/j.cell.2014.01.029
extern: '1'
external_id:
pmid:
- '24630728'
intvolume: ' 156'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2014.01.029
month: '03'
oa: 1
oa_version: Published Version
page: 1286-1297
pmid: 1
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse
eukaryotes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 156
year: '2014'
...
---
_id: '9479'
abstract:
- lang: eng
text: Centromeres mediate chromosome segregation and are defined by the centromere-specific
histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from
centromeres is a general property of terminally differentiated cells, and the
persistence of CenH3 increases the risk of diseases such as cancer. However, active
mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen
vegetative cells, which transport engulfed sperm by extended tip growth, undergo
loss of CenH3; centromeric heterochromatin decondensation; and bulk activation
of silent rRNA genes, accompanied by their translocation into the nucleolus. Here,
we show that these processes are blocked by mutations in the evolutionarily conserved
AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97
proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier
(SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates
with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as
well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations.
In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are
uniquely clustered together within the nucleolus and all major rRNA gene variants,
including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant
vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed
centromeric heterochromatin at the external periphery of the nucleolus. Our results
indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres
and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus
for ribosome production, which fuels single nucleus-driven pollen tube growth
and is essential for plant reproduction.
article_processing_charge: No
article_type: original
author:
- first_name: Zsuzsanna
full_name: Mérai, Zsuzsanna
last_name: Mérai
- first_name: Nina
full_name: Chumak, Nina
last_name: Chumak
- first_name: Marcelina
full_name: García-Aguilar, Marcelina
last_name: García-Aguilar
- first_name: Tzung-Fu
full_name: Hsieh, Tzung-Fu
last_name: Hsieh
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Vera K.
full_name: Schoft, Vera K.
last_name: Schoft
- first_name: János
full_name: Bindics, János
last_name: Bindics
- first_name: Lucyna
full_name: Ślusarz, Lucyna
last_name: Ślusarz
- first_name: Stéphanie
full_name: Arnoux, Stéphanie
last_name: Arnoux
- first_name: Susanne
full_name: Opravil, Susanne
last_name: Opravil
- first_name: Karl
full_name: Mechtler, Karl
last_name: Mechtler
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Hisashi
full_name: Tamaru, Hisashi
last_name: Tamaru
citation:
ama: Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone
Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and
activates ribosomal RNA genes. Proceedings of the National Academy of Sciences.
2014;111(45):16166-16171. doi:10.1073/pnas.1418564111
apa: Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft,
V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles
sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA
genes. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1418564111
chicago: Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh,
Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular
Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin,
and Activates Ribosomal RNA Genes.” Proceedings of the National Academy of
Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1418564111.
ieee: Z. Mérai et al., “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles
sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA
genes,” Proceedings of the National Academy of Sciences, vol. 111, no.
45. National Academy of Sciences, pp. 16166–16171, 2014.
ista: Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics
J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru
H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated
centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings
of the National Academy of Sciences. 111(45), 16166–16171.
mla: Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles
Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA
Genes.” Proceedings of the National Academy of Sciences, vol. 111, no.
45, National Academy of Sciences, 2014, pp. 16166–71, doi:10.1073/pnas.1418564111.
short: Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft,
J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L.
Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014)
16166–16171.
date_created: 2021-06-07T07:23:43Z
date_published: 2014-11-11T00:00:00Z
date_updated: 2021-12-14T08:23:26Z
day: '11'
department:
- _id: DaZi
doi: 10.1073/pnas.1418564111
extern: '1'
external_id:
pmid:
- '25344531'
intvolume: ' 111'
issue: '45'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1418564111
month: '11'
oa: 1
oa_version: Published Version
page: 16166-16171
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres,
decondenses heterochromatin, and activates ribosomal RNA genes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 111
year: '2014'
...
---
_id: '9459'
abstract:
- lang: eng
text: Nucleosome remodelers of the DDM1/Lsh family are required for DNA methylation
of transposable elements, but the reason for this is unknown. How DDM1 interacts
with other methylation pathways, such as small-RNA-directed DNA methylation (RdDM),
which is thought to mediate plant asymmetric methylation through DRM enzymes,
is also unclear. Here, we show that most asymmetric methylation is facilitated
by DDM1 and mediated by the methyltransferase CMT2 separately from RdDM. We find
that heterochromatic sequences preferentially require DDM1 for DNA methylation
and that this preference depends on linker histone H1. RdDM is instead inhibited
by heterochromatin and absolutely requires the nucleosome remodeler DRD1. Together,
DDM1 and RdDM mediate nearly all transposon methylation and collaborate to repress
transposition and regulate the methylation and expression of genes. Our results
indicate that DDM1 provides DNA methyltransferases access to H1-containing heterochromatin
to allow stable silencing of transposable elements in cooperation with the RdDM
pathway.
article_processing_charge: No
article_type: original
author:
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Devin
full_name: Coleman-Derr, Devin
last_name: Coleman-Derr
- first_name: Leor
full_name: Eshed-Williams, Leor
last_name: Eshed-Williams
- first_name: Ka
full_name: Thao, Ka
last_name: Thao
- first_name: Stacey L.
full_name: Harmer, Stacey L.
last_name: Harmer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zemach A, Kim MY, Hsieh P-H, et al. The Arabidopsis nucleosome remodeler DDM1
allows DNA methyltransferases to access H1-containing heterochromatin. Cell.
2013;153(1):193-205. doi:10.1016/j.cell.2013.02.033
apa: Zemach, A., Kim, M. Y., Hsieh, P.-H., Coleman-Derr, D., Eshed-Williams, L.,
Thao, K., … Zilberman, D. (2013). The Arabidopsis nucleosome remodeler DDM1 allows
DNA methyltransferases to access H1-containing heterochromatin. Cell. Elsevier.
https://doi.org/10.1016/j.cell.2013.02.033
chicago: Zemach, Assaf, M. Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor
Eshed-Williams, Ka Thao, Stacey L. Harmer, and Daniel Zilberman. “The Arabidopsis
Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing
Heterochromatin.” Cell. Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.02.033.
ieee: A. Zemach et al., “The Arabidopsis nucleosome remodeler DDM1 allows
DNA methyltransferases to access H1-containing heterochromatin,” Cell,
vol. 153, no. 1. Elsevier, pp. 193–205, 2013.
ista: Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer
SL, Zilberman D. 2013. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases
to access H1-containing heterochromatin. Cell. 153(1), 193–205.
mla: Zemach, Assaf, et al. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA
Methyltransferases to Access H1-Containing Heterochromatin.” Cell, vol.
153, no. 1, Elsevier, 2013, pp. 193–205, doi:10.1016/j.cell.2013.02.033.
short: A. Zemach, M.Y. Kim, P.-H. Hsieh, D. Coleman-Derr, L. Eshed-Williams, K.
Thao, S.L. Harmer, D. Zilberman, Cell 153 (2013) 193–205.
date_created: 2021-06-04T12:23:28Z
date_published: 2013-03-28T00:00:00Z
date_updated: 2021-12-14T08:25:35Z
day: '28'
department:
- _id: DaZi
doi: 10.1016/j.cell.2013.02.033
extern: '1'
external_id:
pmid:
- '23540698'
intvolume: ' 153'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2013.02.033
month: '03'
oa: 1
oa_version: Published Version
page: 193-205
pmid: 1
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to
access H1-containing heterochromatin
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 153
year: '2013'
...
---
_id: '9481'
abstract:
- lang: eng
text: Arabidopsis thaliana endosperm, a transient tissue that nourishes the embryo,
exhibits extensive localized DNA demethylation on maternally inherited chromosomes.
Demethylation mediates parent-of-origin–specific (imprinted) gene expression but
is apparently unnecessary for the extensive accumulation of maternally biased
small RNA (sRNA) molecules detected in seeds. Endosperm DNA in the distantly related
monocots rice and maize is likewise locally hypomethylated, but whether this hypomethylation
is generally parent-of-origin specific is unknown. Imprinted expression of sRNA
also remains uninvestigated in monocot seeds. Here, we report high-coverage sequencing
of the Kitaake rice cultivar that enabled us to show that localized hypomethylation
in rice endosperm occurs solely on the maternal genome, preferring regions of
high DNA accessibility. Maternally expressed imprinted genes are enriched for
hypomethylation at putative promoter regions and transcriptional termini and paternally
expressed genes at promoters and gene bodies, mirroring our recent results in
A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are
dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are
expressed from both parental genomes and correlate with hypomethylation. Overlaps
between imprinted sRNA loci and imprinted genes expressed from opposite alleles
suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling
tissues primarily originate from small class II (cut-and-paste) transposable elements,
those in endosperm are more uniformly derived, including sequences from other
transposon classes, as well as genic and intergenic regions. Our data indicate
that the endosperm exhibits a unique pattern of sRNA expression and suggest that
localized hypomethylation of maternal endosperm DNA is conserved in flowering
plants.
article_processing_charge: No
article_type: original
author:
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Randy
full_name: Ruan, Randy
last_name: Ruan
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Manoj K.
full_name: Sharma, Manoj K.
last_name: Sharma
- first_name: Rita
full_name: Sharma, Rita
last_name: Sharma
- first_name: Pamela C
full_name: Ronald, Pamela C
last_name: Ronald
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Rodrigues JA, Ruan R, Nishimura T, et al. Imprinted expression of genes and
small RNA is associated with localized hypomethylation of the maternal genome
in rice endosperm. Proceedings of the National Academy of Sciences. 2013;110(19):7934-7939.
doi:10.1073/pnas.1306164110
apa: Rodrigues, J. A., Ruan, R., Nishimura, T., Sharma, M. K., Sharma, R., Ronald,
P. C., … Zilberman, D. (2013). Imprinted expression of genes and small RNA is
associated with localized hypomethylation of the maternal genome in rice endosperm.
Proceedings of the National Academy of Sciences. National Academy of Sciences.
https://doi.org/10.1073/pnas.1306164110
chicago: Rodrigues, Jessica A., Randy Ruan, Toshiro Nishimura, Manoj K. Sharma,
Rita Sharma, Pamela C Ronald, Robert L. Fischer, and Daniel Zilberman. “Imprinted
Expression of Genes and Small RNA Is Associated with Localized Hypomethylation
of the Maternal Genome in Rice Endosperm.” Proceedings of the National Academy
of Sciences. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1306164110.
ieee: J. A. Rodrigues et al., “Imprinted expression of genes and small RNA
is associated with localized hypomethylation of the maternal genome in rice endosperm,”
Proceedings of the National Academy of Sciences, vol. 110, no. 19. National
Academy of Sciences, pp. 7934–7939, 2013.
ista: Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Fischer
RL, Zilberman D. 2013. Imprinted expression of genes and small RNA is associated
with localized hypomethylation of the maternal genome in rice endosperm. Proceedings
of the National Academy of Sciences. 110(19), 7934–7939.
mla: Rodrigues, Jessica A., et al. “Imprinted Expression of Genes and Small RNA
Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.”
Proceedings of the National Academy of Sciences, vol. 110, no. 19, National
Academy of Sciences, 2013, pp. 7934–39, doi:10.1073/pnas.1306164110.
short: J.A. Rodrigues, R. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, P.C. Ronald,
R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 110
(2013) 7934–7939.
date_created: 2021-06-07T07:31:02Z
date_published: 2013-05-07T00:00:00Z
date_updated: 2021-12-14T08:26:44Z
day: '07'
department:
- _id: DaZi
doi: 10.1073/pnas.1306164110
extern: '1'
external_id:
pmid:
- '23613580'
intvolume: ' 110'
issue: '19'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1306164110
month: '05'
oa: 1
oa_version: Published Version
page: 7934-7939
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Imprinted expression of genes and small RNA is associated with localized hypomethylation
of the maternal genome in rice endosperm
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 110
year: '2013'
...
---
_id: '9520'
abstract:
- lang: eng
text: Plants undergo alternation of generation in which reproductive cells develop
in the plant body ("sporophytic generation") and then differentiate into a multicellular
gamete-forming "gametophytic generation." Different populations of helper cells
assist in this transgenerational journey, with somatic tissues supporting early
development and single nurse cells supporting gametogenesis. New data reveal a
two-way relationship between early reproductive cells and their helpers involving
complex epigenetic and signaling networks determining cell number and fate. Later,
the egg cell plays a central role in specifying accessory cells, whereas in both
gametophytes, companion cells contribute non-cell-autonomously to the epigenetic
landscape of the gamete genomes.
article_processing_charge: No
article_type: review
author:
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Hugh
full_name: Dickinson, Hugh
last_name: Dickinson
citation:
ama: 'Feng X, Zilberman D, Dickinson H. A conversation across generations: Soma-germ
cell crosstalk in plants. Developmental Cell. 2013;24(3):215-225. doi:10.1016/j.devcel.2013.01.014'
apa: 'Feng, X., Zilberman, D., & Dickinson, H. (2013). A conversation across
generations: Soma-germ cell crosstalk in plants. Developmental Cell. Elsevier.
https://doi.org/10.1016/j.devcel.2013.01.014'
chicago: 'Feng, Xiaoqi, Daniel Zilberman, and Hugh Dickinson. “A Conversation across
Generations: Soma-Germ Cell Crosstalk in Plants.” Developmental Cell. Elsevier,
2013. https://doi.org/10.1016/j.devcel.2013.01.014.'
ieee: 'X. Feng, D. Zilberman, and H. Dickinson, “A conversation across generations:
Soma-germ cell crosstalk in plants,” Developmental Cell, vol. 24, no. 3.
