---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21716'
abstract:
- lang: eng
text: Male germline development in plants is highly sensitive to heat stress, with
elevated temperatures frequently impairing male fertility and consequently reducing
seed production. Indeed, recent global warming has decreased major crop yields,
emphasizing the urgent need to elucidate the molecular and cellular mechanisms
underlying heat-induced male sterility. This review synthesizes current knowledge
on how heat stress disrupts microsporogenesis and microgametogenesis, and how
plants counteract these stresses through diverse thermotolerance mechanisms. We
emphasize temperature-sensitive processes, including meiotic progression in male
germ cells, programmed cell death of somatic tapetal nurse cells, and post-meiotic
pollen tube development. We further discuss how epigenetic regulators enhance
thermotolerance by reprogramming DNA methylation landscapes and modulating histone
variant distribution. Finally, we propose future directions aimed at understanding
the mechanisms of reproductive thermotolerance from the epigenetic perspective.
acknowledgement: This work was supported by JSPS KAKENHI (grant number JP22J01430)
and the Osamu Hayaishi Memorial Scholarship for Study Abroad for H.N.
article_number: '102881'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Hiroki
full_name: Nagai, Hiroki
id: 608df3e6-e2ab-11ed-8890-c9318cec7da4
last_name: Nagai
orcid: 0000-0003-1671-9434
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: NAGAI H, Feng X. Genetic and epigenetic mechanisms underlying male reproductive
thermotolerance. Current Opinion in Plant Biology. 2026;91(6). doi:10.1016/j.pbi.2026.102881
apa: NAGAI, H., & Feng, X. (2026). Genetic and epigenetic mechanisms underlying
male reproductive thermotolerance. Current Opinion in Plant Biology. Elsevier.
https://doi.org/10.1016/j.pbi.2026.102881
chicago: NAGAI, HIROKI, and Xiaoqi Feng. “Genetic and Epigenetic Mechanisms Underlying
Male Reproductive Thermotolerance.” Current Opinion in Plant Biology. Elsevier,
2026. https://doi.org/10.1016/j.pbi.2026.102881.
ieee: H. NAGAI and X. Feng, “Genetic and epigenetic mechanisms underlying male reproductive
thermotolerance,” Current Opinion in Plant Biology, vol. 91, no. 6. Elsevier,
2026.
ista: NAGAI H, Feng X. 2026. Genetic and epigenetic mechanisms underlying male reproductive
thermotolerance. Current Opinion in Plant Biology. 91(6), 102881.
mla: NAGAI, HIROKI, and Xiaoqi Feng. “Genetic and Epigenetic Mechanisms Underlying
Male Reproductive Thermotolerance.” Current Opinion in Plant Biology, vol.
91, no. 6, 102881, Elsevier, 2026, doi:10.1016/j.pbi.2026.102881.
short: H. NAGAI, X. Feng, Current Opinion in Plant Biology 91 (2026).
corr_author: '1'
date_created: 2026-04-12T22:01:50Z
date_published: 2026-04-01T00:00:00Z
date_updated: 2026-05-04T11:15:57Z
day: '01'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.1016/j.pbi.2026.102881
has_accepted_license: '1'
intvolume: ' 91'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.pbi.2026.102881
month: '04'
oa: 1
oa_version: Published Version
publication: Current Opinion in Plant Biology
publication_identifier:
eissn:
- 1879-0356
issn:
- 1369-5266
publication_status: epub_ahead
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic and epigenetic mechanisms underlying male reproductive thermotolerance
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: 91
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '20220'
abstract:
- lang: eng
text: Stress granules (SG) are biomolecular condensates that represent an adaptive
response of cells to various stresses, including heat. However, the cell type–specific
function and relevance of SG formation, especially during reproductive development,
are largely not understood. Here, we show that the meiotic A-type cyclin TARDY
ASYNCHRONOUS MEIOSIS (TAM) is recruited to SGs in male meiocytes of Arabidopsis
after exposure to heat. We find that the amino terminus of TAM is necessary and
sufficient for the localization of proteins to meiotic SGs. Swapping the amino
terminus of TAM with the one of its sister protein CYCA1;1 resulted in a separation-of-function
allele of TAM, which prevents the partitioning of TAM to SGs while restoring a
wild-type phenotype in a tam mutant background under nonheat stress conditions.
Notably, plants expressing this TAM version prematurely terminate meiosis under
heat resulting in unreduced gametes. Thus, the formation of TAM-containing SGs
is necessary for genome stability under heat stress.
acknowledged_ssus:
- _id: Bio
acknowledgement: "We thank L. Strader (Duke University, Durham) and A. Holehouse (Washington
University, Saint Louis) for discussion and input in LLPS. We thank T. Nakagawa
(Shimane University, Matsue) for providing the pGWB604 Gateway vector containing
bar gene identified by Meiji Seika Kaisha Ltd. We thank M. Heese (Hamburg University)
for the critical reading and comments on this manuscript. We further thank J. Mehrmann
(Hamburg University) for technical assistance. We thank the ISTA imaging facility
for assistance for microscopy.\r\nThis project has received funding from JST-PRESTO
(JPMJPR18H7), JST-CREST (JPMJCR18H4), European Union’s Horizon 2020 under MSCA grant
101034413, and a federal grant from the state of Hamburg (LFF-BiCon)."
article_processing_charge: Yes
article_type: original
author:
- first_name: Joke G
full_name: De Jaeger-Braet, Joke G
id: 26bd38d3-c59a-11ee-a1af-d7a988cafcc5
last_name: De Jaeger-Braet
- first_name: Merle
full_name: Hartmann, Merle
last_name: Hartmann
- first_name: Lev
full_name: Böttger, Lev
last_name: Böttger
- first_name: Chao
full_name: Yang, Chao
id: 082e3e6e-8069-11ed-8390-c8cce7b1aaca
last_name: Yang
- first_name: Takahiro
full_name: Hamada, Takahiro
last_name: Hamada
- first_name: Stefan
full_name: Hoth, Stefan
last_name: Hoth
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Magdalena
full_name: Weingartner, Magdalena
last_name: Weingartner
- first_name: Arp
full_name: Schnittger, Arp
last_name: Schnittger
citation:
ama: De Jaeger-Braet JG, Hartmann M, Böttger L, et al. The recruitment of the A-type
cyclin TAM to stress granules is crucial for meiotic fidelity under heat. Science
Advances. 2025;11(32):eadr5694. doi:10.1126/sciadv.adr5694
apa: De Jaeger-Braet, J. G., Hartmann, M., Böttger, L., Yang, C., Hamada, T., Hoth,
S., … Schnittger, A. (2025). The recruitment of the A-type cyclin TAM to stress
granules is crucial for meiotic fidelity under heat. Science Advances.
AAAS. https://doi.org/10.1126/sciadv.adr5694
chicago: De Jaeger-Braet, Joke G, Merle Hartmann, Lev Böttger, Chao Yang, Takahiro
Hamada, Stefan Hoth, Xiaoqi Feng, Magdalena Weingartner, and Arp Schnittger. “The
Recruitment of the A-Type Cyclin TAM to Stress Granules Is Crucial for Meiotic
Fidelity under Heat.” Science Advances. AAAS, 2025. https://doi.org/10.1126/sciadv.adr5694.
ieee: J. G. De Jaeger-Braet et al., “The recruitment of the A-type cyclin
TAM to stress granules is crucial for meiotic fidelity under heat,” Science
Advances, vol. 11, no. 32. AAAS, p. eadr5694, 2025.
ista: De Jaeger-Braet JG, Hartmann M, Böttger L, Yang C, Hamada T, Hoth S, Feng
X, Weingartner M, Schnittger A. 2025. The recruitment of the A-type cyclin TAM
to stress granules is crucial for meiotic fidelity under heat. Science Advances.
11(32), eadr5694.
mla: De Jaeger-Braet, Joke G., et al. “The Recruitment of the A-Type Cyclin TAM
to Stress Granules Is Crucial for Meiotic Fidelity under Heat.” Science Advances,
vol. 11, no. 32, AAAS, 2025, p. eadr5694, doi:10.1126/sciadv.adr5694.
short: J.G. De Jaeger-Braet, M. Hartmann, L. Böttger, C. Yang, T. Hamada, S. Hoth,
X. Feng, M. Weingartner, A. Schnittger, Science Advances 11 (2025) eadr5694.
date_created: 2025-08-24T22:01:30Z
date_published: 2025-08-08T00:00:00Z
date_updated: 2025-09-30T14:24:10Z
day: '08'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.1126/sciadv.adr5694
ec_funded: 1
external_id:
isi:
- '001549102600016'
file:
- access_level: open_access
checksum: 0f1ae246acc9b075f01bf4afe382c8ba
content_type: application/pdf
creator: dernst
date_created: 2025-09-02T07:05:37Z
date_updated: 2025-09-02T07:05:37Z
file_id: '20270'
file_name: 2025_ScienceAdvance_DeJaegerBraet.pdf
file_size: 10876817
relation: main_file
success: 1
file_date_updated: 2025-09-02T07:05:37Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '32'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '08'
oa: 1
oa_version: Published Version
page: eadr5694
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: The recruitment of the A-type cyclin TAM to stress granules is crucial for
meiotic fidelity under heat
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 11
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19436'
abstract:
- lang: eng
text: Dynamic DNA methylation represses transposable elements (TEs) and regulates
gene activity, playing a pivotal role in plant development. Although substantial
progress has been made in understanding DNA methylation reprogramming during germline
development in Arabidopsis thaliana, whether similar mechanisms exist in other
dicot plants remains unclear. Here, we analyzed DNA methylation levels in meiocytes,
microspores, and pollens of Brassica Rapa using whole-genome bisulfite sequencing
(WGBS). Global DNA methylation analysis revealed similar CHH methylation reprogramming
compared to Arabidopsis, while distinct patterns were observed in the dynamics
of global CG and CHG methylation in B. rapa. Differentially methylated region
(DMR) analysis identified specifically methylated loci in the male sex cells of
B. Rapa with a stronger tendency to target genes, similar to observations in Arabidopsis.
Additionally, we found that the activity and genomic targeting preference of the
small RNA-directed DNA methylation (RdDM) were altered during B. Rapa male germline
development. A subset of long terminal repeat (LTR) TEs were activated, possibly
due to the dynamic regulation of DNA methylation during male sexual development
in B. Rapa. These findings provided new insights into the evolution of epigenetic
reprogramming mechanisms in plants.
acknowledgement: We thank Prof. Ying Li of Nanjing Agricultural University for her
help in providing seeds of K2 materials. This work was carried out with the support
of National Natural Science Foundation of China (Grant No. 32070608).
article_number: '16'
article_processing_charge: Yes
article_type: original
author:
- first_name: Jun
full_name: Zhang, Jun
last_name: Zhang
- first_name: Di
full_name: Wu, Di
last_name: Wu
- first_name: Yating
full_name: Zhang, Yating
last_name: Zhang
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Hongbo
full_name: Gao, Hongbo
id: 77c2e73a-eabd-11ef-aee9-8093a2ba7a93
last_name: Gao
citation:
ama: Zhang J, Wu D, Zhang Y, Feng X, Gao H. DNA methylation dynamics in male germline
development in Brassica Rapa. Molecular Horticulture. 2025;5. doi:10.1186/s43897-024-00137-9
apa: Zhang, J., Wu, D., Zhang, Y., Feng, X., & Gao, H. (2025). DNA methylation
dynamics in male germline development in Brassica Rapa. Molecular Horticulture.