Elsevier, pp. 215–225, 2013.'
ista: 'Feng X, Zilberman D, Dickinson H. 2013. A conversation across generations:
Soma-germ cell crosstalk in plants. Developmental Cell. 24(3), 215–225.'
mla: 'Feng, Xiaoqi, et al. “A Conversation across Generations: Soma-Germ Cell Crosstalk
in Plants.” Developmental Cell, vol. 24, no. 3, Elsevier, 2013, pp. 215–25,
doi:10.1016/j.devcel.2013.01.014.'
short: X. Feng, D. Zilberman, H. Dickinson, Developmental Cell 24 (2013) 215–225.
date_created: 2021-06-08T06:14:50Z
date_published: 2013-02-11T00:00:00Z
date_updated: 2023-05-08T11:00:59Z
day: '11'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1016/j.devcel.2013.01.014
extern: '1'
external_id:
pmid:
- '23410937'
intvolume: ' 24'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.devcel.2013.01.014
month: '02'
oa: 1
oa_version: Published Version
page: 215-225
pmid: 1
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'A conversation across generations: Soma-germ cell crosstalk in plants'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2013'
...
---
_id: '9451'
abstract:
- lang: eng
text: The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes
DNA demethylation before fertilization, but the targeting preferences, mechanism,
and biological significance of this process remain unclear. Here, we show that
active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for
all of the demethylation in the central cell and preferentially targets small,
AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative
cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation
of similar sequences, and lack of DEMETER in vegetative cells causes reduced small
RNA–directed DNA methylation of transposons in sperm. Our results demonstrate
that demethylation in companion cells reinforces transposon methylation in plant
gametes and likely contributes to stable silencing of transposable elements across
generations.
article_processing_charge: No
article_type: original
author:
- first_name: Christian A.
full_name: Ibarra, Christian A.
last_name: Ibarra
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
last_name: Feng
- first_name: Vera K.
full_name: Schoft, Vera K.
last_name: Schoft
- first_name: Tzung-Fu
full_name: Hsieh, Tzung-Fu
last_name: Hsieh
- first_name: Rie
full_name: Uzawa, Rie
last_name: Uzawa
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: Nina
full_name: Chumak, Nina
last_name: Chumak
- first_name: Adriana
full_name: Machlicova, Adriana
last_name: Machlicova
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Denisse
full_name: Rojas, Denisse
last_name: Rojas
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Hisashi
full_name: Tamaru, Hisashi
last_name: Tamaru
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion
cells reinforces transposon methylation in gametes. Science. 2012;337(6100):1360-1364.
doi:10.1126/science.1224839
apa: Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues,
J. A., … Zilberman, D. (2012). Active DNA demethylation in plant companion cells
reinforces transposon methylation in gametes. Science. American Association
for the Advancement of Science. https://doi.org/10.1126/science.1224839
chicago: Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie
Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in
Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science.
American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1224839.
ieee: C. A. Ibarra et al., “Active DNA demethylation in plant companion cells
reinforces transposon methylation in gametes,” Science, vol. 337, no. 6100.
American Association for the Advancement of Science, pp. 1360–1364, 2012.
ista: Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, Rodrigues JA, Zemach A,
Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman
D. 2012. Active DNA demethylation in plant companion cells reinforces transposon
methylation in gametes. Science. 337(6100), 1360–1364.
mla: Ibarra, Christian A., et al. “Active DNA Demethylation in Plant Companion Cells
Reinforces Transposon Methylation in Gametes.” Science, vol. 337, no. 6100,
American Association for the Advancement of Science, 2012, pp. 1360–64, doi:10.1126/science.1224839.
short: C.A. Ibarra, X. Feng, V.K. Schoft, T.-F. Hsieh, R. Uzawa, J.A. Rodrigues,
A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R.L. Fischer, H.
Tamaru, D. Zilberman, Science 337 (2012) 1360–1364.
date_created: 2021-06-04T07:51:31Z
date_published: 2012-09-14T00:00:00Z
date_updated: 2021-12-14T08:28:51Z
day: '14'
ddc:
- '580'
department:
- _id: DaZi
doi: 10.1126/science.1224839
extern: '1'
external_id:
pmid:
- '22984074'
has_accepted_license: '1'
intvolume: ' 337'
issue: '6100'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034762/
month: '09'
oa: 1
oa_version: Published Version
page: 1360-1364
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Active DNA demethylation in plant companion cells reinforces transposon methylation
in gametes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 337
year: '2012'
...
---
_id: '9535'
abstract:
- lang: eng
text: The most well-studied function of DNA methylation in eukaryotic cells is the
transcriptional silencing of genes and transposons. More recent results showed
that many eukaryotes methylate the bodies of genes as well and that this methylation
correlates with transcriptional activity rather than repression. The purpose of
gene body methylation remains mysterious, but is potentially related to the histone
variant H2A.Z. Studies in plants and animals have shown that the genome-wide distributions
of H2A.Z and DNA methylation are strikingly anticorrelated. Furthermore, we and
other investigators have shown that this relationship is likely to be the result
of an ancient but unknown mechanism by which DNA methylation prevents the incorporation
of H2A.Z. Recently, we discovered strong correlations between the presence of
H2A.Z within gene bodies, the degree to which a gene's expression varies across
tissue types or environmental conditions, and transcriptional misregulation in
an h2a.z mutant. We propose that one basal function of gene body methylation is
the establishment of constitutive expression patterns within housekeeping genes
by excluding H2A.Z from their bodies.
article_processing_charge: No
article_type: review
author:
- first_name: D.
full_name: Coleman-Derr, D.
last_name: Coleman-Derr
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Coleman-Derr D, Zilberman D. DNA methylation, H2A.Z, and the regulation of
constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology.
2012;77:147-154. doi:10.1101/sqb.2012.77.014944
apa: Coleman-Derr, D., & Zilberman, D. (2012). DNA methylation, H2A.Z, and the
regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative
Biology. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/sqb.2012.77.014944
chicago: Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the
Regulation of Constitutive Expression.” Cold Spring Harbor Symposia on Quantitative
Biology. Cold Spring Harbor Laboratory Press, 2012. https://doi.org/10.1101/sqb.2012.77.014944.
ieee: D. Coleman-Derr and D. Zilberman, “DNA methylation, H2A.Z, and the regulation
of constitutive expression,” Cold Spring Harbor Symposia on Quantitative Biology,
vol. 77. Cold Spring Harbor Laboratory Press, pp. 147–154, 2012.
ista: Coleman-Derr D, Zilberman D. 2012. DNA methylation, H2A.Z, and the regulation
of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology.
77, 147–154.
mla: Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation
of Constitutive Expression.” Cold Spring Harbor Symposia on Quantitative Biology,
vol. 77, Cold Spring Harbor Laboratory Press, 2012, pp. 147–54, doi:10.1101/sqb.2012.77.014944.
short: D. Coleman-Derr, D. Zilberman, Cold Spring Harbor Symposia on Quantitative
Biology 77 (2012) 147–154.
date_created: 2021-06-08T13:01:23Z
date_published: 2012-12-18T00:00:00Z
date_updated: 2021-12-14T08:33:09Z
day: '18'
department:
- _id: DaZi
doi: 10.1101/sqb.2012.77.014944
extern: '1'
external_id:
pmid:
- '23250988'
intvolume: ' 77'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/sqb.2012.77.014944
month: '12'
oa: 1
oa_version: Published Version
page: 147-154
pmid: 1
publication: Cold Spring Harbor Symposia on Quantitative Biology
publication_identifier:
eissn:
- 1943-4456
issn:
- 0091-7451
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation, H2A.Z, and the regulation of constitutive expression
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 77
year: '2012'
...
---
_id: '9499'
abstract:
- lang: eng
text: EMBRYONIC FLOWER1 (EMF1) is a plant-specific gene crucial to Arabidopsis vegetative
development. Loss of function mutants in the EMF1 gene mimic the phenotype caused
by mutations in Polycomb Group protein (PcG) genes, which encode epigenetic repressors
that regulate many aspects of eukaryotic development. In Arabidopsis, Polycomb
Repressor Complex 2 (PRC2), made of PcG proteins, catalyzes trimethylation of
lysine 27 on histone H3 (H3K27me3) and PRC1-like proteins catalyze H2AK119 ubiquitination.
Despite functional similarity to PcG proteins, EMF1 lacks sequence homology with
known PcG proteins; thus, its role in the PcG mechanism is unclear. To study the
EMF1 functions and its mechanism of action, we performed genome-wide mapping of
EMF1 binding and H3K27me3 modification sites in Arabidopsis seedlings. The EMF1
binding pattern is similar to that of H3K27me3 modification on the chromosomal
and genic level. ChIPOTLe peak finding and clustering analyses both show that
the highly trimethylated genes also have high enrichment levels of EMF1 binding,
termed EMF1_K27 genes. EMF1 interacts with regulatory genes, which are silenced
to allow vegetative growth, and with genes specifying cell fates during growth
and differentiation. H3K27me3 marks not only these genes but also some genes that
are involved in endosperm development and maternal effects. Transcriptome analysis,
coupled with the H3K27me3 pattern, of EMF1_K27 genes in emf1 and PRC2 mutants
showed that EMF1 represses gene activities via diverse mechanisms and plays a
novel role in the PcG mechanism.
article_number: e1002512
article_processing_charge: No
article_type: original
author:
- first_name: Sang Yeol
full_name: Kim, Sang Yeol
last_name: Kim
- first_name: Jungeun
full_name: Lee, Jungeun
last_name: Lee
- first_name: Leor
full_name: Eshed-Williams, Leor
last_name: Eshed-Williams
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Z. Renee
full_name: Sung, Z. Renee
last_name: Sung
citation:
ama: Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. EMF1 and PRC2 cooperate
to repress key regulators of Arabidopsis development. PLoS Genetics. 2012;8(3).
doi:10.1371/journal.pgen.1002512
apa: Kim, S. Y., Lee, J., Eshed-Williams, L., Zilberman, D., & Sung, Z. R. (2012).
EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development.
PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002512
chicago: Kim, Sang Yeol, Jungeun Lee, Leor Eshed-Williams, Daniel Zilberman, and
Z. Renee Sung. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis
Development.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002512.
ieee: S. Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, and Z. R. Sung, “EMF1
and PRC2 cooperate to repress key regulators of Arabidopsis development,” PLoS
Genetics, vol. 8, no. 3. Public Library of Science, 2012.
ista: Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. 2012. EMF1 and PRC2
cooperate to repress key regulators of Arabidopsis development. PLoS Genetics.
8(3), e1002512.
mla: Kim, Sang Yeol, et al. “EMF1 and PRC2 Cooperate to Repress Key Regulators of
Arabidopsis Development.” PLoS Genetics, vol. 8, no. 3, e1002512, Public
Library of Science, 2012, doi:10.1371/journal.pgen.1002512.
short: S.Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, Z.R. Sung, PLoS Genetics
8 (2012).
date_created: 2021-06-07T11:07:56Z
date_published: 2012-03-22T00:00:00Z
date_updated: 2021-12-14T08:31:14Z
day: '22'
department:
- _id: DaZi
doi: 10.1371/journal.pgen.1002512
extern: '1'
external_id:
pmid:
- '22457632'
intvolume: ' 8'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1371/journal.pgen.1002512
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Genetics
publication_identifier:
eissn:
- 1553-7404
issn:
- 1553-7390
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 8
year: '2012'
...