Springer Nature. https://doi.org/10.1186/s43897-024-00137-9
chicago: Zhang, Jun, Di Wu, Yating Zhang, Xiaoqi Feng, and Hongbo Gao. “DNA Methylation
Dynamics in Male Germline Development in Brassica Rapa.” Molecular Horticulture.
Springer Nature, 2025. https://doi.org/10.1186/s43897-024-00137-9.
ieee: J. Zhang, D. Wu, Y. Zhang, X. Feng, and H. Gao, “DNA methylation dynamics
in male germline development in Brassica Rapa,” Molecular Horticulture,
vol. 5. Springer Nature, 2025.
ista: Zhang J, Wu D, Zhang Y, Feng X, Gao H. 2025. DNA methylation dynamics in male
germline development in Brassica Rapa. Molecular Horticulture. 5, 16.
mla: Zhang, Jun, et al. “DNA Methylation Dynamics in Male Germline Development in
Brassica Rapa.” Molecular Horticulture, vol. 5, 16, Springer Nature, 2025,
doi:10.1186/s43897-024-00137-9.
short: J. Zhang, D. Wu, Y. Zhang, X. Feng, H. Gao, Molecular Horticulture 5 (2025).
corr_author: '1'
date_created: 2025-03-23T23:01:25Z
date_published: 2025-03-04T00:00:00Z
date_updated: 2025-09-30T11:17:08Z
day: '04'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.1186/s43897-024-00137-9
external_id:
isi:
- '001436233900001'
pmid:
- '40033451'
file:
- access_level: open_access
checksum: 6d1e0e9b0e1902e4a711f81c5c17a070
content_type: application/pdf
creator: dernst
date_created: 2025-03-25T12:15:32Z
date_updated: 2025-03-25T12:15:32Z
file_id: '19460'
file_name: 2025_MolecularHorticulture_Zhang.pdf
file_size: 3014980
relation: main_file
success: 1
file_date_updated: 2025-03-25T12:15:32Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Molecular Horticulture
publication_identifier:
eissn:
- 2730-9401
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation dynamics in male germline development in Brassica Rapa
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 5
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19602'
abstract:
- lang: eng
text: N4-methylcytosine (4mC) is an important DNA modification in prokaryotes, but
its relevance and even its presence in eukaryotes have been mysterious. Here we
show that spermatogenesis in the liverwort Marchantia polymorpha involves two
waves of extensive DNA methylation reprogramming. First, 5-methylcytosine (5mC)
expands from transposons to the entire genome. Notably, the second wave installs
4mC throughout genic regions, covering over 50% of CG sites in sperm. 4mC requires
a methyltransferase (MpDN4MT1a) that is specifically expressed during late spermiogenesis.
Deletion of MpDN4MT1a alters the sperm transcriptome, causes sperm swimming and
fertility defects, and impairs post-fertilization development. Our results reveal
extensive 4mC in a eukaryote, identify a family of eukaryotic methyltransferases,
and elucidate the biological functions of 4mC in reproductive development, thereby
expanding the repertoire of functional eukaryotic DNA modifications.
acknowledged_ssus:
- _id: Bio
- _id: ScienComp
acknowledgement: We thank Sir Richard Roberts (NEB) for the kind gift of anti-4mC
antibodies. We are also grateful to the JIC Small Molecule Mass Spectrometry (Lionel
Hill) and Chemistry (Martin Rejzek) platforms as well as the High Resolution Metabolomics
Laboratory (Manfred Beckmann, Aberystwyth University) for their assistance with
LC-MS. Additionally, we acknowledge the assistance of the JIC Bioimaging Facility
and ISTA Imaging and Optics Facility for microscopy. Finally, we appreciate the
High Performance Computing resources provided by the ISTA Scientific Computing Facility
and Norwich BioScience Institute Partnership Computing Infrastructure. This work
was funded by a Sainsbury Charitable Foundation studentship (J.W.), a UKRI-BBSRC
Doctoral Training Partnerships studentship (BBT0087171 to J.T.), a European Research
Council Starting Grant (“SexMeth” 804981 to J.W., S.X., and X.F.), two Biotechnology
and Biological Sciences Research Council (BBSRC) grants (BBS0096201 and BBP0135111
to J.Z., M.V., and X.F.), an EMBO Long Term Fellowship (Y.L.), an ISTA Bridge Fellowship
(S.X.), and ISTA core funding (Y.Y. and X.F.).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: James
full_name: Walker, James
last_name: Walker
- first_name: Jingyi
full_name: Zhang, Jingyi
last_name: Zhang
- first_name: Yalin
full_name: Liu, Yalin
last_name: Liu
- first_name: Shujuan
full_name: Xu, Shujuan
id: 9724dd9d-f591-11ee-bd51-e97ed0652286
last_name: Xu
- first_name: Yiming
full_name: Yu, Yiming
id: 318e643b-8b61-11ed-b69e-aafa103ec8dd
last_name: Yu
orcid: 0000-0002-9919-7282
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: Weizhi
full_name: Ouyang, Weizhi
id: fec73395-8b60-11ed-b69e-927fda99c743
last_name: Ouyang
- first_name: Judit
full_name: Tálas, Judit
last_name: Tálas
- first_name: Liam
full_name: Dolan, Liam
last_name: Dolan
- first_name: Keiji
full_name: Nakajima, Keiji
last_name: Nakajima
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: Walker J, Zhang J, Liu Y, et al. Extensive N4 cytosine methylation is essential
for Marchantia sperm function. Cell. 2025;188(11):2890-2906.e14. doi:10.1016/j.cell.2025.03.014
apa: Walker, J., Zhang, J., Liu, Y., Xu, S., Yu, Y., Vickers, M., … Feng, X. (2025).
Extensive N4 cytosine methylation is essential for Marchantia sperm function.
Cell. Elsevier. https://doi.org/10.1016/j.cell.2025.03.014
chicago: Walker, James, Jingyi Zhang, Yalin Liu, Shujuan Xu, Yiming Yu, Martin Vickers,
Weizhi Ouyang, et al. “Extensive N4 Cytosine Methylation Is Essential for Marchantia
Sperm Function.” Cell. Elsevier, 2025. https://doi.org/10.1016/j.cell.2025.03.014.
ieee: J. Walker et al., “Extensive N4 cytosine methylation is essential for
Marchantia sperm function,” Cell, vol. 188, no. 11. Elsevier, p. 2890–2906.e14,
2025.
ista: Walker J, Zhang J, Liu Y, Xu S, Yu Y, Vickers M, Ouyang W, Tálas J, Dolan
L, Nakajima K, Feng X. 2025. Extensive N4 cytosine methylation is essential for
Marchantia sperm function. Cell. 188(11), 2890–2906.e14.
mla: Walker, James, et al. “Extensive N4 Cytosine Methylation Is Essential for Marchantia
Sperm Function.” Cell, vol. 188, no. 11, Elsevier, 2025, p. 2890–2906.e14,
doi:10.1016/j.cell.2025.03.014.
short: J. Walker, J. Zhang, Y. Liu, S. Xu, Y. Yu, M. Vickers, W. Ouyang, J. Tálas,
L. Dolan, K. Nakajima, X. Feng, Cell 188 (2025) 2890–2906.e14.
corr_author: '1'
date_created: 2025-04-20T22:01:28Z
date_published: 2025-05-29T00:00:00Z
date_updated: 2026-04-28T13:36:51Z
day: '29'
ddc:
- '570'
department:
- _id: XiFe
doi: 10.1016/j.cell.2025.03.014
ec_funded: 1
external_id:
isi:
- '001504744800006'
pmid:
- '40209706'
file:
- access_level: open_access
checksum: 0dcc2feb368dfe7c4890093366b2dacb
content_type: application/pdf
creator: dernst
date_created: 2025-12-29T13:40:32Z
date_updated: 2025-12-29T13:40:32Z
file_id: '20871'
file_name: 2025_Cell_Walker.pdf
file_size: 11622960
relation: main_file
success: 1
file_date_updated: 2025-12-29T13:40:32Z
has_accepted_license: '1'
intvolume: ' 188'
isi: 1
issue: '11'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 2890-2906.e14
pmid: 1
project:
- _id: bdb51a6e-d553-11ed-ba76-c2025f3d5725
call_identifier: H2020
grant_number: '804981'
name: Establishment, modulation and inheritance of sexual lineage specific DNA methylation
in plants
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/from-bacterial-immunity-to-plant-sex/
scopus_import: '1'
status: public
title: Extensive N4 cytosine methylation is essential for Marchantia sperm function
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 188
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15375'
abstract:
- lang: eng
text: In the eukaryotic nucleus, heterochromatin forms highly condensed, visible
foci known as heterochromatin foci (HF). These HF are enriched with linker histone
H1, a key player in heterochromatin condensation and silencing. However, it is
unknown how H1 aggregates HF and condenses heterochromatin. In this study, we
established that H1 facilitates heterochromatin condensation by enhancing inter-
and intrachromosomal interactions between and within heterochromatic regions of
the Arabidopsis (Arabidopsis thaliana) genome. We demonstrated that H1 drives
HF formation via phase separation, which requires its C-terminal intrinsically
disordered region (C-IDR). A truncated H1 lacking the C-IDR fails to form foci
or recover HF in the h1 mutant background, whereas C-IDR with a short stretch
of the globular domain (18 out of 71 amino acids) is sufficient to rescue both
defects. In addition, C-IDR is essential for H1's roles in regulating nucleosome
repeat length and DNA methylation in Arabidopsis, indicating that phase separation
capability is required for chromatin functions of H1. Our data suggest that bacterial
H1-like proteins, which have been shown to condense DNA, are intrinsically disordered
and capable of mediating phase separation. Therefore, we propose that phase separation
mediated by H1 or H1-like proteins may represent an ancient mechanism for condensing
chromatin and DNA.