---
_id: '9497'
abstract:
- lang: eng
text: The regulation of eukaryotic chromatin relies on interactions between many
epigenetic factors, including histone modifications, DNA methylation, and the
incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic
histone variants that is enriched at the transcriptional start sites of genes,
has been implicated in a variety of chromosomal processes. Recently, we reported
a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic
hallmark of heterochromatin that has also been found in the bodies of active genes
in plants and animals. Here, we investigate the basis of this anticorrelation
using a novel h2a.z loss-of-function line in Arabidopsis thaliana. Through genome-wide
bisulfite sequencing, we demonstrate that loss of H2A.Z in Arabidopsis has only
a minor effect on the level or profile of DNA methylation in genes, and we propose
that the global anticorrelation between DNA methylation and H2A.Z is primarily
caused by the exclusion of H2A.Z from methylated DNA. RNA sequencing and genomic
mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at
the TSS, is correlated with lower transcription levels and higher measures of
gene responsiveness. Loss of H2A.Z causes misregulation of many genes that are
disproportionately associated with response to environmental and developmental
stimuli. We propose that H2A.Z deposition in gene bodies promotes variability
in levels and patterns of gene expression, and that a major function of genic
DNA methylation is to exclude H2A.Z from constitutively expressed genes.
article_number: e1002988
article_processing_charge: No
article_type: original
author:
- first_name: Devin
full_name: Coleman-Derr, Devin
last_name: Coleman-Derr
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Coleman-Derr D, Zilberman D. Deposition of histone variant H2A.Z within gene
bodies regulates responsive genes. PLoS Genetics. 2012;8(10). doi:10.1371/journal.pgen.1002988
apa: Coleman-Derr, D., & Zilberman, D. (2012). Deposition of histone variant
H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. Public
Library of Science. https://doi.org/10.1371/journal.pgen.1002988
chicago: Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant
H2A.Z within Gene Bodies Regulates Responsive Genes.” PLoS Genetics. Public
Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002988.
ieee: D. Coleman-Derr and D. Zilberman, “Deposition of histone variant H2A.Z within
gene bodies regulates responsive genes,” PLoS Genetics, vol. 8, no. 10.
Public Library of Science, 2012.
ista: Coleman-Derr D, Zilberman D. 2012. Deposition of histone variant H2A.Z within
gene bodies regulates responsive genes. PLoS Genetics. 8(10), e1002988.
mla: Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z
within Gene Bodies Regulates Responsive Genes.” PLoS Genetics, vol. 8,
no. 10, e1002988, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002988.
short: D. Coleman-Derr, D. Zilberman, PLoS Genetics 8 (2012).
date_created: 2021-06-07T10:55:27Z
date_published: 2012-10-11T00:00:00Z
date_updated: 2021-12-14T08:29:57Z
day: '11'
department:
- _id: DaZi
doi: 10.1371/journal.pgen.1002988
extern: '1'
external_id:
pmid:
- '23071449'
intvolume: ' 8'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1371/journal.pgen.1002988
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Genetics
publication_identifier:
eissn:
- 1553-7404
issn:
- 1553-7390
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Deposition of histone variant H2A.Z within gene bodies regulates responsive
genes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 8
year: '2012'
...
---
_id: '9528'
abstract:
- lang: eng
text: Accumulating evidence points toward diverse functions for plant chromatin.
Remarkable progress has been made over the last few years in elucidating the mechanisms
for a number of these functions. Activity of the histone demethylase IBM1 accurately
targets DNA methylation to silent repeats and transposable elements, not to genes.
A genetic screen uncovered the surprising role of H2A.Z-containing nucleosomes
in sensing precise differences in ambient temperature and consequent gene regulation.
Precise maintenance of chromosome number is assured by a histone modification
that suppresses inappropriate DNA replication and by centromeric histone H3 regulation
of chromosome segregation. Histones and noncoding RNAs regulate FLOWERING LOCUS
C, the expression of which quantitatively measures the duration of cold exposure,
functioning as memory of winter. These findings are a testament to the power of
using plants to research chromatin organization, and demonstrate examples of how
chromatin functions to achieve biological accuracy, precision, and memory.
article_processing_charge: No
article_type: review
author:
- first_name: Jason T.
full_name: Huff, Jason T.
last_name: Huff
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Huff JT, Zilberman D. Regulation of biological accuracy, precision, and memory
by plant chromatin organization. Current Opinion in Genetics and Development.
2012;22(2):132-138. doi:10.1016/j.gde.2012.01.007
apa: Huff, J. T., & Zilberman, D. (2012). Regulation of biological accuracy,
precision, and memory by plant chromatin organization. Current Opinion in Genetics
and Development. Elsevier. https://doi.org/10.1016/j.gde.2012.01.007
chicago: Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy,
Precision, and Memory by Plant Chromatin Organization.” Current Opinion in
Genetics and Development. Elsevier, 2012. https://doi.org/10.1016/j.gde.2012.01.007.
ieee: J. T. Huff and D. Zilberman, “Regulation of biological accuracy, precision,
and memory by plant chromatin organization,” Current Opinion in Genetics and
Development, vol. 22, no. 2. Elsevier, pp. 132–138, 2012.
ista: Huff JT, Zilberman D. 2012. Regulation of biological accuracy, precision,
and memory by plant chromatin organization. Current Opinion in Genetics and Development.
22(2), 132–138.
mla: Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision,
and Memory by Plant Chromatin Organization.” Current Opinion in Genetics and
Development, vol. 22, no. 2, Elsevier, 2012, pp. 132–38, doi:10.1016/j.gde.2012.01.007.
short: J.T. Huff, D. Zilberman, Current Opinion in Genetics and Development 22 (2012)
132–138.
date_created: 2021-06-08T08:58:52Z
date_published: 2012-04-01T00:00:00Z
date_updated: 2021-12-14T08:32:38Z
department:
- _id: DaZi
doi: 10.1016/j.gde.2012.01.007
extern: '1'
external_id:
pmid:
- '22336527'
intvolume: ' 22'
issue: '2'
language:
- iso: eng
month: '04'
oa_version: None
page: 132-138
pmid: 1
publication: Current Opinion in Genetics and Development
publication_identifier:
issn:
- 0959-437X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Regulation of biological accuracy, precision, and memory by plant chromatin
organization
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 22
year: '2012'
...
---
_id: '9483'
abstract:
- lang: eng
text: Imprinted genes are expressed primarily or exclusively from either the maternal
or paternal allele, a phenomenon that occurs in flowering plants and mammals.
Flowering plant imprinted gene expression has been described primarily in endosperm,
a terminal nutritive tissue consumed by the embryo during seed development or
after germination. Imprinted expression in Arabidopsis thaliana endosperm is orchestrated
by differences in cytosine DNA methylation between the paternal and maternal genomes
as well as by Polycomb group proteins. Currently, only 11 imprinted A. thaliana
genes are known. Here, we use extensive sequencing of cDNA libraries to identify
9 paternally expressed and 34 maternally expressed imprinted genes in A. thaliana
endosperm that are regulated by the DNA-demethylating glycosylase DEMETER, the
DNA methyltransferase MET1, and/or the core Polycomb group protein FIE. These
genes encode transcription factors, proteins involved in hormone signaling, components
of the ubiquitin protein degradation pathway, regulators of histone and DNA methylation,
and small RNA pathway proteins. We also identify maternally expressed genes that
may be regulated by unknown mechanisms or deposited from maternal tissues. We
did not detect any imprinted genes in the embryo. Our results show that imprinted
gene expression is an extensive mechanistically complex phenomenon that likely
affects multiple aspects of seed development.
article_processing_charge: No
article_type: original
author:
- first_name: Tzung-Fu
full_name: Hsieh, Tzung-Fu
last_name: Hsieh
- first_name: Juhyun
full_name: Shin, Juhyun
last_name: Shin
- first_name: Rie
full_name: Uzawa, Rie
last_name: Uzawa
- first_name: Pedro
full_name: Silva, Pedro
last_name: Silva
- first_name: Stephanie
full_name: Cohen, Stephanie
last_name: Cohen
- first_name: Matthew J.
full_name: Bauer, Matthew J.
last_name: Bauer
- first_name: Meryl
full_name: Hashimoto, Meryl
last_name: Hashimoto
- first_name: Ryan C.
full_name: Kirkbride, Ryan C.
last_name: Kirkbride
- first_name: John J.
full_name: Harada, John J.
last_name: Harada
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
citation:
ama: Hsieh T-F, Shin J, Uzawa R, et al. Regulation of imprinted gene expression
in Arabidopsis endosperm. Proceedings of the National Academy of Sciences.
2011;108(5):1755-1762. doi:10.1073/pnas.1019273108
apa: Hsieh, T.-F., Shin, J., Uzawa, R., Silva, P., Cohen, S., Bauer, M. J., … Fischer,
R. L. (2011). Regulation of imprinted gene expression in Arabidopsis endosperm.
Proceedings of the National Academy of Sciences. National Academy of Sciences.
https://doi.org/10.1073/pnas.1019273108
chicago: Hsieh, Tzung-Fu, Juhyun Shin, Rie Uzawa, Pedro Silva, Stephanie Cohen,
Matthew J. Bauer, Meryl Hashimoto, et al. “Regulation of Imprinted Gene Expression
in Arabidopsis Endosperm.” Proceedings of the National Academy of Sciences.
National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1019273108.
ieee: T.-F. Hsieh et al., “Regulation of imprinted gene expression in Arabidopsis
endosperm,” Proceedings of the National Academy of Sciences, vol. 108,
no. 5. National Academy of Sciences, pp. 1755–1762, 2011.
ista: Hsieh T-F, Shin J, Uzawa R, Silva P, Cohen S, Bauer MJ, Hashimoto M, Kirkbride
RC, Harada JJ, Zilberman D, Fischer RL. 2011. Regulation of imprinted gene expression
in Arabidopsis endosperm. Proceedings of the National Academy of Sciences. 108(5),
1755–1762.
mla: Hsieh, Tzung-Fu, et al. “Regulation of Imprinted Gene Expression in Arabidopsis
Endosperm.” Proceedings of the National Academy of Sciences, vol. 108,
no. 5, National Academy of Sciences, 2011, pp. 1755–62, doi:10.1073/pnas.1019273108.
short: T.-F. Hsieh, J. Shin, R. Uzawa, P. Silva, S. Cohen, M.J. Bauer, M. Hashimoto,
R.C. Kirkbride, J.J. Harada, D. Zilberman, R.L. Fischer, Proceedings of the National
Academy of Sciences 108 (2011) 1755–1762.
date_created: 2021-06-07T07:40:38Z
date_published: 2011-02-01T00:00:00Z
date_updated: 2021-12-14T08:33:49Z
day: '01'
department:
- _id: DaZi
doi: 10.1073/pnas.1019273108
extern: '1'
external_id:
pmid:
- '21257907'
intvolume: ' 108'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1019273108
month: '02'
oa: 1
oa_version: Published Version
page: 1755-1762
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Regulation of imprinted gene expression in Arabidopsis endosperm
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 108
year: '2011'
...
---
_id: '9522'
abstract:
- lang: eng
text: Little is known about chromatin remodeling events immediately after fertilization.
A recent report by Autran et al. (2011) in Cell now shows that chromatin regulatory
pathways that silence transposable elements are responsible for global delayed
activation of gene expression in the early Arabidopsis embryo.
article_processing_charge: No
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zilberman D. Balancing Parental Contributions in Plant Embryonic Gene Activation.
Vol 20. Elsevier; 2011:735-736. doi:10.1016/j.devcel.2011.05.018
apa: Zilberman, D. (2011). Balancing parental contributions in plant embryonic
gene activation. Developmental Cell (Vol. 20, pp. 735–736). Elsevier.
https://doi.org/10.1016/j.devcel.2011.05.018
chicago: Zilberman, Daniel. Balancing Parental Contributions in Plant Embryonic
Gene Activation. Developmental Cell. Vol. 20. Elsevier, 2011. https://doi.org/10.1016/j.devcel.2011.05.018.
ieee: D. Zilberman, Balancing parental contributions in plant embryonic gene
activation, vol. 20, no. 6. Elsevier, 2011, pp. 735–736.
ista: Zilberman D. 2011. Balancing parental contributions in plant embryonic gene
activation, Elsevier,p.
mla: Zilberman, Daniel. “Balancing Parental Contributions in Plant Embryonic Gene
Activation.” Developmental Cell, vol. 20, no. 6, Elsevier, 2011, pp. 735–36,
doi:10.1016/j.devcel.2011.05.018.
short: D. Zilberman, Balancing Parental Contributions in Plant Embryonic Gene Activation,
Elsevier, 2011.
date_created: 2021-06-08T06:23:39Z
date_published: 2011-06-14T00:00:00Z
date_updated: 2021-12-14T08:34:37Z
day: '14'
department:
- _id: DaZi
doi: 10.1016/j.devcel.2011.05.018
extern: '1'
external_id:
pmid:
- '21664571'
intvolume: ' 20'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.devcel.2011.05.018
month: '06'
oa: 1
oa_version: Published Version
page: 735-736
pmid: 1
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Balancing parental contributions in plant embryonic gene activation
type: other_academic_publication
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 20
year: '2011'
...