acknowledged_ssus:
- _id: Bio
- _id: ScienComp
acknowledgement: "This work was funded by ISTA core support (Y.Y. and X.F.) and grants
from the National Natural Science Foundation of China (31871443 to L.W. and P.L.;
32100417 to L.W.).\r\nWe thank the ISTA Imaging and Optics Facility for assistance
with microscopy and the ISTA Scientific Computing Facility for high-performance
computing resources."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Yiming
full_name: Yu, Yiming
id: 318e643b-8b61-11ed-b69e-aafa103ec8dd
last_name: Yu
- first_name: Liang
full_name: Wang, Liang
last_name: Wang
- first_name: Jingyi
full_name: Zhang, Jingyi
last_name: Zhang
- first_name: Zhengyong
full_name: Bai, Zhengyong
last_name: Bai
- first_name: Guohong
full_name: Li, Guohong
last_name: Li
- first_name: Pilong
full_name: Li, Pilong
last_name: Li
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: He S, Yu Y, Wang L, et al. Linker histone H1 drives heterochromatin condensation
via phase separation in Arabidopsis. The Plant Cell. 2024;36(5):1829-1843.
doi:10.1093/plcell/koae034
apa: He, S., Yu, Y., Wang, L., Zhang, J., Bai, Z., Li, G., … Feng, X. (2024). Linker
histone H1 drives heterochromatin condensation via phase separation in Arabidopsis.
The Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koae034
chicago: He, Shengbo, Yiming Yu, Liang Wang, Jingyi Zhang, Zhengyong Bai, Guohong
Li, Pilong Li, and Xiaoqi Feng. “Linker Histone H1 Drives Heterochromatin Condensation
via Phase Separation in Arabidopsis.” The Plant Cell. Oxford University
Press, 2024. https://doi.org/10.1093/plcell/koae034.
ieee: S. He et al., “Linker histone H1 drives heterochromatin condensation
via phase separation in Arabidopsis,” The Plant Cell, vol. 36, no. 5. Oxford
University Press, pp. 1829–1843, 2024.
ista: He S, Yu Y, Wang L, Zhang J, Bai Z, Li G, Li P, Feng X. 2024. Linker histone
H1 drives heterochromatin condensation via phase separation in Arabidopsis. The
Plant Cell. 36(5), 1829–1843.
mla: He, Shengbo, et al. “Linker Histone H1 Drives Heterochromatin Condensation
via Phase Separation in Arabidopsis.” The Plant Cell, vol. 36, no. 5, Oxford
University Press, 2024, pp. 1829–43, doi:10.1093/plcell/koae034.
short: S. He, Y. Yu, L. Wang, J. Zhang, Z. Bai, G. Li, P. Li, X. Feng, The Plant
Cell 36 (2024) 1829–1843.
corr_author: '1'
date_created: 2024-05-12T22:01:01Z
date_published: 2024-05-01T00:00:00Z
date_updated: 2025-09-08T07:21:17Z
day: '01'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.1093/plcell/koae034
external_id:
isi:
- '001180817000001'
pmid:
- '38309957'
file:
- access_level: open_access
checksum: eed76c848fe3d8fe9a53943181aaa53c
content_type: application/pdf
creator: dernst
date_created: 2025-04-23T07:43:12Z
date_updated: 2025-04-23T07:43:12Z
file_id: '19611'
file_name: 2024_PlantCell_He.pdf
file_size: 50791962
relation: main_file
success: 1
file_date_updated: 2025-04-23T07:43:12Z
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1829-1843
pmid: 1
publication: The Plant Cell
publication_identifier:
eissn:
- 1532-298X
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Linker histone H1 drives heterochromatin condensation via phase separation
in Arabidopsis
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 36
year: '2024'
...
---
_id: '12668'
abstract:
- lang: eng
text: "Background: Plant and animal embryogenesis have conserved and distinct features.
Cell fate transitions occur during embryogenesis in both plants and animals. The
epigenomic processes regulating plant embryogenesis remain largely elusive.\r\n\r\nResults:
Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis
of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific
and proximal–distal distinct chromatin accessibility and dynamics concordant with
transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3,
H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific
epigenomic dynamics during zygotic genome activation. Polycomb repressive complex
2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later
H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to
establish a permissive chromatin environment facilitating the access of transcription
factors to cis-elements for fate patterning. Embryonic maturation is characterized
by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates
in restricting totipotency while preventing extensive organogenesis. Finally,
epigenomic signatures are correlated with biased expression among homeolog triads
and divergent expression after polyploidization, revealing an epigenomic contributor
to subgenome diversification in an allohexaploid genome.\r\n\r\nConclusions: Collectively,
we present an invaluable resource for comparative and mechanistic analysis of
the epigenomic regulation of crop embryogenesis."
article_number: '7'
article_processing_charge: No
article_type: original
author:
- first_name: Long
full_name: Zhao, Long
last_name: Zhao
- first_name: Yiman
full_name: Yang, Yiman
last_name: Yang
- first_name: Jinchao
full_name: Chen, Jinchao
last_name: Chen
- first_name: Xuelei
full_name: Lin, Xuelei
last_name: Lin
- first_name: Hao
full_name: Zhang, Hao
last_name: Zhang
- first_name: Hao
full_name: Wang, Hao
last_name: Wang
- first_name: Hongzhe
full_name: Wang, Hongzhe
last_name: Wang
- first_name: Xiaomin
full_name: Bie, Xiaomin
last_name: Bie
- first_name: Jiafu
full_name: Jiang, Jiafu
last_name: Jiang
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Xiangdong
full_name: Fu, Xiangdong
last_name: Fu
- first_name: Xiansheng
full_name: Zhang, Xiansheng
last_name: Zhang
- first_name: Zhuo
full_name: Du, Zhuo
last_name: Du
- first_name: Jun
full_name: Xiao, Jun
last_name: Xiao
citation:
ama: Zhao L, Yang Y, Chen J, et al. Dynamic chromatin regulatory programs during
embryogenesis of hexaploid wheat. Genome Biology. 2023;24. doi:10.1186/s13059-022-02844-2
apa: Zhao, L., Yang, Y., Chen, J., Lin, X., Zhang, H., Wang, H., … Xiao, J. (2023).
Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat.
Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-022-02844-2
chicago: Zhao, Long, Yiman Yang, Jinchao Chen, Xuelei Lin, Hao Zhang, Hao Wang,
Hongzhe Wang, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis
of Hexaploid Wheat.” Genome Biology. Springer Nature, 2023. https://doi.org/10.1186/s13059-022-02844-2.
ieee: L. Zhao et al., “Dynamic chromatin regulatory programs during embryogenesis
of hexaploid wheat,” Genome Biology, vol. 24. Springer Nature, 2023.
ista: Zhao L, Yang Y, Chen J, Lin X, Zhang H, Wang H, Wang H, Bie X, Jiang J, Feng
X, Fu X, Zhang X, Du Z, Xiao J. 2023. Dynamic chromatin regulatory programs during
embryogenesis of hexaploid wheat. Genome Biology. 24, 7.
mla: Zhao, Long, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis
of Hexaploid Wheat.” Genome Biology, vol. 24, 7, Springer Nature, 2023,
doi:10.1186/s13059-022-02844-2.
short: L. Zhao, Y. Yang, J. Chen, X. Lin, H. Zhang, H. Wang, H. Wang, X. Bie, J.
Jiang, X. Feng, X. Fu, X. Zhang, Z. Du, J. Xiao, Genome Biology 24 (2023).
date_created: 2023-02-23T09:13:49Z
date_published: 2023-01-13T00:00:00Z
date_updated: 2023-05-08T10:52:49Z
day: '13'
department:
- _id: XiFe
doi: 10.1186/s13059-022-02844-2
extern: '1'
external_id:
pmid:
- '36639687'
intvolume: ' 24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1186/s13059-022-02844-2
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
issn:
- 1474-760X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2023'
...
---
_id: '12669'
abstract:
- lang: eng
text: The study of RNAs has become one of the most influential research fields in
contemporary biology and biomedicine. In the last few years, new sequencing technologies
have produced an explosion of new and exciting discoveries in the field but have
also given rise to many open questions. Defining these questions, together with
old, long-standing gaps in our knowledge, is the spirit of this article. The breadth
of topics within RNA biology research is vast, and every aspect of the biology
of these molecules contains countless exciting open questions. Here, we asked
12 groups to discuss their most compelling question among some plant RNA biology
topics. The following vignettes cover RNA alternative splicing; RNA dynamics;
RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding
RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis
and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each
section, we will present the current state-of-the-art in plant RNA biology research
before asking the questions that will surely motivate future discoveries in the
field. We hope this article will spark a debate about the future perspective on
RNA biology and provoke novel reflections in the reader.
article_number: koac346
article_processing_charge: No
article_type: original
author:
- first_name: Pablo A
full_name: Manavella, Pablo A
last_name: Manavella
- first_name: Micaela A
full_name: Godoy Herz, Micaela A
last_name: Godoy Herz
- first_name: Alberto R
full_name: Kornblihtt, Alberto R
last_name: Kornblihtt
- first_name: Reed
full_name: Sorenson, Reed
last_name: Sorenson
- first_name: Leslie E
full_name: Sieburth, Leslie E
last_name: Sieburth
- first_name: Kentaro
full_name: Nakaminami, Kentaro
last_name: Nakaminami
- first_name: Motoaki
full_name: Seki, Motoaki
last_name: Seki
- first_name: Yiliang
full_name: Ding, Yiliang
last_name: Ding
- first_name: Qianwen
full_name: Sun, Qianwen
last_name: Sun
- first_name: Hunseung
full_name: Kang, Hunseung
last_name: Kang
- first_name: Federico D
full_name: Ariel, Federico D
last_name: Ariel
- first_name: Martin
full_name: Crespi, Martin
last_name: Crespi
- first_name: Axel J
full_name: Giudicatti, Axel J
last_name: Giudicatti
- first_name: Qiang
full_name: Cai, Qiang
last_name: Cai
- first_name: Hailing
full_name: Jin, Hailing
last_name: Jin
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Yijun
full_name: Qi, Yijun
last_name: Qi
- first_name: Craig S
full_name: Pikaard, Craig S
last_name: Pikaard
citation:
ama: 'Manavella PA, Godoy Herz MA, Kornblihtt AR, et al. Beyond transcription: compelling
open questions in plant RNA biology. The Plant Cell. 2023;35(6). doi:10.1093/plcell/koac346'
apa: 'Manavella, P. A., Godoy Herz, M. A., Kornblihtt, A. R., Sorenson, R., Sieburth,
L. E., Nakaminami, K., … Pikaard, C. S. (2023). Beyond transcription: compelling
open questions in plant RNA biology. The Plant Cell. Oxford University
Press. https://doi.org/10.1093/plcell/koac346'
chicago: 'Manavella, Pablo A, Micaela A Godoy Herz, Alberto R Kornblihtt, Reed Sorenson,
Leslie E Sieburth, Kentaro Nakaminami, Motoaki Seki, et al. “Beyond Transcription:
Compelling Open Questions in Plant RNA Biology.” The Plant Cell. Oxford
University Press, 2023. https://doi.org/10.1093/plcell/koac346.'
ieee: 'P. A. Manavella et al., “Beyond transcription: compelling open questions
in plant RNA biology,” The Plant Cell, vol. 35, no. 6. Oxford University
Press, 2023.'
ista: 'Manavella PA, Godoy Herz MA, Kornblihtt AR, Sorenson R, Sieburth LE, Nakaminami
K, Seki M, Ding Y, Sun Q, Kang H, Ariel FD, Crespi M, Giudicatti AJ, Cai Q, Jin
H, Feng X, Qi Y, Pikaard CS. 2023. Beyond transcription: compelling open questions
in plant RNA biology. The Plant Cell. 35(6), koac346.'
mla: 'Manavella, Pablo A., et al. “Beyond Transcription: Compelling Open Questions
in Plant RNA Biology.” The Plant Cell, vol. 35, no. 6, koac346, Oxford
University Press, 2023, doi:10.1093/plcell/koac346.'
short: P.A. Manavella, M.A. Godoy Herz, A.R. Kornblihtt, R. Sorenson, L.E. Sieburth,
K. Nakaminami, M. Seki, Y. Ding, Q. Sun, H. Kang, F.D. Ariel, M. Crespi, A.J.
Giudicatti, Q. Cai, H. Jin, X. Feng, Y. Qi, C.S. Pikaard, The Plant Cell 35 (2023).
date_created: 2023-02-23T09:14:59Z
date_published: 2023-06-01T00:00:00Z
date_updated: 2023-10-04T09:48:43Z
day: '01'
department:
- _id: XiFe
doi: 10.1093/plcell/koac346
extern: '1'
external_id:
pmid:
- '36477566'
intvolume: ' 35'
issue: '6'
keyword:
- Cell Biology
- Plant Science
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/plcell/koac346
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: The Plant Cell
publication_identifier:
eissn:
- 1532-298X
issn:
- 1040-4651
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Beyond transcription: compelling open questions in plant RNA biology'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2023'
...
---
_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).
corr_author: '1'
date_created: 2023-02-23T09:17:44Z
date_published: 2023-03-28T00:00:00Z
date_updated: 2025-04-14T07:57:43Z
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: '12670'
abstract:
- lang: eng
text: DNA methylation plays essential homeostatic functions in eukaryotic genomes.
In animals, DNA methylation is also developmentally regulated and, in turn, regulates
development. In the past two decades, huge research effort has endorsed the understanding
that DNA methylation plays a similar role in plant development, especially during
sexual reproduction. The power of whole-genome sequencing and cell isolation techniques,
as well as bioinformatics tools, have enabled recent studies to reveal dynamic
changes in DNA methylation during germline development. Furthermore, the combination
of these technological advances with genetics, developmental biology and cell
biology tools has revealed functional methylation reprogramming events that control
gene and transposon activities in flowering plant germlines. In this review, we
discuss the major advances in our knowledge of DNA methylation dynamics during
male and female germline development in flowering plants.
article_processing_charge: No
article_type: review
author:
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: He S, Feng X. DNA methylation dynamics during germline development. Journal
of Integrative Plant Biology. 2022;64(12):2240-2251. doi:10.1111/jipb.13422
apa: He, S., & Feng, X. (2022). DNA methylation dynamics during germline development.
Journal of Integrative Plant Biology. Wiley. https://doi.org/10.1111/jipb.13422
chicago: He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline
Development.” Journal of Integrative Plant Biology. Wiley, 2022. https://doi.org/10.1111/jipb.13422.
ieee: S. He and X. Feng, “DNA methylation dynamics during germline development,”
Journal of Integrative Plant Biology, vol. 64, no. 12. Wiley, pp. 2240–2251,
2022.
ista: He S, Feng X. 2022. DNA methylation dynamics during germline development.
Journal of Integrative Plant Biology. 64(12), 2240–2251.
mla: He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline Development.”
Journal of Integrative Plant Biology, vol. 64, no. 12, Wiley, 2022, pp.
2240–51, doi:10.1111/jipb.13422.
short: S. He, X. Feng, Journal of Integrative Plant Biology 64 (2022) 2240–2251.
date_created: 2023-02-23T09:15:57Z
date_published: 2022-12-07T00:00:00Z
date_updated: 2024-10-14T12:03:14Z
day: '07'
department:
- _id: XiFe
doi: 10.1111/jipb.13422
extern: '1'
external_id:
pmid:
- '36478632'
intvolume: ' 64'
issue: '12'
keyword:
- Plant Science
- General Biochemistry
- Genetics and Molecular Biology
- Biochemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jipb.13422
month: '12'
oa: 1
oa_version: Published Version
page: 2240-2251
pmid: 1
publication: Journal of Integrative Plant Biology
publication_identifier:
eissn:
- 1744-7909
issn:
- 1672-9072
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation dynamics during germline development
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 64
year: '2022'
...
---
_id: '12671'
abstract:
- lang: eng
text: Sperm chromatin is typically transformed by protamines into a compact and
transcriptionally inactive state1,2. Sperm cells of flowering plants lack protamines,
yet they have small, transcriptionally active nuclei with chromatin condensed
through an unknown mechanism3,4. Here we show that a histone variant, H2B.8, mediates
sperm chromatin and nuclear condensation in Arabidopsis thaliana. Loss of H2B.8
causes enlarged sperm nuclei with dispersed chromatin, whereas ectopic expression
in somatic cells produces smaller nuclei with aggregated chromatin. This result
demonstrates that H2B.8 is sufficient for chromatin condensation. H2B.8 aggregates
transcriptionally inactive AT-rich chromatin into phase-separated condensates,
which facilitates nuclear compaction without reducing transcription. Reciprocal
crosses show that mutation of h2b.8 reduces male transmission, which suggests
that H2B.8-mediated sperm compaction is important for fertility. Altogether, our
results reveal a new mechanism of nuclear compaction through global aggregation
of unexpressed chromatin. We propose that H2B.8 is an evolutionary innovation
of flowering plants that achieves nuclear condensation compatible with active
transcription.
article_processing_charge: No
article_type: original
author:
- first_name: Toby
full_name: Buttress, Toby
last_name: Buttress
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Liang
full_name: Wang, Liang
last_name: Wang
- first_name: Shaoli
full_name: Zhou, Shaoli
last_name: Zhou
- first_name: Gerhard
full_name: Saalbach, Gerhard
last_name: Saalbach
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: Guohong
full_name: Li, Guohong
last_name: Li
- first_name: Pilong
full_name: Li, Pilong
last_name: Li
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: Buttress T, He S, Wang L, et al. Histone H2B.8 compacts flowering plant sperm
through chromatin phase separation. Nature. 2022;611(7936):614-622. doi:10.1038/s41586-022-05386-6
apa: Buttress, T., He, S., Wang, L., Zhou, S., Saalbach, G., Vickers, M., … Feng,
X. (2022). Histone H2B.8 compacts flowering plant sperm through chromatin phase
separation. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05386-6
chicago: Buttress, Toby, Shengbo He, Liang Wang, Shaoli Zhou, Gerhard Saalbach,
Martin Vickers, Guohong Li, Pilong Li, and Xiaoqi Feng. “Histone H2B.8 Compacts
Flowering Plant Sperm through Chromatin Phase Separation.” Nature. Springer
Nature, 2022. https://doi.org/10.1038/s41586-022-05386-6.
ieee: T. Buttress et al., “Histone H2B.8 compacts flowering plant sperm through
chromatin phase separation,” Nature, vol. 611, no. 7936. Springer Nature,
pp. 614–622, 2022.
ista: Buttress T, He S, Wang L, Zhou S, Saalbach G, Vickers M, Li G, Li P, Feng
X. 2022. Histone H2B.8 compacts flowering plant sperm through chromatin phase
separation. Nature. 611(7936), 614–622.
mla: Buttress, Toby, et al. “Histone H2B.8 Compacts Flowering Plant Sperm through
Chromatin Phase Separation.” Nature, vol. 611, no. 7936, Springer Nature,
2022, pp. 614–22, doi:10.1038/s41586-022-05386-6.
short: T. Buttress, S. He, L. Wang, S. Zhou, G. Saalbach, M. Vickers, G. Li, P.
Li, X. Feng, Nature 611 (2022) 614–622.
date_created: 2023-02-23T09:17:05Z
date_published: 2022-11-17T00:00:00Z
date_updated: 2024-10-14T12:03:36Z
day: '17'
department:
- _id: XiFe
doi: 10.1038/s41586-022-05386-6
extern: '1'
external_id:
pmid:
- '36323776'
intvolume: ' 611'
issue: '7936'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41586-022-05386-6
month: '11'
oa: 1
oa_version: Published Version
page: 614-622
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 H2B.8 compacts flowering plant sperm through chromatin phase separation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 611
year: '2022'
...