---
_id: '9485'
abstract:
- lang: eng
text: 'Cytosine methylation silences transposable elements in plants, vertebrates,
and fungi but also regulates gene expression. Plant methylation is catalyzed by
three families of enzymes, each with a preferred sequence context: CG, CHG (H
= A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis
thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally
hypomethylated in the CG context while retaining high non-CG methylation. Global
methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition
remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all
sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas
CG hypomethylation is localized. CHH methylation of small transposable elements
is increased in embryos, suggesting that endosperm demethylation enhances transposon
silencing. Genes preferentially expressed in endosperm, including those coding
for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated
in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm
biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is
conserved among angiosperms and has a profound effect on gene expression in cereal
crops.'
article_processing_charge: No
article_type: original
author:
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Pedro
full_name: Silva, Pedro
last_name: Silva
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Bradley
full_name: Dotson, Bradley
last_name: Dotson
- first_name: Matthew D.
full_name: Brooks, Matthew D.
last_name: Brooks
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zemach A, Kim MY, Silva P, et al. Local DNA hypomethylation activates genes
in rice endosperm. Proceedings of the National Academy of Sciences. 2010;107(43):18729-18734.
doi:10.1073/pnas.1009695107
apa: Zemach, A., Kim, M. Y., Silva, P., Rodrigues, J. A., Dotson, B., Brooks, M.
D., & Zilberman, D. (2010). Local DNA hypomethylation activates genes in rice
endosperm. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1009695107
chicago: Zemach, Assaf, M. Yvonne Kim, Pedro Silva, Jessica A. Rodrigues, Bradley
Dotson, Matthew D. Brooks, and Daniel Zilberman. “Local DNA Hypomethylation Activates
Genes in Rice Endosperm.” Proceedings of the National Academy of Sciences.
National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.1009695107.
ieee: A. Zemach et al., “Local DNA hypomethylation activates genes in rice
endosperm,” Proceedings of the National Academy of Sciences, vol. 107,
no. 43. National Academy of Sciences, pp. 18729–18734, 2010.
ista: Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, Brooks MD, Zilberman D.
2010. Local DNA hypomethylation activates genes in rice endosperm. Proceedings
of the National Academy of Sciences. 107(43), 18729–18734.
mla: Zemach, Assaf, et al. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.”
Proceedings of the National Academy of Sciences, vol. 107, no. 43, National
Academy of Sciences, 2010, pp. 18729–34, doi:10.1073/pnas.1009695107.
short: A. Zemach, M.Y. Kim, P. Silva, J.A. Rodrigues, B. Dotson, M.D. Brooks, D.
Zilberman, Proceedings of the National Academy of Sciences 107 (2010) 18729–18734.
date_created: 2021-06-07T09:31:01Z
date_published: 2010-10-26T00:00:00Z
date_updated: 2021-12-14T08:40:02Z
day: '26'
department:
- _id: DaZi
doi: 10.1073/pnas.1009695107
extern: '1'
external_id:
pmid:
- '20937895'
intvolume: ' 107'
issue: '43'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1009695107
month: '10'
oa: 1
oa_version: Published Version
page: 18729-18734
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Local DNA hypomethylation activates genes in rice endosperm
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 107
year: '2010'
...
---
_id: '9489'
abstract:
- lang: eng
text: Cytosine methylation is an ancient process with conserved enzymology but diverse
biological functions that include defense against transposable elements and regulation
of gene expression. Here we will discuss the evolution and biological significance
of eukaryotic DNA methylation, the likely drivers of that evolution, and major
remaining mysteries.
article_processing_charge: No
article_type: review
author:
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zemach A, Zilberman D. Evolution of eukaryotic DNA methylation and the pursuit
of safer sex. Current Biology. 2010;20(17):R780-R785. doi:10.1016/j.cub.2010.07.007
apa: Zemach, A., & Zilberman, D. (2010). Evolution of eukaryotic DNA methylation
and the pursuit of safer sex. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2010.07.007
chicago: Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation
and the Pursuit of Safer Sex.” Current Biology. Elsevier, 2010. https://doi.org/10.1016/j.cub.2010.07.007.
ieee: A. Zemach and D. Zilberman, “Evolution of eukaryotic DNA methylation and the
pursuit of safer sex,” Current Biology, vol. 20, no. 17. Elsevier, pp.
R780–R785, 2010.
ista: Zemach A, Zilberman D. 2010. Evolution of eukaryotic DNA methylation and the
pursuit of safer sex. Current Biology. 20(17), R780–R785.
mla: Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation
and the Pursuit of Safer Sex.” Current Biology, vol. 20, no. 17, Elsevier,
2010, pp. R780–85, doi:10.1016/j.cub.2010.07.007.
short: A. Zemach, D. Zilberman, Current Biology 20 (2010) R780–R785.
date_created: 2021-06-07T09:45:27Z
date_published: 2010-09-14T00:00:00Z
date_updated: 2021-12-14T08:52:34Z
day: '14'
department:
- _id: DaZi
doi: 10.1016/j.cub.2010.07.007
extern: '1'
external_id:
pmid:
- '20833323'
intvolume: ' 20'
issue: '17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2010.07.007
month: '09'
oa: 1
oa_version: Published Version
page: R780-R785
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolution of eukaryotic DNA methylation and the pursuit of safer sex
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 20
year: '2010'
...
---
_id: '9452'
abstract:
- lang: eng
text: Eukaryotic cytosine methylation represses transcription but also occurs in
the bodies of active genes, and the extent of methylation biology conservation
is unclear. We quantified DNA methylation in 17 eukaryotic genomes and found that
gene body methylation is conserved between plants and animals, whereas selective
methylation of transposons is not. We show that methylation of plant transposons
in the CHG context extends to green algae and that exclusion of histone H2A.Z
from methylated DNA is conserved between plants and animals, and we present evidence
for RNA-directed DNA methylation of fungal genes. Our data demonstrate that extant
DNA methylation systems are mosaics of conserved and derived features, and indicate
that gene body methylation is an ancient property of eukaryotic genomes.
article_processing_charge: No
article_type: original
author:
- first_name: 'Assaf '
full_name: 'Zemach, Assaf '
last_name: Zemach
- first_name: Ivy E.
full_name: McDaniel, Ivy E.
last_name: McDaniel
- first_name: Pedro
full_name: Silva, Pedro
last_name: Silva
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zemach A, McDaniel IE, Silva P, Zilberman D. Genome-wide evolutionary analysis
of eukaryotic DNA methylation. Science. 2010;328(5980):916-919. doi:10.1126/science.1186366
apa: Zemach, A., McDaniel, I. E., Silva, P., & Zilberman, D. (2010). Genome-wide
evolutionary analysis of eukaryotic DNA methylation. Science. American
Association for the Advancement of Science. https://doi.org/10.1126/science.1186366
chicago: Zemach, Assaf , Ivy E. McDaniel, Pedro Silva, and Daniel Zilberman. “Genome-Wide
Evolutionary Analysis of Eukaryotic DNA Methylation.” Science. American
Association for the Advancement of Science, 2010. https://doi.org/10.1126/science.1186366.
ieee: A. Zemach, I. E. McDaniel, P. Silva, and D. Zilberman, “Genome-wide evolutionary
analysis of eukaryotic DNA methylation,” Science, vol. 328, no. 5980. American
Association for the Advancement of Science, pp. 916–919, 2010.
ista: Zemach A, McDaniel IE, Silva P, Zilberman D. 2010. Genome-wide evolutionary
analysis of eukaryotic DNA methylation. Science. 328(5980), 916–919.
mla: Zemach, Assaf, et al. “Genome-Wide Evolutionary Analysis of Eukaryotic DNA
Methylation.” Science, vol. 328, no. 5980, American Association for the
Advancement of Science, 2010, pp. 916–19, doi:10.1126/science.1186366.
short: A. Zemach, I.E. McDaniel, P. Silva, D. Zilberman, Science 328 (2010) 916–919.
date_created: 2021-06-04T08:26:08Z
date_published: 2010-05-14T00:00:00Z
date_updated: 2021-12-14T08:35:37Z
day: '14'
department:
- _id: DaZi
doi: 10.1126/science.1186366
extern: '1'
external_id:
pmid:
- '20395474 '
intvolume: ' 328'
issue: '5980'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '05'
oa_version: None
page: 916-919
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genome-wide evolutionary analysis of eukaryotic DNA methylation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 328
year: '2010'
...
---
_id: '9453'
abstract:
- lang: eng
text: Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis
thaliana endosperm by cytosine demethylation of the maternal genome mediated by
the DNA glycosylase DEMETER, but the extent of the methylation changes is not
known. Here, we show that virtually the entire endosperm genome is demethylated,
coupled with extensive local non-CG hypermethylation of small interfering RNA–targeted
sequences. Mutation of DEMETER partially restores endosperm CG methylation to
levels found in other tissues, indicating that CG demethylation is specific to
maternal sequences. Endosperm demethylation is accompanied by CHH hypermethylation
of embryo transposable elements. Our findings demonstrate extensive reconfiguration
of the endosperm methylation landscape that likely reinforces transposon silencing
in the embryo.
article_processing_charge: No
article_type: original
author:
- first_name: Tzung-Fu
full_name: Hsieh, Tzung-Fu
last_name: Hsieh
- first_name: Christian A.
full_name: Ibarra, Christian A.
last_name: Ibarra
- first_name: Pedro
full_name: Silva, Pedro
last_name: Silva
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: Leor
full_name: Eshed-Williams, Leor
last_name: Eshed-Williams
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Hsieh T-F, Ibarra CA, Silva P, et al. Genome-wide demethylation of Arabidopsis
endosperm. Science. 2009;324(5933):1451-1454. doi:10.1126/science.1172417
apa: Hsieh, T.-F., Ibarra, C. A., Silva, P., Zemach, A., Eshed-Williams, L., Fischer,
R. L., & Zilberman, D. (2009). Genome-wide demethylation of Arabidopsis endosperm.
Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1172417
chicago: Hsieh, Tzung-Fu, Christian A. Ibarra, Pedro Silva, Assaf Zemach, Leor Eshed-Williams,
Robert L. Fischer, and Daniel Zilberman. “Genome-Wide Demethylation of Arabidopsis
Endosperm.” Science. American Association for the Advancement of Science,
2009. https://doi.org/10.1126/science.1172417.
ieee: T.-F. Hsieh et al., “Genome-wide demethylation of Arabidopsis endosperm,”
Science, vol. 324, no. 5933. American Association for the Advancement of
Science, pp. 1451–1454, 2009.
ista: Hsieh T-F, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, Fischer RL, Zilberman
D. 2009. Genome-wide demethylation of Arabidopsis endosperm. Science. 324(5933),
1451–1454.
mla: Hsieh, Tzung-Fu, et al. “Genome-Wide Demethylation of Arabidopsis Endosperm.”
Science, vol. 324, no. 5933, American Association for the Advancement of
Science, 2009, pp. 1451–54, doi:10.1126/science.1172417.
short: T.-F. Hsieh, C.A. Ibarra, P. Silva, A. Zemach, L. Eshed-Williams, R.L. Fischer,
D. Zilberman, Science 324 (2009) 1451–1454.
date_created: 2021-06-04T08:55:41Z
date_published: 2009-06-12T00:00:00Z
date_updated: 2021-12-14T08:53:26Z
day: '12'
department:
- _id: DaZi
doi: 10.1126/science.1172417
extern: '1'
external_id:
pmid:
- '19520962'
intvolume: ' 324'
issue: '5933'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4044190/
month: '06'
oa: 1
oa_version: Submitted Version
page: 1451-1454
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genome-wide demethylation of Arabidopsis endosperm
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 324
year: '2009'
...
---
_id: '9537'
abstract:
- lang: eng
text: DNA methylation is an ancient process found in all domains of life. Although
the enzymes that mediate methylation have remained highly conserved, DNA methylation
has been adapted for a variety of uses throughout evolution, including defense
against transposable elements and control of gene expression. Defects in DNA methylation
are linked to human diseases, including cancer. Methylation has been lost several
times in the course of animal and fungal evolution, thus limiting the opportunity
for study in common model organisms. In the past decade, plants have emerged as
a premier model system for genetic dissection of DNA methylation. A recent combination
of plant genetics with powerful genomic approaches has led to a number of exciting
discoveries and promises many more.
article_processing_charge: No
article_type: review
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zilberman D. The evolving functions of DNA methylation. Current Opinion
in Plant Biology. 2008;11(5):554-559. doi:10.1016/j.pbi.2008.07.004
apa: Zilberman, D. (2008). The evolving functions of DNA methylation. Current
Opinion in Plant Biology. Elsevier . https://doi.org/10.1016/j.pbi.2008.07.004
chicago: Zilberman, Daniel. “The Evolving Functions of DNA Methylation.” Current
Opinion in Plant Biology. Elsevier , 2008. https://doi.org/10.1016/j.pbi.2008.07.004.
ieee: D. Zilberman, “The evolving functions of DNA methylation,” Current Opinion
in Plant Biology, vol. 11, no. 5. Elsevier , pp. 554–559, 2008.
ista: Zilberman D. 2008. The evolving functions of DNA methylation. Current Opinion
in Plant Biology. 11(5), 554–559.
mla: Zilberman, Daniel. “The Evolving Functions of DNA Methylation.” Current
Opinion in Plant Biology, vol. 11, no. 5, Elsevier , 2008, pp. 554–59, doi:10.1016/j.pbi.2008.07.004.
short: D. Zilberman, Current Opinion in Plant Biology 11 (2008) 554–559.
date_created: 2021-06-08T13:13:37Z
date_published: 2008-10-01T00:00:00Z
date_updated: 2021-12-14T08:54:07Z
department:
- _id: DaZi
doi: 10.1016/j.pbi.2008.07.004
extern: '1'
external_id:
pmid:
- '18774331'
intvolume: ' 11'
issue: '5'
language:
- iso: eng
month: '10'
oa_version: None
page: 554-559
pmid: 1
publication: Current Opinion in Plant Biology
publication_identifier:
issn:
- 1369-5266
publication_status: published
publisher: 'Elsevier '
quality_controlled: '1'
scopus_import: '1'
status: public
title: The evolving functions of DNA methylation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 11
year: '2008'
...