---
_id: '12186'
abstract:
- lang: eng
text: Activation of cell-surface and intracellular receptor-mediated immunity results
in rapid transcriptional reprogramming that underpins disease resistance. However,
the mechanisms by which co-activation of both immune systems lead to transcriptional
changes are not clear. Here, we combine RNA-seq and ATAC-seq to define changes
in gene expression and chromatin accessibility. Activation of cell-surface or
intracellular receptor-mediated immunity, or both, increases chromatin accessibility
at induced defence genes. Analysis of ATAC-seq and RNA-seq data combined with
publicly available information on transcription factor DNA-binding motifs enabled
comparison of individual gene regulatory networks activated by cell-surface or
intracellular receptor-mediated immunity, or by both. These results and analyses
reveal overlapping and conserved transcriptional regulatory mechanisms between
the two immune systems.
acknowledgement: "We thank the Gatsby Foundation (UK) for funding to the JDGJ laboratory.
PD acknowledges support from the European Union’s Horizon 2020 Research and Innovation
Program under Marie Skłodowska Curie Actions (grant agreement: 656243) and a Future
Leader Fellowship from the Biotechnology and Biological Sciences Research Council
(BBSRC) (grant agreement: BB/R012172/1). TS, RKS, DM, and JDGJ were supported by
the Gatsby Foundation funding to the\r\nSainsbury Laboratory. NMP and KV were supported
by a BOF grant from Ghent University (grant agreement: BOF24Y2019001901). WG and
RZ were supported by the Scottish Government Rural and Environment Science and Analytical
Services division (RESAS), and RZ also acknowledges the support from a BBSRC Bioinformatics
and Biological Resources Fund (grant agreement: BB/S020160/1).BPMN was supported
by the Norwich Research Park (NRP) Biosciences Doctoral Training Partnership (DTP)
funded by the BBSRC (grant agreement: BB/M011216/1). SH and XF were supported by
a BBSRC Responsive Mode grant (grant agreement: BB/S009620/1) and a European Research
Council Starting grant ‘SexMeth’ (grant agreement: 804981). CL was supported by
Deutsche Forschungsgemeinschaft (grant agreement: LI 2862/4). "
article_processing_charge: No
article_type: original
author:
- first_name: Pingtao
full_name: Ding, Pingtao
last_name: Ding
- first_name: Toshiyuki
full_name: Sakai, Toshiyuki
last_name: Sakai
- first_name: Ram
full_name: Krishna Shrestha, Ram
last_name: Krishna Shrestha
- first_name: Nicolas
full_name: Manosalva Perez, Nicolas
last_name: Manosalva Perez
- first_name: Wenbin
full_name: Guo, Wenbin
last_name: Guo
- first_name: Bruno Pok Man
full_name: Ngou, Bruno Pok Man
last_name: Ngou
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Chang
full_name: Liu, Chang
last_name: Liu
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Runxuan
full_name: Zhang, Runxuan
last_name: Zhang
- first_name: Klaas
full_name: Vandepoele, Klaas
last_name: Vandepoele
- first_name: Dan
full_name: MacLean, Dan
last_name: MacLean
- first_name: Jonathan D G
full_name: Jones, Jonathan D G
last_name: Jones
citation:
ama: Ding P, Sakai T, Krishna Shrestha R, et al. Chromatin accessibility landscapes
activated by cell-surface and intracellular immune receptors. Journal of Experimental
Botany. 2021;72(22):7927-7941. doi:10.1093/jxb/erab373
apa: Ding, P., Sakai, T., Krishna Shrestha, R., Manosalva Perez, N., Guo, W., Ngou,
B. P. M., … Jones, J. D. G. (2021). Chromatin accessibility landscapes activated
by cell-surface and intracellular immune receptors. Journal of Experimental
Botany. Oxford University Press. https://doi.org/10.1093/jxb/erab373
chicago: Ding, Pingtao, Toshiyuki Sakai, Ram Krishna Shrestha, Nicolas Manosalva
Perez, Wenbin Guo, Bruno Pok Man Ngou, Shengbo He, et al. “Chromatin Accessibility
Landscapes Activated by Cell-Surface and Intracellular Immune Receptors.” Journal
of Experimental Botany. Oxford University Press, 2021. https://doi.org/10.1093/jxb/erab373.
ieee: P. Ding et al., “Chromatin accessibility landscapes activated by cell-surface
and intracellular immune receptors,” Journal of Experimental Botany, vol.
72, no. 22. Oxford University Press, pp. 7927–7941, 2021.
ista: Ding P, Sakai T, Krishna Shrestha R, Manosalva Perez N, Guo W, Ngou BPM, He
S, Liu C, Feng X, Zhang R, Vandepoele K, MacLean D, Jones JDG. 2021. Chromatin
accessibility landscapes activated by cell-surface and intracellular immune receptors.
Journal of Experimental Botany. 72(22), 7927–7941.
mla: Ding, Pingtao, et al. “Chromatin Accessibility Landscapes Activated by Cell-Surface
and Intracellular Immune Receptors.” Journal of Experimental Botany, vol.
72, no. 22, Oxford University Press, 2021, pp. 7927–41, doi:10.1093/jxb/erab373.
short: P. Ding, T. Sakai, R. Krishna Shrestha, N. Manosalva Perez, W. Guo, B.P.M.
Ngou, S. He, C. Liu, X. Feng, R. Zhang, K. Vandepoele, D. MacLean, J.D.G. Jones,
Journal of Experimental Botany 72 (2021) 7927–7941.
date_created: 2023-01-16T09:14:35Z
date_published: 2021-08-13T00:00:00Z
date_updated: 2023-05-08T11:01:18Z
day: '13'
department:
- _id: XiFe
doi: 10.1093/jxb/erab373
extern: '1'
external_id:
pmid:
- '34387350'
intvolume: ' 72'
issue: '22'
keyword:
- Plant Science
- Physiology
language:
- iso: eng
month: '08'
oa_version: None
page: 7927-7941
pmid: 1
publication: Journal of Experimental Botany
publication_identifier:
issn:
- 0022-0957
- 1460-2431
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromatin accessibility landscapes activated by cell-surface and intracellular
immune receptors
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 72
year: '2021'
...
---
OA_place: repository
OA_type: green
_id: '12187'
abstract:
- lang: eng
text: Genomes of germ cells present an existential vulnerability to organisms because
germ cell mutations will propagate to future generations. Transposable elements
are one source of such mutations. In the small flowering plant Arabidopsis, Long
et al. found that genome methylation in the male germline is directed by small
interfering RNAs (siRNAs) imperfectly transcribed from transposons (see the Perspective
by Mosher). These germline siRNAs silence germline transposons and establish inherited
methylation patterns in sperm, thus maintaining the integrity of the plant genome
across generations.
acknowledgement: 'We thank the John Innes Centre Bioimaging Facility (S. Lopez, E.
Wegel, and K. Findlay) for their assistance with microscopy and the Norwich BioScience
Institute Partnership Computing Infrastructure for Science Group for high-performance
computing resources. Funding: This work was funded by a European Research Council
Starting Grant (“SexMeth” 804981; J.L., J.W., and X.F.), a Sainsbury Charitable
Foundation studentship (J.W.), two Biotechnology and Biological Sciences Research
Council (BBSRC) grants (BBS0096201 and BBP0135111; W.S., M.V., and X.F.), two John
Innes Foundation studentships (B.A. and S.D.), and a BBSRC David Phillips Fellowship
(BBL0250431; H.G. and X.F.). Author contributions: J.L., J.W., and X.F. designed
the study and wrote the manuscript; J.L., W.S., B.A., H.G., and S.D. performed the
experiments; and J.L., J.W., B.A., H.G., S.D., M.V., and X.F. analyzed the data.
Competing interests: The authors declare no competing interests. Data and material
availability: All sequencing data have been deposited in the Gene Expression Omnibus
(GEO) under accession no. GSE161625. Accession nos. of published datasets used in
this study are listed in table S6. Published software used in this study include
Bowtie v1.2.2 (https://doi.org/10.1002/0471250953.bi1107s32), Bismark v0.22.2 (https://doi.org/10.1093/bioinformatics/btr167),
Kallisto v0.43.0 (https://doi.org/10.1038/nbt0816-888d), Shortstack v3.8.5 (https://doi.org/10.1534/g3.116.030452),
and Cutadapt v1.15 (https://doi.org/10.1089/cmb.2017.0096). TrimGalore v0.4.1 and
MarkDuplicates v1.141 are available from https://github.com/FelixKrueger/TrimGalore
and https://github.com/broadinstitute/picard, respectively. All remaining data are
in the main paper or the supplementary materials.'
article_processing_charge: No
article_type: original
author:
- first_name: Jincheng
full_name: Long, Jincheng
last_name: Long
- first_name: James
full_name: Walker, James
last_name: Walker
- first_name: Wenjing
full_name: She, Wenjing
last_name: She
- first_name: Billy
full_name: Aldridge, Billy
last_name: Aldridge
- first_name: Hongbo
full_name: Gao, Hongbo
last_name: Gao
- first_name: Samuel
full_name: Deans, Samuel
last_name: Deans
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: Long J, Walker J, She W, et al. Nurse cell-derived small RNAs define paternal
epigenetic inheritance in Arabidopsis. Science. 2021;373(6550). doi:10.1126/science.abh0556
apa: Long, J., Walker, J., She, W., Aldridge, B., Gao, H., Deans, S., … Feng, X.
(2021). Nurse cell-derived small RNAs define paternal epigenetic inheritance in
Arabidopsis. Science. American Association for the Advancement of Science.
https://doi.org/10.1126/science.abh0556
chicago: Long, Jincheng, James Walker, Wenjing She, Billy Aldridge, Hongbo Gao,
Samuel Deans, Martin Vickers, and Xiaoqi Feng. “Nurse Cell-Derived Small RNAs
Define Paternal Epigenetic Inheritance in Arabidopsis.” Science. American
Association for the Advancement of Science, 2021. https://doi.org/10.1126/science.abh0556.
ieee: J. Long et al., “Nurse cell-derived small RNAs define paternal epigenetic
inheritance in Arabidopsis,” Science, vol. 373, no. 6550. American Association
for the Advancement of Science, 2021.
ista: Long J, Walker J, She W, Aldridge B, Gao H, Deans S, Vickers M, Feng X. 2021.
Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis.
Science. 373(6550).
mla: Long, Jincheng, et al. “Nurse Cell-Derived Small RNAs Define Paternal Epigenetic
Inheritance in Arabidopsis.” Science, vol. 373, no. 6550, American Association
for the Advancement of Science, 2021, doi:10.1126/science.abh0556.
short: J. Long, J. Walker, W. She, B. Aldridge, H. Gao, S. Deans, M. Vickers, X.