---
_id: '9457'
abstract:
- lang: eng
text: Eukaryotic chromatin is separated into functional domains differentiated by
posttranslational histone modifications, histone variants, and DNA methylation1–6.
Methylation is associated with repression of transcriptional initiation in plants
and animals, and is frequently found in transposable elements. Proper methylation
patterns are critical for eukaryotic development4,5, and aberrant methylation-induced
silencing of tumor suppressor genes is a common feature of human cancer7. In contrast
to methylation, the histone variant H2A.Z is preferentially deposited by the Swr1
ATPase complex near 5′ ends of genes where it promotes transcriptional competence8–20.
How DNA methylation and H2A.Z influence transcription remains largely unknown.
Here we show that in the plant Arabidopsis thaliana, regions of DNA methylation
are quantitatively deficient in H2A.Z. Exclusion of H2A.Z is seen at sites of
DNA methylation in the bodies of actively transcribed genes and in methylated
transposons. Mutation of the MET1 DNA methyltransferase, which causes both losses
and gains of DNA methylation4,5, engenders opposite changes in H2A.Z deposition,
while mutation of the PIE1 subunit of the Swr1 complex that deposits H2A.Z17 leads
to genome-wide hypermethylation. Our findings indicate that DNA methylation can
influence chromatin structure and effect gene silencing by excluding H2A.Z, and
that H2A.Z protects genes from DNA methylation.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Devin
full_name: Coleman-Derr, Devin
last_name: Coleman-Derr
- first_name: Tracy
full_name: Ballinger, Tracy
last_name: Ballinger
- first_name: Steven
full_name: Henikoff, Steven
last_name: Henikoff
citation:
ama: Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. Histone H2A.Z and DNA
methylation are mutually antagonistic chromatin marks. Nature. 2008;456(7218):125-129.
doi:10.1038/nature07324
apa: Zilberman, D., Coleman-Derr, D., Ballinger, T., & Henikoff, S. (2008).
Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature.
Springer Nature. https://doi.org/10.1038/nature07324
chicago: Zilberman, Daniel, Devin Coleman-Derr, Tracy Ballinger, and Steven Henikoff.
“Histone H2A.Z and DNA Methylation Are Mutually Antagonistic Chromatin Marks.”
Nature. Springer Nature, 2008. https://doi.org/10.1038/nature07324.
ieee: D. Zilberman, D. Coleman-Derr, T. Ballinger, and S. Henikoff, “Histone H2A.Z
and DNA methylation are mutually antagonistic chromatin marks,” Nature,
vol. 456, no. 7218. Springer Nature, pp. 125–129, 2008.
ista: Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. 2008. Histone H2A.Z
and DNA methylation are mutually antagonistic chromatin marks. Nature. 456(7218),
125–129.
mla: Zilberman, Daniel, et al. “Histone H2A.Z and DNA Methylation Are Mutually Antagonistic
Chromatin Marks.” Nature, vol. 456, no. 7218, Springer Nature, 2008, pp.
125–29, doi:10.1038/nature07324.
short: D. Zilberman, D. Coleman-Derr, T. Ballinger, S. Henikoff, Nature 456 (2008)
125–129.
date_created: 2021-06-04T11:49:32Z
date_published: 2008-11-06T00:00:00Z
date_updated: 2021-12-14T08:54:36Z
day: '06'
department:
- _id: DaZi
doi: 10.1038/nature07324
extern: '1'
external_id:
pmid:
- '18815594'
intvolume: ' 456'
issue: '7218'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877514/
month: '11'
oa: 1
oa_version: Submitted Version
page: 125-129
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 456
year: '2008'
...
---
_id: '9487'
abstract:
- lang: eng
text: Cytosine DNA methylation is considered to be a stable epigenetic mark, but
active demethylation has been observed in both plants and animals. In Arabidopsis
thaliana, DNA glycosylases of the DEMETER (DME) family remove methylcytosines
from DNA. Demethylation by DME is necessary for genomic imprinting, and demethylation
by a related protein, REPRESSOR OF SILENCING1, prevents gene silencing in a transgenic
background. However, the extent and function of demethylation by DEMETER-LIKE
(DML) proteins in WT plants is not known. Using genome-tiling microarrays, we
mapped DNA methylation in mutant and WT plants and identified 179 loci actively
demethylated by DML enzymes. Mutations in DML genes lead to locus-specific DNA
hypermethylation. Reintroducing WT DML genes restores most loci to the normal
pattern of methylation, although at some loci, hypermethylated epialleles persist.
Of loci demethylated by DML enzymes, >80% are near or overlap genes. Genic demethylation
by DML enzymes primarily occurs at the 5′ and 3′ ends, a pattern opposite to the
overall distribution of WT DNA methylation. Our results show that demethylation
by DML DNA glycosylases edits the patterns of DNA methylation within the Arabidopsis
genome to protect genes from potentially deleterious methylation.
article_processing_charge: No
article_type: original
author:
- first_name: Jon
full_name: Penterman, Jon
last_name: Penterman
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Jin Hoe
full_name: Huh, Jin Hoe
last_name: Huh
- first_name: Tracy
full_name: Ballinger, Tracy
last_name: Ballinger
- first_name: Steven
full_name: Henikoff, Steven
last_name: Henikoff
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
citation:
ama: Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. DNA
demethylation in the Arabidopsis genome. Proceedings of the National Academy
of Sciences. 2007;104(16):6752-6757. doi:10.1073/pnas.0701861104
apa: Penterman, J., Zilberman, D., Huh, J. H., Ballinger, T., Henikoff, S., &
Fischer, R. L. (2007). DNA demethylation in the Arabidopsis genome. Proceedings
of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.0701861104
chicago: Penterman, Jon, Daniel Zilberman, Jin Hoe Huh, Tracy Ballinger, Steven
Henikoff, and Robert L. Fischer. “DNA Demethylation in the Arabidopsis Genome.”
Proceedings of the National Academy of Sciences. National Academy of Sciences,
2007. https://doi.org/10.1073/pnas.0701861104.
ieee: J. Penterman, D. Zilberman, J. H. Huh, T. Ballinger, S. Henikoff, and R. L.
Fischer, “DNA demethylation in the Arabidopsis genome,” Proceedings of the
National Academy of Sciences, vol. 104, no. 16. National Academy of Sciences,
pp. 6752–6757, 2007.
ista: Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. 2007.
DNA demethylation in the Arabidopsis genome. Proceedings of the National Academy
of Sciences. 104(16), 6752–6757.
mla: Penterman, Jon, et al. “DNA Demethylation in the Arabidopsis Genome.” Proceedings
of the National Academy of Sciences, vol. 104, no. 16, National Academy of
Sciences, 2007, pp. 6752–57, doi:10.1073/pnas.0701861104.
short: J. Penterman, D. Zilberman, J.H. Huh, T. Ballinger, S. Henikoff, R.L. Fischer,
Proceedings of the National Academy of Sciences 104 (2007) 6752–6757.
date_created: 2021-06-07T09:38:21Z
date_published: 2007-04-17T00:00:00Z
date_updated: 2021-12-14T08:55:12Z
day: '17'
department:
- _id: DaZi
doi: 10.1073/pnas.0701861104
extern: '1'
external_id:
pmid:
- '17409185'
intvolume: ' 104'
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.0701861104
month: '04'
oa: 1
oa_version: Published Version
page: 6752-6757
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA demethylation in the Arabidopsis genome
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 104
year: '2007'
...
---
_id: '9504'
article_processing_charge: No
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zilberman D. The Human Promoter Methylome. Vol 39. Nature Publishing
Group; 2007:442-443. doi:10.1038/ng0407-442
apa: Zilberman, D. (2007). The human promoter methylome. Nature Genetics
(Vol. 39, pp. 442–443). Nature Publishing Group. https://doi.org/10.1038/ng0407-442
chicago: Zilberman, Daniel. The Human Promoter Methylome. Nature Genetics.
Vol. 39. Nature Publishing Group, 2007. https://doi.org/10.1038/ng0407-442.
ieee: D. Zilberman, The human promoter methylome, vol. 39, no. 4. Nature
Publishing Group, 2007, pp. 442–443.
ista: Zilberman D. 2007. The human promoter methylome, Nature Publishing Group,p.
mla: Zilberman, Daniel. “The Human Promoter Methylome.” Nature Genetics,
vol. 39, no. 4, Nature Publishing Group, 2007, pp. 442–43, doi:10.1038/ng0407-442.
short: D. Zilberman, The Human Promoter Methylome, Nature Publishing Group, 2007.
date_created: 2021-06-07T12:08:24Z
date_published: 2007-04-01T00:00:00Z
date_updated: 2021-12-14T08:55:46Z
day: '01'
department:
- _id: DaZi
doi: 10.1038/ng0407-442
extern: '1'
external_id:
pmid:
- '17392803'
intvolume: ' 39'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 442-443
pmid: 1
publication: Nature Genetics
publication_identifier:
eissn:
- 1546-1718
issn:
- 1061-4036
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
status: public
title: The human promoter methylome
type: other_academic_publication
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 39
year: '2007'
...
---
_id: '9524'
abstract:
- lang: eng
text: Cytosine methylation is the most common covalent modification of DNA in eukaryotes.
DNA methylation has an important role in many aspects of biology, including development
and disease. Methylation can be detected using bisulfite conversion, methylation-sensitive
restriction enzymes, methyl-binding proteins and anti-methylcytosine antibodies.
Combining these techniques with DNA microarrays and high-throughput sequencing
has made the mapping of DNA methylation feasible on a genome-wide scale. Here
we discuss recent developments and future directions for identifying and mapping
methylation, in an effort to help colleagues to identify the approaches that best
serve their research interests.
article_processing_charge: No
article_type: review
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Steven
full_name: Henikoff, Steven
last_name: Henikoff
citation:
ama: Zilberman D, Henikoff S. Genome-wide analysis of DNA methylation patterns.
Development. 2007;134(22):3959-3965. doi:10.1242/dev.001131
apa: Zilberman, D., & Henikoff, S. (2007). Genome-wide analysis of DNA methylation
patterns. Development. The Company of Biologists. https://doi.org/10.1242/dev.001131
chicago: Zilberman, Daniel, and Steven Henikoff. “Genome-Wide Analysis of DNA Methylation
Patterns.” Development. The Company of Biologists, 2007. https://doi.org/10.1242/dev.001131.
ieee: D. Zilberman and S. Henikoff, “Genome-wide analysis of DNA methylation patterns,”
Development, vol. 134, no. 22. The Company of Biologists, pp. 3959–3965,
2007.
ista: Zilberman D, Henikoff S. 2007. Genome-wide analysis of DNA methylation patterns.
Development. 134(22), 3959–3965.
mla: Zilberman, Daniel, and Steven Henikoff. “Genome-Wide Analysis of DNA Methylation
Patterns.” Development, vol. 134, no. 22, The Company of Biologists, 2007,
pp. 3959–65, doi:10.1242/dev.001131.
short: D. Zilberman, S. Henikoff, Development 134 (2007) 3959–3965.
date_created: 2021-06-08T06:29:50Z
date_published: 2007-11-15T00:00:00Z
date_updated: 2021-12-14T08:57:58Z
day: '15'
department:
- _id: DaZi
doi: 10.1242/dev.001131
extern: '1'
external_id:
pmid:
- '17928417'
intvolume: ' 134'
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1242/dev.001131
month: '11'
oa: 1
oa_version: Published Version
page: 3959-3965
pmid: 1
publication: Development
publication_identifier:
eissn:
- 1477-9129
issn:
- 0950-1991
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genome-wide analysis of DNA methylation patterns
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 134
year: '2007'
...
---
_id: '9505'
abstract:
- lang: eng
text: 'Cytosine methylation, a common form of DNA modification that antagonizes
transcription, is found at transposons and repeats in vertebrates, plants and
fungi. Here we have mapped DNA methylation in the entire Arabidopsis thaliana
genome at high resolution. DNA methylation covers transposons and is present within
a large fraction of A. thaliana genes. Methylation within genes is conspicuously
biased away from gene ends, suggesting a dependence on RNA polymerase transit.