Feng, Science 373 (2021).
date_created: 2023-01-16T09:15:14Z
date_published: 2021-07-02T00:00:00Z
date_updated: 2026-03-19T10:52:21Z
day: '02'
department:
- _id: XiFe
doi: 10.1126/science.abh0556
extern: '1'
external_id:
pmid:
- '34210850'
intvolume: ' 373'
issue: '6550'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2021.01.25.428150
month: '07'
oa: 1
oa_version: Preprint
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: Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 373
year: '2021'
...
---
_id: '12188'
abstract:
- lang: eng
text: Molecular mechanisms enabling the switching and maintenance of epigenetic
states are not fully understood. Distinct histone modifications are often associated
with ON/OFF epigenetic states, but how these states are stably maintained through
DNA replication, yet in certain situations switch from one to another remains
unclear. Here, we address this problem through identification of Arabidopsis INCURVATA11
(ICU11) as a Polycomb Repressive Complex 2 accessory protein. ICU11 robustly immunoprecipitated
in vivo with PRC2 core components and the accessory proteins, EMBRYONIC FLOWER
1 (EMF1), LIKE HETEROCHROMATIN PROTEIN1 (LHP1), and TELOMERE_REPEAT_BINDING FACTORS
(TRBs). ICU11 encodes a 2-oxoglutarate-dependent dioxygenase, an activity associated
with histone demethylation in other organisms, and mutant plants show defects
in multiple aspects of the Arabidopsis epigenome. To investigate its primary molecular
function we identified the Arabidopsis FLOWERING LOCUS C (FLC) as a direct target
and found icu11 disrupted the cold-induced, Polycomb-mediated silencing underlying
vernalization. icu11 prevented reduction in H3K36me3 levels normally seen during
the early cold phase, supporting a role for ICU11 in H3K36me3 demethylation. This
was coincident with an attenuation of H3K27me3 at the internal nucleation site
in FLC, and reduction in H3K27me3 levels across the body of the gene after plants
were returned to the warm. Thus, ICU11 is required for the cold-induced epigenetic
switching between the mutually exclusive chromatin states at FLC, from the active
H3K36me3 state to the silenced H3K27me3 state. These data support the importance
of physical coupling of histone modification activities to promote epigenetic
switching between opposing chromatin states.
acknowledgement: We would like to thank Scott Berry for help with ICU-GFP nuclear
localization microscopy, Hao Yu and Lisha Shen for assistance with 6mA DNA methylation
analysis, Donna Gibson for graphic design assistance, and members of the C.D. and
Howard laboratories for helpful discussions. This work was funded by the European
Research Council grants to “MEXTIM” (to C.D.) and “SexMeth” (to X. Feng), by the
Biotechnological and Biological Sciences Research Council (BBSRC) Institute Strategic
Programmes GRO (BB/J004588/1), GEN (BB/P013511/1), BBSRC grant (to X. Feng) (BB/S009620/1),
and the Marie Sklodowska–Curie Postdoctoral Fellowships “UNRAVEL” (to R.H.B.) and
"WISDOM" (to X. Fang). Additional funding via the Wellcome Trust through a Senior
Research Fellowship (to J.R.) (103139) and a multiuser equipment grant (108504).
The Wellcome Centre for Cell Biology is supported by core funding from the Wellcome
Trust (203149).
article_processing_charge: No
article_type: original
author:
- first_name: Rebecca H.
full_name: Bloomer, Rebecca H.
last_name: Bloomer
- first_name: Claire E.
full_name: Hutchison, Claire E.
last_name: Hutchison
- first_name: Isabel
full_name: Bäurle, Isabel
last_name: Bäurle
- first_name: James
full_name: Walker, James
last_name: Walker
- first_name: Xiaofeng
full_name: Fang, Xiaofeng
last_name: Fang
- first_name: Pumi
full_name: Perera, Pumi
last_name: Perera
- first_name: Christos N.
full_name: Velanis, Christos N.
last_name: Velanis
- first_name: Serin
full_name: Gümüs, Serin
last_name: Gümüs
- first_name: Christos
full_name: Spanos, Christos
last_name: Spanos
- first_name: Juri
full_name: Rappsilber, Juri
last_name: Rappsilber
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Justin
full_name: Goodrich, Justin
last_name: Goodrich
- first_name: Caroline
full_name: Dean, Caroline
last_name: Dean
citation:
ama: Bloomer RH, Hutchison CE, Bäurle I, et al. The Arabidopsis epigenetic regulator
ICU11 as an accessory protein of polycomb repressive complex 2. Proceedings
of the National Academy of Sciences. 2020;117(28):16660-16666. doi:10.1073/pnas.1920621117
apa: Bloomer, R. H., Hutchison, C. E., Bäurle, I., Walker, J., Fang, X., Perera,
P., … Dean, C. (2020). The Arabidopsis epigenetic regulator ICU11 as an accessory
protein of polycomb repressive complex 2. Proceedings of the National Academy
of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1920621117
chicago: Bloomer, Rebecca H., Claire E. Hutchison, Isabel Bäurle, James Walker,
Xiaofeng Fang, Pumi Perera, Christos N. Velanis, et al. “The Arabidopsis Epigenetic
Regulator ICU11 as an Accessory Protein of Polycomb Repressive Complex 2.” Proceedings
of the National Academy of Sciences. Proceedings of the National Academy of
Sciences, 2020. https://doi.org/10.1073/pnas.1920621117.
ieee: R. H. Bloomer et al., “The Arabidopsis epigenetic regulator ICU11
as an accessory protein of polycomb repressive complex 2,” Proceedings of the
National Academy of Sciences, vol. 117, no. 28. Proceedings of the National
Academy of Sciences, pp. 16660–16666, 2020.
ista: Bloomer RH, Hutchison CE, Bäurle I, Walker J, Fang X, Perera P, Velanis CN,
Gümüs S, Spanos C, Rappsilber J, Feng X, Goodrich J, Dean C. 2020. The Arabidopsis
epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex
2. Proceedings of the National Academy of Sciences. 117(28), 16660–16666.
mla: Bloomer, Rebecca H., et al. “The Arabidopsis Epigenetic Regulator ICU11 as
an Accessory Protein of Polycomb Repressive Complex 2.” Proceedings of the
National Academy of Sciences, vol. 117, no. 28, Proceedings of the National
Academy of Sciences, 2020, pp. 16660–66, doi:10.1073/pnas.1920621117.
short: R.H. Bloomer, C.E. Hutchison, I. Bäurle, J. Walker, X. Fang, P. Perera, C.N.
Velanis, S. Gümüs, C. Spanos, J. Rappsilber, X. Feng, J. Goodrich, C. Dean, Proceedings
of the National Academy of Sciences 117 (2020) 16660–16666.
date_created: 2023-01-16T09:15:44Z
date_published: 2020-05-22T00:00:00Z
date_updated: 2023-05-08T10:53:55Z
day: '22'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.1073/pnas.1920621117
extern: '1'
external_id:
pmid:
- '32601198'
file:
- access_level: open_access
checksum: cedee184cb12f454f2fba4158ff47db9
content_type: application/pdf
creator: alisjak
date_created: 2023-02-07T11:29:55Z
date_updated: 2023-02-07T11:29:55Z
file_id: '12526'
file_name: 2020_PNAS_Bloomer.pdf
file_size: 1105414
relation: main_file
success: 1
file_date_updated: 2023-02-07T11:29:55Z
has_accepted_license: '1'
intvolume: ' 117'
issue: '28'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368280/
month: '05'
oa: 1
oa_version: Published Version
page: 16660-16666
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb
repressive complex 2
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: 117
year: '2020'
...
---
_id: '12189'
abstract:
- lang: eng
text: Meiotic crossovers (COs) are important for reshuffling genetic information
between homologous chromosomes and they are essential for their correct segregation.
COs are unevenly distributed along chromosomes and the underlying mechanisms controlling
CO localization are not well understood. We previously showed that meiotic COs
are mis-localized in the absence of AXR1, an enzyme involved in the neddylation/rubylation
protein modification pathway in Arabidopsis thaliana. Here, we report that in
axr1-/-, male meiocytes show a strong defect in chromosome pairing whereas the
formation of the telomere bouquet is not affected. COs are also redistributed
towards subtelomeric chromosomal ends where they frequently form clusters, in
contrast to large central regions depleted in recombination. The CO suppressed
regions correlate with DNA hypermethylation of transposable elements (TEs) in
the CHH context in axr1-/- meiocytes. Through examining somatic methylomes, we
found axr1-/- affects DNA methylation in a plant, causing hypermethylation in
all sequence contexts (CG, CHG and CHH) in TEs. Impairment of the main pathways
involved in DNA methylation is epistatic over axr1-/- for DNA methylation in somatic
cells but does not restore regular chromosome segregation during meiosis. Collectively,
our findings reveal that the neddylation pathway not only regulates hormonal perception
and CO distribution but is also, directly or indirectly, a major limiting pathway
of TE DNA methylation in somatic cells.
acknowledgement: The authors wish to thank Cécile Raynaud, Eric Jenczewski, Rajeev
Kumar, Raphaël Mercier and Jean Molinier for critical reading of the manuscript.
article_number: e1008894
article_processing_charge: No
article_type: original
author:
- first_name: Nicolas
full_name: Christophorou, Nicolas
last_name: Christophorou
- first_name: Wenjing
full_name: She, Wenjing
last_name: She
- first_name: Jincheng
full_name: Long, Jincheng
last_name: Long
- first_name: Aurélie
full_name: Hurel, Aurélie
last_name: Hurel
- first_name: Sébastien
full_name: Beaubiat, Sébastien
last_name: Beaubiat
- first_name: Yassir
full_name: Idir, Yassir
last_name: Idir
- first_name: Marina
full_name: Tagliaro-Jahns, Marina
last_name: Tagliaro-Jahns
- first_name: Aurélie
full_name: Chambon, Aurélie
last_name: Chambon
- first_name: Victor
full_name: Solier, Victor
last_name: Solier
- first_name: Daniel
full_name: Vezon, Daniel
last_name: Vezon
- first_name: Mathilde
full_name: Grelon, Mathilde
last_name: Grelon
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Nicolas
full_name: Bouché, Nicolas
last_name: Bouché
- first_name: Christine
full_name: Mézard, Christine
last_name: Mézard
citation:
ama: Christophorou N, She W, Long J, et al. AXR1 affects DNA methylation independently
of its role in regulating meiotic crossover localization. PLOS Genetics.
2020;16(6). doi:10.1371/journal.pgen.1008894
apa: Christophorou, N., She, W., Long, J., Hurel, A., Beaubiat, S., Idir, Y., …
Mézard, C. (2020). AXR1 affects DNA methylation independently of its role in regulating
meiotic crossover localization. PLOS Genetics. Public Library of Science
(PLoS). https://doi.org/10.1371/journal.pgen.1008894
chicago: Christophorou, Nicolas, Wenjing She, Jincheng Long, Aurélie Hurel, Sébastien
Beaubiat, Yassir Idir, Marina Tagliaro-Jahns, et al. “AXR1 Affects DNA Methylation
Independently of Its Role in Regulating Meiotic Crossover Localization.” PLOS
Genetics. Public Library of Science (PLoS), 2020. https://doi.org/10.1371/journal.pgen.1008894.
ieee: N. Christophorou et al., “AXR1 affects DNA methylation independently
of its role in regulating meiotic crossover localization,” PLOS Genetics,
vol. 16, no. 6. Public Library of Science (PLoS), 2020.
ista: Christophorou N, She W, Long J, Hurel A, Beaubiat S, Idir Y, Tagliaro-Jahns
M, Chambon A, Solier V, Vezon D, Grelon M, Feng X, Bouché N, Mézard C. 2020. AXR1
affects DNA methylation independently of its role in regulating meiotic crossover
localization. PLOS Genetics. 16(6), e1008894.
mla: Christophorou, Nicolas, et al. “AXR1 Affects DNA Methylation Independently
of Its Role in Regulating Meiotic Crossover Localization.” PLOS Genetics,
vol. 16, no. 6, e1008894, Public Library of Science (PLoS), 2020, doi:10.1371/journal.pgen.1008894.
short: N. Christophorou, W. She, J. Long, A. Hurel, S. Beaubiat, Y. Idir, M. Tagliaro-Jahns,
A. Chambon, V. Solier, D. Vezon, M. Grelon, X. Feng, N. Bouché, C. Mézard, PLOS
Genetics 16 (2020).
date_created: 2023-01-16T09:16:10Z
date_published: 2020-06-29T00:00:00Z
date_updated: 2023-05-08T10:54:39Z
day: '29'
department:
- _id: XiFe
doi: 10.1371/journal.pgen.1008894
extern: '1'
external_id:
pmid:
- '32598340'
intvolume: ' 16'
issue: '6'
keyword:
- Cancer Research
- Genetics (clinical)
- Genetics
- Molecular Biology
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7351236/
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLOS Genetics
publication_identifier:
issn:
- 1553-7404
publication_status: published
publisher: Public Library of Science (PLoS)
quality_controlled: '1'
scopus_import: '1'
status: public
title: AXR1 affects DNA methylation independently of its role in regulating meiotic
crossover localization
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2020'
...
---
_id: '12190'
abstract:
- lang: eng
text: Meiotic crossover frequency varies within genomes, which influences genetic
diversity and adaptation. In turn, genetic variation within populations can act
to modify crossover frequency in cis and trans. To identify genetic variation
that controls meiotic crossover frequency, we screened Arabidopsis accessions
using fluorescent recombination reporters. We mapped a genetic modifier of crossover
frequency in Col × Bur populations of Arabidopsis to a premature stop codon within
TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase
II general transcription factor TFIID. The Arabidopsis taf4b mutation is a rare
variant found in the British Isles, originating in South-West Ireland. Using genetics,
genomics, and immunocytology, we demonstrate a genome-wide decrease in taf4b crossovers,
with strongest reduction in the sub-telomeric regions. Using RNA sequencing (RNA-seq)
from purified meiocytes, we show that TAF4b expression is meiocyte enriched, whereas
its paralog TAF4 is broadly expressed. Consistent with the role of TFIID in promoting
gene expression, RNA-seq of wild-type and taf4b meiocytes identified widespread
transcriptional changes, including in genes that regulate the meiotic cell cycle
and recombination. Therefore, TAF4b duplication is associated with acquisition
of meiocyte-specific expression and promotion of germline transcription, which
act directly or indirectly to elevate crossovers. This identifies a novel mode
of meiotic recombination control via a general transcription factor.
acknowledgement: "We thank Gregory Copenhaver (University of North Carolina), Avraham
Levy (The Weizmann Institute), and Scott Poethig (University of Pennsylvania) for
FTLs; Piotr Ziolkowski for Col-420/Bur seed; Sureshkumar Balasubramanian\r\n(Monash
University) for providing British and Irish Arabidopsis accessions; Mathilde Grelon
(INRA, Versailles) for providing the MLH1 antibody; and the Gurdon Institute for
access to microscopes. This work was supported by a BBSRC DTP studentship (E.J.L.),
European Research Area Network for Coordinating Action in Plant Sciences/BBSRC ‘‘DeCOP’’
(BB/M004937/1; C.L.), a BBSRC David Phillips Fellowship (BB/L025043/1; H.G. and
X.F.), the European Research Council (CoG ‘‘SynthHotspot,’’ A.J.T., C.L., and I.R.H.;
StG ‘‘SexMeth,’’ X.F.), and a Sainsbury Charitable Foundation Studentship (A.R.B.)."
article_processing_charge: No
article_type: original
author:
- first_name: Emma J.
full_name: Lawrence, Emma J.
last_name: Lawrence
- first_name: Hongbo
full_name: Gao, Hongbo
last_name: Gao
- first_name: Andrew J.
full_name: Tock, Andrew J.
last_name: Tock
- first_name: Christophe
full_name: Lambing, Christophe
last_name: Lambing
- first_name: Alexander R.
full_name: Blackwell, Alexander R.
last_name: Blackwell
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Ian R.
full_name: Henderson, Ian R.
last_name: Henderson
citation:
ama: Lawrence EJ, Gao H, Tock AJ, et al. Natural variation in TBP-ASSOCIATED FACTOR
4b controls meiotic crossover and germline transcription in Arabidopsis. Current
Biology. 2019;29(16):2676-2686.e3. doi:10.1016/j.cub.2019.06.084
apa: Lawrence, E. J., Gao, H., Tock, A. J., Lambing, C., Blackwell, A. R., Feng,
X., & Henderson, I. R. (2019). Natural variation in TBP-ASSOCIATED FACTOR
4b controls meiotic crossover and germline transcription in Arabidopsis. Current
Biology. Elsevier. https://doi.org/10.1016/j.cub.2019.06.084
chicago: Lawrence, Emma J., Hongbo Gao, Andrew J. Tock, Christophe Lambing, Alexander
R. Blackwell, Xiaoqi Feng, and Ian R. Henderson. “Natural Variation in TBP-ASSOCIATED
FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.”
Current Biology. Elsevier, 2019. https://doi.org/10.1016/j.cub.2019.06.084.
ieee: E. J. Lawrence et al., “Natural variation in TBP-ASSOCIATED FACTOR
4b controls meiotic crossover and germline transcription in Arabidopsis,” Current
Biology, vol. 29, no. 16. Elsevier, p. 2676–2686.e3, 2019.
ista: Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR.
2019. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover
and germline transcription in Arabidopsis. Current Biology. 29(16), 2676–2686.e3.
mla: Lawrence, Emma J., et al. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls
Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology,
vol. 29, no. 16, Elsevier, 2019, p. 2676–2686.e3, doi:10.1016/j.cub.2019.06.084.
short: E.J. Lawrence, H. Gao, A.J. Tock, C. Lambing, A.R. Blackwell, X. Feng, I.R.
Henderson, Current Biology 29 (2019) 2676–2686.e3.
date_created: 2023-01-16T09:16:33Z
date_published: 2019-08-19T00:00:00Z
date_updated: 2025-01-14T14:31:02Z
day: '19'
department:
- _id: XiFe
doi: 10.1016/j.cub.2019.06.084
extern: '1'
external_id:
pmid:
- '31378616'
intvolume: ' 29'
issue: '16'
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '08'
oa_version: None
page: 2676-2686.e3
pmid: 1
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and
germline transcription in Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2019'
...
---
_id: '12192'
abstract:
- lang: eng
text: Transposable elements (TEs), the movement of which can damage the genome,
are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in
the sperm companion cell – vegetative cell (VC) – of the flowering plant Arabidopsis
thaliana. However, the extent and mechanism of this activation are unknown. Here
we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed
DNA demethylation. We further demonstrate that DEMETER access to some of these
TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically
expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent
mechanism. We demonstrate that H1 is required for heterochromatin condensation
in plant cells and show that H1 overexpression creates heterochromatic foci in
the VC progenitor cell. Taken together, our results demonstrate that the natural
depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation,
heterochromatin relaxation, and TE activation.
acknowledgement: We thank David Twell for the pDONR-P4-P1R-pLAT52 and pDONR-P2R-P3-mRFP
vectors, the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder)
for their assistance with microscopy, and the Norwich BioScience Institute Partnership
Computing infrastructure for Science Group for High Performance Computing resources.
This work was funded by a Biotechnology and Biological Sciences Research Council
(BBSRC) David Phillips Fellowship (BB/L025043/1; SH, JZ and XF), a European Research
Council Starting Grant ('SexMeth' 804981; XF) and a Grant to Exceptional Researchers
by the Gatsby Charitable Foundation (SH and XF).
article_number: '42530'
article_processing_charge: No
article_type: original
author:
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: Jingyi
full_name: Zhang, Jingyi
last_name: Zhang
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells
causes DNA demethylation, heterochromatin decondensation and transposon activation.
eLife. 2019;8. doi:10.7554/elife.42530
apa: He, S., Vickers, M., Zhang, J., & Feng, X. (2019). Natural depletion of
histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation
and transposon activation. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.42530
chicago: He, Shengbo, Martin Vickers, Jingyi Zhang, and Xiaoqi Feng. “Natural Depletion
of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation
and Transposon Activation.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/elife.42530.
ieee: S. He, M. Vickers, J. Zhang, and X. Feng, “Natural depletion of histone H1
in sex cells causes DNA demethylation, heterochromatin decondensation and transposon
activation,” eLife, vol. 8. eLife Sciences Publications, 2019.
ista: He S, Vickers M, Zhang J, Feng X. 2019. Natural depletion of histone H1 in
sex cells causes DNA demethylation, heterochromatin decondensation and transposon
activation. eLife. 8, 42530.
mla: He, Shengbo, et al. “Natural Depletion of Histone H1 in Sex Cells Causes DNA
Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife,
vol. 8, 42530, eLife Sciences Publications, 2019, doi:10.7554/elife.42530.
short: S. He, M. Vickers, J. Zhang, X. Feng, ELife 8 (2019).
date_created: 2023-01-16T09:17:21Z
date_published: 2019-05-28T00:00:00Z
date_updated: 2025-01-14T14:31:41Z
day: '28'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.7554/elife.42530
extern: '1'
external_id:
unknown:
- '31135340'
file:
- access_level: open_access
checksum: ea6b89c20d59e5eb3646916fe5d568ad
content_type: application/pdf
creator: alisjak
date_created: 2023-02-07T09:42:46Z
date_updated: 2023-02-07T09:42:46Z
file_id: '12525'
file_name: 2019_elife_He.pdf
file_size: 2493837
relation: main_file
success: 1
file_date_updated: 2023-02-07T09:42:46Z
has_accepted_license: '1'
intvolume: ' 8'
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin
decondensation and transposon activation
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: 8
year: '2019'
...