Genic methylation is strongly influenced by transcription: moderately transcribed
genes are most likely to be methylated, whereas genes at either extreme are least
likely. In turn, transcription is influenced by methylation: short methylated
genes are poorly expressed, and loss of methylation in the body of a gene leads
to enhanced transcription. Our results indicate that genic transcription and DNA
methylation are closely interwoven processes.'
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Mary
full_name: Gehring, Mary
last_name: Gehring
- first_name: Robert K.
full_name: Tran, Robert K.
last_name: Tran
- first_name: Tracy
full_name: Ballinger, Tracy
last_name: Ballinger
- first_name: Steven
full_name: Henikoff, Steven
last_name: Henikoff
citation:
ama: Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. Genome-wide analysis
of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation
and transcription. Nature Genetics. 2006;39(1):61-69. doi:10.1038/ng1929
apa: Zilberman, D., Gehring, M., Tran, R. K., Ballinger, T., & Henikoff, S.
(2006). Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers
an interdependence between methylation and transcription. Nature Genetics.
Nature Publishing Group. https://doi.org/10.1038/ng1929
chicago: Zilberman, Daniel, Mary Gehring, Robert K. Tran, Tracy Ballinger, and Steven
Henikoff. “Genome-Wide Analysis of Arabidopsis Thaliana DNA Methylation Uncovers
an Interdependence between Methylation and Transcription.” Nature Genetics.
Nature Publishing Group, 2006. https://doi.org/10.1038/ng1929.
ieee: D. Zilberman, M. Gehring, R. K. Tran, T. Ballinger, and S. Henikoff, “Genome-wide
analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between
methylation and transcription,” Nature Genetics, vol. 39, no. 1. Nature
Publishing Group, pp. 61–69, 2006.
ista: Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. 2006. Genome-wide
analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between
methylation and transcription. Nature Genetics. 39(1), 61–69.
mla: Zilberman, Daniel, et al. “Genome-Wide Analysis of Arabidopsis Thaliana DNA
Methylation Uncovers an Interdependence between Methylation and Transcription.”
Nature Genetics, vol. 39, no. 1, Nature Publishing Group, 2006, pp. 61–69,
doi:10.1038/ng1929.
short: D. Zilberman, M. Gehring, R.K. Tran, T. Ballinger, S. Henikoff, Nature Genetics
39 (2006) 61–69.
date_created: 2021-06-07T12:19:31Z
date_published: 2006-11-26T00:00:00Z
date_updated: 2021-12-14T09:02:51Z
day: '26'
department:
- _id: DaZi
doi: 10.1038/ng1929
extern: '1'
external_id:
pmid:
- '17128275'
intvolume: ' 39'
issue: '1'
language:
- iso: eng
month: '11'
oa_version: None
page: 61-69
pmid: 1
publication: Nature Genetics
publication_identifier:
eissn:
- 1546-1718
issn:
- 1061-4036
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence
between methylation and transcription
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 39
year: '2006'
...
---
_id: '9491'
abstract:
- lang: eng
text: Cytosine DNA methylation in vertebrates is widespread, but methylation in
plants is found almost exclusively at transposable elements and repetitive DNA
[1]. Within regions of methylation, methylcytosines are typically found in CG,
CNG, and asymmetric contexts. CG sites are maintained by a plant homolog of mammalian
Dnmt1 acting on hemi-methylated DNA after replication. Methylation of CNG and
asymmetric sites appears to be maintained at each cell cycle by other mechanisms.
We report a new type of DNA methylation in Arabidopsis, dense CG methylation clusters
found at scattered sites throughout the genome. These clusters lack non-CG methylation
and are preferentially found in genes, although they are relatively deficient
toward the 5′ end. CG methylation clusters are present in lines derived from different
accessions and in mutants that eliminate de novo methylation, indicating that
CG methylation clusters are stably maintained at specific sites. Because 5-methylcytosine
is mutagenic, the appearance of CG methylation clusters over evolutionary time
predicts a genome-wide deficiency of CG dinucleotides and an excess of C(A/T)G
trinucleotides within transcribed regions. This is exactly what we find, implying
that CG methylation clusters have contributed profoundly to plant gene evolution.
We suggest that CG methylation clusters silence cryptic promoters that arise sporadically
within transcription units.
article_processing_charge: No
article_type: original
author:
- first_name: Robert K.
full_name: Tran, Robert K.
last_name: Tran
- first_name: Jorja G.
full_name: Henikoff, Jorja G.
last_name: Henikoff
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Renata F.
full_name: Ditt, Renata F.
last_name: Ditt
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
- first_name: Steven
full_name: Henikoff, Steven
last_name: Henikoff
citation:
ama: Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. DNA methylation
profiling identifies CG methylation clusters in Arabidopsis genes. Current
Biology. 2005;15(2):154-159. doi:10.1016/j.cub.2005.01.008
apa: Tran, R. K., Henikoff, J. G., Zilberman, D., Ditt, R. F., Jacobsen, S. E.,
& Henikoff, S. (2005). DNA methylation profiling identifies CG methylation
clusters in Arabidopsis genes. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2005.01.008
chicago: Tran, Robert K., Jorja G. Henikoff, Daniel Zilberman, Renata F. Ditt, Steven
E. Jacobsen, and Steven Henikoff. “DNA Methylation Profiling Identifies CG Methylation
Clusters in Arabidopsis Genes.” Current Biology. Elsevier, 2005. https://doi.org/10.1016/j.cub.2005.01.008.
ieee: R. K. Tran, J. G. Henikoff, D. Zilberman, R. F. Ditt, S. E. Jacobsen, and
S. Henikoff, “DNA methylation profiling identifies CG methylation clusters in
Arabidopsis genes,” Current Biology, vol. 15, no. 2. Elsevier, pp. 154–159,
2005.
ista: Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. 2005.
DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes.
Current Biology. 15(2), 154–159.
mla: Tran, Robert K., et al. “DNA Methylation Profiling Identifies CG Methylation
Clusters in Arabidopsis Genes.” Current Biology, vol. 15, no. 2, Elsevier,
2005, pp. 154–59, doi:10.1016/j.cub.2005.01.008.
short: R.K. Tran, J.G. Henikoff, D. Zilberman, R.F. Ditt, S.E. Jacobsen, S. Henikoff,
Current Biology 15 (2005) 154–159.
date_created: 2021-06-07T10:24:30Z
date_published: 2005-01-26T00:00:00Z
date_updated: 2021-12-14T09:12:26Z
day: '26'
department:
- _id: DaZi
doi: 10.1016/j.cub.2005.01.008
extern: '1'
external_id:
pmid:
- '15668172 '
intvolume: ' 15'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2005.01.008
month: '01'
oa: 1
oa_version: Published Version
page: 154-159
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation profiling identifies CG methylation clusters in Arabidopsis
genes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 15
year: '2005'
...
---
_id: '9514'
abstract:
- lang: eng
text: "Background:\r\nDNA methylation occurs at preferred sites in eukaryotes. In
Arabidopsis, DNA cytosine methylation is maintained by three subfamilies of methyltransferases
with distinct substrate specificities and different modes of action. Targeting
of cytosine methylation at selected loci has been found to sometimes involve histone
H3 methylation and small interfering (si)RNAs. However, the relationship between
different cytosine methylation pathways and their preferred targets is not known.\r\nResults:\r\nWe
used a microarray-based profiling method to explore the involvement of Arabidopsis
CMT3 and DRM DNA methyltransferases, a histone H3 lysine-9 methyltransferase (KYP)
and an Argonaute-related siRNA silencing component (AGO4) in methylating target
loci. We found that KYP targets are also CMT3 targets, suggesting that histone
methylation maintains CNG methylation genome-wide. CMT3 and KYP targets show similar
proximal distributions that correspond to the overall distribution of transposable
elements of all types, whereas DRM targets are distributed more distally along
the chromosome. We find an inverse relationship between element size and loss
of methylation in ago4 and drm mutants.\r\nConclusion:\r\nWe conclude that the
targets of both DNA methylation and histone H3K9 methylation pathways are transposable
elements genome-wide, irrespective of element type and position. Our findings
also suggest that RNA-directed DNA methylation is required to silence isolated
elements that may be too small to be maintained in a silent state by a chromatin-based
mechanism alone. Thus, parallel pathways would be needed to maintain silencing
of transposable elements."
article_number: R90
article_processing_charge: No
article_type: original
author:
- first_name: Robert K.
full_name: Tran, Robert K.
last_name: Tran
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Cecilia
full_name: de Bustos, Cecilia
last_name: de Bustos
- first_name: Renata F.
full_name: Ditt, Renata F.
last_name: Ditt
- first_name: Jorja G.
full_name: Henikoff, Jorja G.
last_name: Henikoff
- first_name: Anders M.
full_name: Lindroth, Anders M.
last_name: Lindroth
- first_name: Jeffrey
full_name: Delrow, Jeffrey
last_name: Delrow
- first_name: Tom
full_name: Boyle, Tom
last_name: Boyle
- first_name: Samson
full_name: Kwong, Samson
last_name: Kwong
- first_name: Terri D.
full_name: Bryson, Terri D.
last_name: Bryson
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
- first_name: Steven
full_name: Henikoff, Steven
last_name: Henikoff
citation:
ama: Tran RK, Zilberman D, de Bustos C, et al. Chromatin and siRNA pathways cooperate
to maintain DNA methylation of small transposable elements in Arabidopsis. Genome
Biology. 2005;6(11). doi:10.1186/gb-2005-6-11-r90
apa: Tran, R. K., Zilberman, D., de Bustos, C., Ditt, R. F., Henikoff, J. G., Lindroth,
A. M., … Henikoff, S. (2005). Chromatin and siRNA pathways cooperate to maintain
DNA methylation of small transposable elements in Arabidopsis. Genome Biology.
Springer Nature. https://doi.org/10.1186/gb-2005-6-11-r90
chicago: Tran, Robert K., Daniel Zilberman, Cecilia de Bustos, Renata F. Ditt, Jorja
G. Henikoff, Anders M. Lindroth, Jeffrey Delrow, et al. “Chromatin and SiRNA Pathways
Cooperate to Maintain DNA Methylation of Small Transposable Elements in Arabidopsis.”
Genome Biology. Springer Nature, 2005. https://doi.org/10.1186/gb-2005-6-11-r90.
ieee: R. K. Tran et al., “Chromatin and siRNA pathways cooperate to maintain
DNA methylation of small transposable elements in Arabidopsis,” Genome Biology,
vol. 6, no. 11. Springer Nature, 2005.
ista: Tran RK, Zilberman D, de Bustos C, Ditt RF, Henikoff JG, Lindroth AM, Delrow
J, Boyle T, Kwong S, Bryson TD, Jacobsen SE, Henikoff S. 2005. Chromatin and siRNA
pathways cooperate to maintain DNA methylation of small transposable elements
in Arabidopsis. Genome Biology. 6(11), R90.
mla: Tran, Robert K., et al. “Chromatin and SiRNA Pathways Cooperate to Maintain
DNA Methylation of Small Transposable Elements in Arabidopsis.” Genome Biology,
vol. 6, no. 11, R90, Springer Nature, 2005, doi:10.1186/gb-2005-6-11-r90.
short: R.K. Tran, D. Zilberman, C. de Bustos, R.F. Ditt, J.G. Henikoff, A.M. Lindroth,
J. Delrow, T. Boyle, S. Kwong, T.D. Bryson, S.E. Jacobsen, S. Henikoff, Genome
Biology 6 (2005).
date_created: 2021-06-07T13:12:41Z
date_published: 2005-10-19T00:00:00Z
date_updated: 2021-12-14T09:09:41Z
day: '19'
department:
- _id: DaZi
doi: 10.1186/gb-2005-6-11-r90
extern: '1'
external_id:
pmid:
- '16277745'
intvolume: ' 6'
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1186/gb-2005-6-11-r90
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
eissn:
- 1465-6906
issn:
- 1474-760X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromatin and siRNA pathways cooperate to maintain DNA methylation of small
transposable elements in Arabidopsis
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 6
year: '2005'
...
---
_id: '9529'
abstract:
- lang: eng
text: Eukaryotic organisms have the remarkable ability to inherit states of gene
activity without altering the underlying DNA sequence. This epigenetic inheritance
can persist over thousands of years, providing an alternative to genetic mutations
as a substrate for natural selection. Epigenetic inheritance might be propagated
by differences in DNA methylation, post-translational histone modifications, and
deposition of histone variants. Mounting evidence also indicates that small interfering
RNA (siRNA)-mediated mechanisms play central roles in setting up and maintaining
states of gene activity. Much of the epigenetic machinery of many organisms, including
Arabidopsis, appears to be directed at silencing viruses and transposable elements,
with epigenetic regulation of endogenous genes being mostly derived from such
processes.
article_processing_charge: No
article_type: review
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Steven
full_name: Henikoff, Steven
last_name: Henikoff
citation:
ama: 'Zilberman D, Henikoff S. Epigenetic inheritance in Arabidopsis: Selective
silence. Current Opinion in Genetics and Development. 2005;15(5):557-562.
doi:10.1016/j.gde.2005.07.002'
apa: 'Zilberman, D., & Henikoff, S. (2005). Epigenetic inheritance in Arabidopsis:
Selective silence. Current Opinion in Genetics and Development. Elsevier.
https://doi.org/10.1016/j.gde.2005.07.002'
chicago: 'Zilberman, Daniel, and Steven Henikoff. “Epigenetic Inheritance in Arabidopsis:
Selective Silence.” Current Opinion in Genetics and Development. Elsevier,
2005. https://doi.org/10.1016/j.gde.2005.07.002.'
ieee: 'D. Zilberman and S. Henikoff, “Epigenetic inheritance in Arabidopsis: Selective
silence,” Current Opinion in Genetics and Development, vol. 15, no. 5.
Elsevier, pp. 557–562, 2005.'
ista: 'Zilberman D, Henikoff S. 2005. Epigenetic inheritance in Arabidopsis: Selective
silence. Current Opinion in Genetics and Development. 15(5), 557–562.'
mla: 'Zilberman, Daniel, and Steven Henikoff. “Epigenetic Inheritance in Arabidopsis:
Selective Silence.” Current Opinion in Genetics and Development, vol. 15,
no. 5, Elsevier, 2005, pp. 557–62, doi:10.1016/j.gde.2005.07.002.'
short: D. Zilberman, S. Henikoff, Current Opinion in Genetics and Development 15
(2005) 557–562.
date_created: 2021-06-08T09:05:56Z
date_published: 2005-10-01T00:00:00Z
date_updated: 2021-12-14T09:13:13Z
department:
- _id: DaZi
doi: 10.1016/j.gde.2005.07.002
extern: '1'
external_id:
pmid:
- '16085410'
intvolume: ' 15'
issue: '5'
language:
- iso: eng
month: '10'
oa_version: None
page: 557-562
pmid: 1
publication: Current Opinion in Genetics and Development
publication_identifier:
issn:
- 0959-437X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Epigenetic inheritance in Arabidopsis: Selective silence'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 15
year: '2005'
...
---
_id: '9493'
abstract:
- lang: eng
text: In a number of organisms, transgenes containing transcribed inverted repeats
(IRs) that produce hairpin RNA can trigger RNA-mediated silencing, which is associated
with 21-24 nucleotide small interfering RNAs (siRNAs). In plants, IR-driven RNA
silencing also causes extensive cytosine methylation of homologous DNA in both
the transgene "trigger" and any other homologous DNA sequences--"targets". Endogenous
genomic sequences, including transposable elements and repeated elements, are
also subject to RNA-mediated silencing. The RNA silencing gene ARGONAUTE4 (AGO4)
is required for maintenance of DNA methylation at several endogenous loci and
for the establishment of methylation at the FWA gene. Here, we show that mutation
of AGO4 substantially reduces the maintenance of DNA methylation triggered by
IR transgenes, but AGO4 loss-of-function does not block the initiation of DNA
methylation by IRs. AGO4 primarily affects non-CG methylation of the target sequences,
while the IR trigger sequences lose methylation in all sequence contexts. Finally,
we find that AGO4 and the DRM methyltransferase genes are required for maintenance
of siRNAs at a subset of endogenous sequences, but AGO4 is not required for the
accumulation of IR-induced siRNAs or a number of endogenous siRNAs, suggesting
that AGO4 may function downstream of siRNA production.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Xiaofeng
full_name: Cao, Xiaofeng
last_name: Cao
- first_name: Lisa K.
full_name: Johansen, Lisa K.
last_name: Johansen
- first_name: Zhixin
full_name: Xie, Zhixin
last_name: Xie
- first_name: James C.
full_name: Carrington, James C.
last_name: Carrington
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
citation:
ama: Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. Role of
Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats.
Current Biology. 2004;14(13):1214-1220. doi:10.1016/j.cub.2004.06.055
apa: Zilberman, D., Cao, X., Johansen, L. K., Xie, Z., Carrington, J. C., &
Jacobsen, S. E. (2004). Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation
triggered by inverted repeats. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2004.06.055
chicago: Zilberman, Daniel, Xiaofeng Cao, Lisa K. Johansen, Zhixin Xie, James C.
Carrington, and Steven E. Jacobsen. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed
DNA Methylation Triggered by Inverted Repeats.” Current Biology. Elsevier,
2004. https://doi.org/10.1016/j.cub.2004.06.055.
ieee: D. Zilberman, X. Cao, L. K. Johansen, Z. Xie, J. C. Carrington, and S. E.
Jacobsen, “Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered
by inverted repeats,” Current Biology, vol. 14, no. 13. Elsevier, pp. 1214–1220,
2004.
ista: Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. 2004.
Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted
repeats. Current Biology. 14(13), 1214–1220.
mla: Zilberman, Daniel, et al. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed DNA
Methylation Triggered by Inverted Repeats.” Current Biology, vol. 14, no.
13, Elsevier, 2004, pp. 1214–20, doi:10.1016/j.cub.2004.06.055.
short: D. Zilberman, X. Cao, L.K. Johansen, Z. Xie, J.C. Carrington, S.E. Jacobsen,
Current Biology 14 (2004) 1214–1220.
date_created: 2021-06-07T10:33:00Z
date_published: 2004-07-13T00:00:00Z
date_updated: 2021-12-14T08:52:00Z
day: '13'
department:
- _id: DaZi
doi: 10.1016/j.cub.2004.06.055
extern: '1'
external_id:
pmid:
- '15242620 '
intvolume: ' 14'
issue: '13'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2004.06.055
month: '07'
oa: 1
oa_version: Published Version
page: 1214-1220
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by
inverted repeats
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 14
year: '2004'
...
---
_id: '9517'
abstract:
- lang: eng
text: Multicellular eukaryotes produce small RNA molecules (approximately 21–24
nucleotides) of two general types, microRNA (miRNA) and short interfering RNA
(siRNA). They collectively function as sequence-specific guides to silence or
regulate genes, transposons, and viruses and to modify chromatin and genome structure.
Formation or activity of small RNAs requires factors belonging to gene families
that encode DICER (or DICER-LIKE [DCL]) and ARGONAUTE proteins and, in the case
of some siRNAs, RNA-dependent RNA polymerase (RDR) proteins. Unlike many animals,
plants encode multiple DCL and RDR proteins. Using a series of insertion mutants
of Arabidopsis thaliana, unique functions for three DCL proteins in miRNA (DCL1),
endogenous siRNA (DCL3), and viral siRNA (DCL2) biogenesis were identified. One
RDR protein (RDR2) was required for all endogenous siRNAs analyzed. The loss of
endogenous siRNA in dcl3 and rdr2 mutants was associated with loss of heterochromatic
marks and increased transcript accumulation at some loci. Defects in siRNA-generation
activity in response to turnip crinkle virus in dcl2 mutant plants correlated
with increased virus susceptibility. We conclude that proliferation and diversification
of DCL and RDR genes during evolution of plants contributed to specialization
of small RNA-directed pathways for development, chromatin structure, and defense.
article_processing_charge: No
article_type: original
author:
- first_name: Zhixin
full_name: Xie, Zhixin
last_name: Xie
- first_name: Lisa K.
full_name: Johansen, Lisa K.
last_name: Johansen
- first_name: Adam M.
full_name: Gustafson, Adam M.
last_name: Gustafson
- first_name: Kristin D.
full_name: Kasschau, Kristin D.
last_name: Kasschau
- first_name: 'Andrew D. '
full_name: 'Lellis, Andrew D. '
last_name: Lellis
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
- first_name: James C.
full_name: Carrington, James C.
last_name: Carrington
citation:
ama: Xie Z, Johansen LK, Gustafson AM, et al. Genetic and functional diversification
of small RNA pathways in plants. PLoS Biology. 2004;2(5):0642-0652. doi:10.1371/journal.pbio.0020104
apa: Xie, Z., Johansen, L. K., Gustafson, A. M., Kasschau, K. D., Lellis, A. D.,
Zilberman, D., … Carrington, J. C. (2004). Genetic and functional diversification
of small RNA pathways in plants. PLoS Biology. Public Library of Science.
https://doi.org/10.1371/journal.pbio.0020104
chicago: Xie, Zhixin, Lisa K. Johansen, Adam M. Gustafson, Kristin D. Kasschau,
Andrew D. Lellis, Daniel Zilberman, Steven E. Jacobsen, and James C. Carrington.
“Genetic and Functional Diversification of Small RNA Pathways in Plants.” PLoS
Biology. Public Library of Science, 2004. https://doi.org/10.1371/journal.pbio.0020104.
ieee: Z. Xie et al., “Genetic and functional diversification of small RNA
pathways in plants,” PLoS Biology, vol. 2, no. 5. Public Library of Science,
pp. 0642–0652, 2004.
ista: Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen
SE, Carrington JC. 2004. Genetic and functional diversification of small RNA pathways
in plants. PLoS Biology. 2(5), 0642–0652.
mla: Xie, Zhixin, et al. “Genetic and Functional Diversification of Small RNA Pathways
in Plants.” PLoS Biology, vol. 2, no. 5, Public Library of Science, 2004,
pp. 0642–52, doi:10.1371/journal.pbio.0020104.
short: Z. Xie, L.K. Johansen, A.M. Gustafson, K.D. Kasschau, A.D. Lellis, D. Zilberman,
S.E. Jacobsen, J.C. Carrington, PLoS Biology 2 (2004) 0642–0652.
date_created: 2021-06-07T14:12:08Z
date_published: 2004-02-24T00:00:00Z
date_updated: 2021-12-14T08:43:57Z
day: '24'
department:
- _id: DaZi
doi: 10.1371/journal.pbio.0020104
extern: '1'
external_id:
pmid:
- '15024409'
intvolume: ' 2'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1371/journal.pbio.0020104
month: '02'
oa: 1
oa_version: Published Version
page: 0642-0652
pmid: 1
publication: PLoS Biology
publication_identifier:
eissn:
- 1545-7885
issn:
- 1544-9173
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic and functional diversification of small RNA pathways in plants
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 2
year: '2004'
...
---
_id: '9511'
abstract:
- lang: eng
text: Recent progress in understanding the silencing of transposable elements in
the model plant Arabidopsis has revealed an interplay between DNA methylation,
histone methylation and small interfering RNAs. DNA and histone methylation are
not always sufficient to maintain silencing, and RNA-based reinforcement can be
needed to maintain as well as initiate it.
article_number: '249'
article_processing_charge: No
article_type: review
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Steven
full_name: Henikoff, Steven
last_name: Henikoff
citation:
ama: 'Zilberman D, Henikoff S. Silencing of transposons in plant genomes: kick them
when they’re down. Genome Biology. 2004;5(12). doi:10.1186/gb-2004-5-12-249'
apa: 'Zilberman, D., & Henikoff, S. (2004). Silencing of transposons in plant
genomes: kick them when they’re down. Genome Biology. Springer Nature.
https://doi.org/10.1186/gb-2004-5-12-249'
chicago: 'Zilberman, Daniel, and Steven Henikoff. “Silencing of Transposons in Plant
Genomes: Kick Them When They’re Down.” Genome Biology. Springer Nature,
2004. https://doi.org/10.1186/gb-2004-5-12-249.'
ieee: 'D. Zilberman and S. Henikoff, “Silencing of transposons in plant genomes:
kick them when they’re down,” Genome Biology, vol. 5, no. 12. Springer
Nature, 2004.'
ista: 'Zilberman D, Henikoff S. 2004. Silencing of transposons in plant genomes:
kick them when they’re down. Genome Biology. 5(12), 249.'
mla: 'Zilberman, Daniel, and Steven Henikoff. “Silencing of Transposons in Plant
Genomes: Kick Them When They’re Down.” Genome Biology, vol. 5, no. 12,
249, Springer Nature, 2004, doi:10.1186/gb-2004-5-12-249.'
short: D. Zilberman, S. Henikoff, Genome Biology 5 (2004).
date_created: 2021-06-07T12:58:06Z
date_published: 2004-11-16T00:00:00Z
date_updated: 2021-12-14T08:44:24Z
day: '16'
department:
- _id: DaZi
doi: 10.1186/gb-2004-5-12-249
extern: '1'
external_id:
pmid:
- '15575975'
intvolume: ' 5'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1186/gb-2004-5-12-249
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
eissn:
- 1465-6906
issn:
- 1474-760X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Silencing of transposons in plant genomes: kick them when they''re down'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 5
year: '2004'
...