---
OA_place: repository
OA_type: green
_id: '12193'
abstract:
- lang: eng
text: DNA methylation regulates eukaryotic gene expression and is extensively reprogrammed
during animal development. However, whether developmental methylation reprogramming
during the sporophytic life cycle of flowering plants regulates genes is presently
unknown. Here we report a distinctive gene-targeted RNA-directed DNA methylation
(RdDM) activity in the Arabidopsis thaliana male sexual lineage that regulates
gene expression in meiocytes. Loss of sexual-lineage-specific RdDM causes mis-splicing
of the MPS1 gene (also known as PRD2), thereby disrupting meiosis. Our results
establish a regulatory paradigm in which de novo methylation creates a cell-lineage-specific
epigenetic signature that controls gene expression and contributes to cellular
function in flowering plants.
acknowledgement: We thank Daniel Zilberman for intellectual contributions to this
work and assistance with manuscript preparation. We also thank Caroline Dean, Kirsten
Bomblies, Vinod Kumar, Siobhan Brady and Sophien Kamoun for comments on the manuscript,
Hugh Dickinson and Josephine Hellberg for developing the meiocyte isolation method,
Giles Oldroyd for the pGWB13-Bar vector, Elisa Fiume for the pMDC107-NTF vector,
Matthew Hartley, Matthew Couchman and Tjelvar Sten Gunnar Olsson for bioinformatics
support, and the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant
Calder) for their assistance with microscopy. This work was funded by a Biotechnology
and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BBL0250431)
to X.F., a BBSRC grant (BBM01973X1) to J.H., and a Sainsbury PhD Studentship to
J.W.
article_processing_charge: No
article_type: original
author:
- first_name: James
full_name: Walker, James
last_name: Walker
- first_name: Hongbo
full_name: Gao, Hongbo
last_name: Gao
- first_name: Jingyi
full_name: Zhang, Jingyi
last_name: Zhang
- first_name: Billy
full_name: Aldridge, Billy
last_name: Aldridge
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: James D.
full_name: Higgins, James D.
last_name: Higgins
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: Walker J, Gao H, Zhang J, et al. Sexual-lineage-specific DNA methylation regulates
meiosis in Arabidopsis. Nature Genetics. 2017;50(1):130-137. doi:10.1038/s41588-017-0008-5
apa: Walker, J., Gao, H., Zhang, J., Aldridge, B., Vickers, M., Higgins, J. D.,
& Feng, X. (2017). Sexual-lineage-specific DNA methylation regulates meiosis
in Arabidopsis. Nature Genetics. Nature Research. https://doi.org/10.1038/s41588-017-0008-5
chicago: Walker, James, Hongbo Gao, Jingyi Zhang, Billy Aldridge, Martin Vickers,
James D. Higgins, and Xiaoqi Feng. “Sexual-Lineage-Specific DNA Methylation Regulates
Meiosis in Arabidopsis.” Nature Genetics. Nature Research, 2017. https://doi.org/10.1038/s41588-017-0008-5.
ieee: J. Walker et al., “Sexual-lineage-specific DNA methylation regulates
meiosis in Arabidopsis,” Nature Genetics, vol. 50, no. 1. Nature Research,
pp. 130–137, 2017.
ista: Walker J, Gao H, Zhang J, Aldridge B, Vickers M, Higgins JD, Feng X. 2017.
Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nature
Genetics. 50(1), 130–137.
mla: Walker, James, et al. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis
in Arabidopsis.” Nature Genetics, vol. 50, no. 1, Nature Research, 2017,
pp. 130–37, doi:10.1038/s41588-017-0008-5.
short: J. Walker, H. Gao, J. Zhang, B. Aldridge, M. Vickers, J.D. Higgins, X. Feng,
Nature Genetics 50 (2017) 130–137.
date_created: 2023-01-16T09:18:05Z
date_published: 2017-12-18T00:00:00Z
date_updated: 2026-03-19T10:51:18Z
day: '18'
department:
- _id: XiFe
doi: 10.1038/s41588-017-0008-5
extern: '1'
external_id:
pmid:
- '29255257'
intvolume: ' 50'
issue: '1'
keyword:
- Genetics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7611288/
month: '12'
oa: 1
oa_version: Submitted Version
page: 130-137
pmid: 1
publication: Nature Genetics
publication_identifier:
eissn:
- 1546-1718
issn:
- 1061-4036
publication_status: published
publisher: Nature Research
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2017'
...
---
_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: '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: '12196'
abstract:
- lang: eng
text: SNC1 (SUPPRESSOR OF NPR1, CONSTITUTIVE 1) is one of a suite of intracellular
Arabidopsis NOD-like receptor (NLR) proteins which, upon activation, result in
the induction of defense responses. However, the molecular mechanisms underlying
NLR activation and the subsequent provocation of immune responses are only partially
characterized. To identify negative regulators of NLR-mediated immunity, a forward
genetic screen was undertaken to search for enhancers of the dwarf, autoimmune
gain-of-function snc1 mutant. To avoid lethality resulting from severe dwarfism,
the screen was conducted using mos4 (modifier of snc1, 4) snc1 plants, which display
wild-type-like morphology and resistance. M2 progeny were screened for mutant,
snc1-enhancing (muse) mutants displaying a reversion to snc1-like phenotypes.
The muse9 mos4 snc1 triple mutant was found to exhibit dwarf morphology, elevated
expression of the pPR2-GUS defense marker reporter gene and enhanced resistance
to the oomycete pathogen Hyaloperonospora arabidopsidis Noco2. Via map-based cloning
and Illumina sequencing, it was determined that the muse9 mutation is in the gene
encoding the SWI/SNF chromatin remodeler SYD (SPLAYED), and was thus renamed syd-10.
The syd-10 single mutant has no observable alteration from wild-type-like resistance,
although the syd-4 T-DNA insertion allele displays enhanced resistance to the
bacterial pathogen Pseudomonas syringae pv. maculicola ES4326. Transcription of
SNC1 is increased in both syd-4 and syd-10. These data suggest that SYD plays
a subtle, specific role in the regulation of SNC1 expression and SNC1-mediated
immunity. SYD may work with other proteins at the chromatin level to repress SNC1
transcription; such regulation is important for fine-tuning the expression of
NLR-encoding genes to prevent unpropitious autoimmunity.
acknowledgement: "This work was supported by the National Sciences and Engineering
Research Council of Canada [Canada Graduate\r\nScholarship–Doctoral to K.J.; Discovery
Grant to X.L.]; the department of Botany at the University of f British Columbia\r\n[the
Dewar Cooper Memorial Fund to X.L.].The authors would like to thank Dr. Yuelin Zhang
and Ms. Yan Li for their assistance with next-generation sequencing, and Mr. Charles
Copeland for critical reading of the manuscript."
article_processing_charge: No
article_type: original
author:
- first_name: Kaeli C.M.
full_name: Johnson, Kaeli C.M.
last_name: Johnson
- first_name: Shitou
full_name: Xia, Shitou
last_name: Xia
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Xin
full_name: Li, Xin
last_name: Li
citation:
ama: Johnson KCM, Xia S, Feng X, Li X. The chromatin remodeler SPLAYED negatively
regulates SNC1-mediated immunity. Plant and Cell Physiology. 2015;56(8):1616-1623.
doi:10.1093/pcp/pcv087
apa: Johnson, K. C. M., Xia, S., Feng, X., & Li, X. (2015). The chromatin remodeler
SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology.
Oxford University Press. https://doi.org/10.1093/pcp/pcv087
chicago: Johnson, Kaeli C.M., Shitou Xia, Xiaoqi Feng, and Xin Li. “The Chromatin
Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.” Plant and Cell
Physiology. Oxford University Press, 2015. https://doi.org/10.1093/pcp/pcv087.
ieee: K. C. M. Johnson, S. Xia, X. Feng, and X. Li, “The chromatin remodeler SPLAYED
negatively regulates SNC1-mediated immunity,” Plant and Cell Physiology,
vol. 56, no. 8. Oxford University Press, pp. 1616–1623, 2015.
ista: Johnson KCM, Xia S, Feng X, Li X. 2015. The chromatin remodeler SPLAYED negatively
regulates SNC1-mediated immunity. Plant and Cell Physiology. 56(8), 1616–1623.
mla: Johnson, Kaeli C. M., et al. “The Chromatin Remodeler SPLAYED Negatively Regulates
SNC1-Mediated Immunity.” Plant and Cell Physiology, vol. 56, no. 8, Oxford
University Press, 2015, pp. 1616–23, doi:10.1093/pcp/pcv087.
short: K.C.M. Johnson, S. Xia, X. Feng, X. Li, Plant and Cell Physiology 56 (2015)
1616–1623.
date_created: 2023-01-16T09:20:22Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2023-05-08T11:03:23Z
department:
- _id: XiFe
doi: 10.1093/pcp/pcv087
extern: '1'
external_id:
pmid:
- '26063389'
intvolume: ' 56'
issue: '8'
keyword:
- Cell Biology
- Plant Science
- Physiology
- General Medicine
language:
- iso: eng
month: '08'
oa_version: None
page: 1616-1623
pmid: 1
publication: Plant and Cell Physiology
publication_identifier:
issn:
- 0032-0781
- 1471-9053
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 56
year: '2015'
...