---
_id: '9454'
article_processing_charge: No
article_type: original
author:
- first_name: Simon W.-L.
full_name: Chan, Simon W.-L.
last_name: Chan
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: ' Zhixin'
full_name: Xie, Zhixin
last_name: Xie
- first_name: ' Lisa K.'
full_name: Johansen, Lisa K.
last_name: Johansen
- first_name: James C.
full_name: Carrington, James C.
last_name: Carrington
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
citation:
ama: Chan SW-L, Zilberman D, Xie Zhixin, Johansen Lisa K., Carrington JC, Jacobsen
SE. RNA silencing genes control de novo DNA methylation. Science. 2004;303(5662):1336.
doi:10.1126/science.1095989
apa: Chan, S. W.-L., Zilberman, D., Xie, Zhixin, Johansen, Lisa K., Carrington,
J. C., & Jacobsen, S. E. (2004). RNA silencing genes control de novo DNA methylation.
Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1095989
chicago: Chan, Simon W.-L., Daniel Zilberman, Zhixin Xie, Lisa K. Johansen, James
C. Carrington, and Steven E. Jacobsen. “RNA Silencing Genes Control de Novo DNA
Methylation.” Science. American Association for the Advancement of Science,
2004. https://doi.org/10.1126/science.1095989.
ieee: S. W.-L. Chan, D. Zilberman, Zhixin Xie, Lisa K. Johansen, J. C. Carrington,
and S. E. Jacobsen, “RNA silencing genes control de novo DNA methylation,” Science,
vol. 303, no. 5662. American Association for the Advancement of Science, p. 1336,
2004.
ista: Chan SW-L, Zilberman D, Xie Zhixin, Johansen Lisa K., Carrington JC, Jacobsen
SE. 2004. RNA silencing genes control de novo DNA methylation. Science. 303(5662),
1336.
mla: Chan, Simon W. L., et al. “RNA Silencing Genes Control de Novo DNA Methylation.”
Science, vol. 303, no. 5662, American Association for the Advancement of
Science, 2004, p. 1336, doi:10.1126/science.1095989.
short: S.W.-L. Chan, D. Zilberman, Zhixin Xie, Lisa K. Johansen, J.C. Carrington,
S.E. Jacobsen, Science 303 (2004) 1336.
date_created: 2021-06-04T11:12:35Z
date_published: 2004-02-27T00:00:00Z
date_updated: 2021-12-14T09:13:53Z
day: '27'
department:
- _id: DaZi
doi: 10.1126/science.1095989
extern: '1'
external_id:
pmid:
- '14988555'
intvolume: ' 303'
issue: '5662'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '02'
oa_version: None
page: '1336'
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: RNA silencing genes control de novo DNA methylation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 303
year: '2004'
...
---
_id: '9495'
abstract:
- lang: eng
text: RNA interference is a conserved process in which double-stranded RNA is processed
into 21–25 nucleotide siRNAs that trigger posttranscriptional gene silencing.
In addition, plants display a phenomenon termed RNA-directed DNA methylation (RdDM)
in which DNA with sequence identity to silenced RNA is de novo methylated at its
cytosine residues. This methylation is not only at canonical CpG sites but also
at cytosines in CpNpG and asymmetric sequence contexts. In this report, we study
the role of the DRM and CMT3 DNA methyltransferase genes in the initiation and
maintenance of RdDM. Neither drm nor cmt3 mutants affected the maintenance of
preestablished RNA-directed CpG methylation. However, drm mutants showed a nearly
complete loss of asymmetric methylation and a partial loss of CpNpG methylation.
The remaining asymmetric and CpNpG methylation was dependent on the activity of
CMT3, showing that DRM and CMT3 act redundantly to maintain non-CpG methylation.
These DNA methyltransferases appear to act downstream of siRNAs, since drm1 drm2
cmt3 triple mutants show a lack of non-CpG methylation but elevated levels of
siRNAs. Finally, we demonstrate that DRM activity is required for the initial
establishment of RdDM in all sequence contexts including CpG, CpNpG, and asymmetric
sites.
article_processing_charge: No
article_type: original
author:
- first_name: Xiaofeng
full_name: Cao, Xiaofeng
last_name: Cao
- first_name: Werner
full_name: Aufsatz, Werner
last_name: Aufsatz
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: M.Florian
full_name: Mette, M.Florian
last_name: Mette
- first_name: Michael S.
full_name: Huang, Michael S.
last_name: Huang
- first_name: Marjori
full_name: Matzke, Marjori
last_name: Matzke
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
citation:
ama: Cao X, Aufsatz W, Zilberman D, et al. Role of the DRM and CMT3 methyltransferases
in RNA-directed DNA methylation. Current Biology. 2003;13(24):2212-2217.
doi:10.1016/j.cub.2003.11.052
apa: Cao, X., Aufsatz, W., Zilberman, D., Mette, M. F., Huang, M. S., Matzke, M.,
& Jacobsen, S. E. (2003). Role of the DRM and CMT3 methyltransferases in RNA-directed
DNA methylation. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2003.11.052
chicago: Cao, Xiaofeng, Werner Aufsatz, Daniel Zilberman, M.Florian Mette, Michael
S. Huang, Marjori Matzke, and Steven E. Jacobsen. “Role of the DRM and CMT3 Methyltransferases
in RNA-Directed DNA Methylation.” Current Biology. Elsevier, 2003. https://doi.org/10.1016/j.cub.2003.11.052.
ieee: X. Cao et al., “Role of the DRM and CMT3 methyltransferases in RNA-directed
DNA methylation,” Current Biology, vol. 13, no. 24. Elsevier, pp. 2212–2217,
2003.
ista: Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke M, Jacobsen SE.
2003. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation.
Current Biology. 13(24), 2212–2217.
mla: Cao, Xiaofeng, et al. “Role of the DRM and CMT3 Methyltransferases in RNA-Directed
DNA Methylation.” Current Biology, vol. 13, no. 24, Elsevier, 2003, pp.
2212–17, doi:10.1016/j.cub.2003.11.052.
short: X. Cao, W. Aufsatz, D. Zilberman, M.F. Mette, M.S. Huang, M. Matzke, S.E.
Jacobsen, Current Biology 13 (2003) 2212–2217.
date_created: 2021-06-07T10:43:02Z
date_published: 2003-12-16T00:00:00Z
date_updated: 2021-12-14T08:41:38Z
day: '16'
department:
- _id: DaZi
doi: 10.1016/j.cub.2003.11.052
extern: '1'
external_id:
pmid:
- '14680640'
intvolume: ' 13'
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2003.11.052
month: '12'
oa: 1
oa_version: Published Version
page: 2212-2217
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 13
year: '2003'
...
---
_id: '9455'
abstract:
- lang: eng
text: Proteins of the ARGONAUTE family are important in diverse posttranscriptional
RNA-mediated gene-silencing systems as well as in transcriptional gene silencing
in Drosophila and fission yeast and in programmed DNA elimination in Tetrahymena.
We cloned ARGONAUTE4 (AGO4) from a screen for mutants that suppress silencing
of the Arabidopsis SUPERMAN(SUP) gene. The ago4-1 mutant reactivated silentSUP
alleles and decreased CpNpG and asymmetric DNA methylation as well as histone
H3 lysine-9 methylation. In addition,ago4-1 blocked histone and DNA methylation
and the accumulation of 25-nucleotide small interfering RNAs (siRNAs) that correspond
to the retroelement AtSN1. These results suggest that AGO4 and long siRNAs direct
chromatin modifications, including histone methylation and non-CpG DNA methylation.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: ' Xiaofeng'
full_name: Cao, Xiaofeng
last_name: Cao
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
citation:
ama: Zilberman D, Cao Xiaofeng, Jacobsen SE. ARGONAUTE4 control of locus-specific
siRNA accumulation and DNA and histone methylation. Science. 2003;299(5607):716-719.
doi:10.1126/science.1079695
apa: Zilberman, D., Cao, Xiaofeng, & Jacobsen, S. E. (2003). ARGONAUTE4 control
of locus-specific siRNA accumulation and DNA and histone methylation. Science.
American Association for the Advancement of Science. https://doi.org/10.1126/science.1079695
chicago: Zilberman, Daniel, Xiaofeng Cao, and Steven E. Jacobsen. “ARGONAUTE4 Control
of Locus-Specific SiRNA Accumulation and DNA and Histone Methylation.” Science.
American Association for the Advancement of Science, 2003. https://doi.org/10.1126/science.1079695.
ieee: D. Zilberman, Xiaofeng Cao, and S. E. Jacobsen, “ARGONAUTE4 control of locus-specific
siRNA accumulation and DNA and histone methylation,” Science, vol. 299,
no. 5607. American Association for the Advancement of Science, pp. 716–719, 2003.
ista: Zilberman D, Cao Xiaofeng, Jacobsen SE. 2003. ARGONAUTE4 control of locus-specific
siRNA accumulation and DNA and histone methylation. Science. 299(5607), 716–719.
mla: Zilberman, Daniel, et al. “ARGONAUTE4 Control of Locus-Specific SiRNA Accumulation
and DNA and Histone Methylation.” Science, vol. 299, no. 5607, American
Association for the Advancement of Science, 2003, pp. 716–19, doi:10.1126/science.1079695.
short: D. Zilberman, Xiaofeng Cao, S.E. Jacobsen, Science 299 (2003) 716–719.
date_created: 2021-06-04T11:26:26Z
date_published: 2003-01-31T00:00:00Z
date_updated: 2021-12-14T08:43:30Z
day: '31'
department:
- _id: DaZi
doi: 10.1126/science.1079695
extern: '1'
external_id:
pmid:
- '12522258'
intvolume: ' 299'
issue: '5607'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '01'
oa_version: None
page: 716-719
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone
methylation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 299
year: '2003'
...
---
_id: '9444'
abstract:
- lang: eng
text: Epigenetic silenced alleles of the Arabidopsis SUPERMANlocus (the clark kent
alleles) are associated with dense hypermethylation at noncanonical cytosines
(CpXpG and asymmetric sites, where X = A, T, C, or G). A genetic screen for suppressors
of a hypermethylated clark kent mutant identified nine loss-of-function alleles
of CHROMOMETHYLASE3(CMT3), a novel cytosine methyltransferase homolog. These cmt3
mutants display a wild-type morphology but exhibit decreased CpXpG methylation
of the SUP gene and of other sequences throughout the genome. They also show reactivated
expression of endogenous retrotransposon sequences. These results show that a
non-CpG DNA methyltransferase is responsible for maintaining epigenetic gene silencing.
article_processing_charge: No
article_type: original
author:
- first_name: A. M.
full_name: Lindroth, A. M.
last_name: Lindroth
- first_name: Xiaofeng
full_name: Cao, Xiaofeng
last_name: Cao
- first_name: James P.
full_name: Jackson, James P.
last_name: Jackson
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Claire M.
full_name: McCallum, Claire M.
last_name: McCallum
- first_name: Steven
full_name: Henikoff, Steven
last_name: Henikoff
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
citation:
ama: Lindroth AM, Cao X, Jackson JP, et al. Requirement of CHROMOMETHYLASE3 for
maintenance of CpXpG methylation. Science. 2001;292(5524):2077-2080. doi:10.1126/science.1059745
apa: Lindroth, A. M., Cao, X., Jackson, J. P., Zilberman, D., McCallum, C. M., Henikoff,
S., & Jacobsen, S. E. (2001). Requirement of CHROMOMETHYLASE3 for maintenance
of CpXpG methylation. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.1059745
chicago: Lindroth, A. M., Xiaofeng Cao, James P. Jackson, Daniel Zilberman, Claire
M. McCallum, Steven Henikoff, and Steven E. Jacobsen. “Requirement of CHROMOMETHYLASE3
for Maintenance of CpXpG Methylation.” Science. American Association for
the Advancement of Science, 2001. https://doi.org/10.1126/science.1059745.
ieee: A. M. Lindroth et al., “Requirement of CHROMOMETHYLASE3 for maintenance
of CpXpG methylation,” Science, vol. 292, no. 5524. American Association
for the Advancement of Science, pp. 2077–2080, 2001.
ista: Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen
SE. 2001. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation.
Science. 292(5524), 2077–2080.
mla: Lindroth, A. M., et al. “Requirement of CHROMOMETHYLASE3 for Maintenance of
CpXpG Methylation.” Science, vol. 292, no. 5524, American Association for
the Advancement of Science, 2001, pp. 2077–80, doi:10.1126/science.1059745.
short: A.M. Lindroth, X. Cao, J.P. Jackson, D. Zilberman, C.M. McCallum, S. Henikoff,
S.E. Jacobsen, Science 292 (2001) 2077–2080.
date_created: 2021-06-02T13:35:16Z
date_published: 2001-06-15T00:00:00Z
date_updated: 2021-12-14T08:40:32Z
day: '15'
department:
- _id: DaZi
doi: 10.1126/science.1059745
extern: '1'
external_id:
pmid:
- '11349138'
intvolume: ' 292'
issue: '5524'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '06'
oa_version: None
page: 2077-2080
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 292
year: '2001'
...