---
_id: '9506'
abstract:
- lang: eng
  text: Methylation in the bodies of active genes is common in animals and vascular
    plants. Evolutionary patterns indicate homeostatic functions for this type of
    methylation.
article_number: '87'
article_processing_charge: No
author:
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
citation:
  ama: Zilberman D. An evolutionary case for functional gene body methylation in plants
    and animals. <i>Genome Biology</i>. 2017;18(1). doi:<a href="https://doi.org/10.1186/s13059-017-1230-2">10.1186/s13059-017-1230-2</a>
  apa: Zilberman, D. (2017). An evolutionary case for functional gene body methylation
    in plants and animals. <i>Genome Biology</i>. Springer Nature. <a href="https://doi.org/10.1186/s13059-017-1230-2">https://doi.org/10.1186/s13059-017-1230-2</a>
  chicago: Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation
    in Plants and Animals.” <i>Genome Biology</i>. Springer Nature, 2017. <a href="https://doi.org/10.1186/s13059-017-1230-2">https://doi.org/10.1186/s13059-017-1230-2</a>.
  ieee: D. Zilberman, “An evolutionary case for functional gene body methylation in
    plants and animals,” <i>Genome Biology</i>, vol. 18, no. 1. Springer Nature, 2017.
  ista: Zilberman D. 2017. An evolutionary case for functional gene body methylation
    in plants and animals. Genome Biology. 18(1), 87.
  mla: Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation
    in Plants and Animals.” <i>Genome Biology</i>, vol. 18, no. 1, 87, Springer Nature,
    2017, doi:<a href="https://doi.org/10.1186/s13059-017-1230-2">10.1186/s13059-017-1230-2</a>.
  short: D. Zilberman, Genome Biology 18 (2017).
date_created: 2021-06-07T12:27:39Z
date_published: 2017-05-09T00:00:00Z
date_updated: 2021-12-14T07:55:02Z
day: '09'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1186/s13059-017-1230-2
extern: '1'
external_id:
  pmid:
  - '28486944'
file:
- access_level: open_access
  checksum: 5a455ad914e7d225b1baa4ab07fd925e
  content_type: application/pdf
  creator: asandaue
  date_created: 2021-06-07T12:31:36Z
  date_updated: 2021-06-07T12:31:36Z
  file_id: '9507'
  file_name: 2017_GenomeBiology_Zilberman.pdf
  file_size: 278183
  relation: main_file
  success: 1
file_date_updated: 2021-06-07T12:31:36Z
has_accepted_license: '1'
intvolume: '        18'
issue: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
  eissn:
  - 1465-6906
  issn:
  - 1474-760X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: An evolutionary case for functional gene body methylation in plants and animals
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 18
year: '2017'
...
---
_id: '9514'
abstract:
- lang: eng
  text: "Background:\r\nDNA methylation occurs at preferred sites in eukaryotes. In
    Arabidopsis, DNA cytosine methylation is maintained by three subfamilies of methyltransferases
    with distinct substrate specificities and different modes of action. Targeting
    of cytosine methylation at selected loci has been found to sometimes involve histone
    H3 methylation and small interfering (si)RNAs. However, the relationship between
    different cytosine methylation pathways and their preferred targets is not known.\r\nResults:\r\nWe
    used a microarray-based profiling method to explore the involvement of Arabidopsis
    CMT3 and DRM DNA methyltransferases, a histone H3 lysine-9 methyltransferase (KYP)
    and an Argonaute-related siRNA silencing component (AGO4) in methylating target
    loci. We found that KYP targets are also CMT3 targets, suggesting that histone
    methylation maintains CNG methylation genome-wide. CMT3 and KYP targets show similar
    proximal distributions that correspond to the overall distribution of transposable
    elements of all types, whereas DRM targets are distributed more distally along
    the chromosome. We find an inverse relationship between element size and loss
    of methylation in ago4 and drm mutants.\r\nConclusion:\r\nWe conclude that the
    targets of both DNA methylation and histone H3K9 methylation pathways are transposable
    elements genome-wide, irrespective of element type and position. Our findings
    also suggest that RNA-directed DNA methylation is required to silence isolated
    elements that may be too small to be maintained in a silent state by a chromatin-based
    mechanism alone. Thus, parallel pathways would be needed to maintain silencing
    of transposable elements."
article_number: R90
article_processing_charge: No
article_type: original
author:
- first_name: Robert K.
  full_name: Tran, Robert K.
  last_name: Tran
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
- first_name: Cecilia
  full_name: de Bustos, Cecilia
  last_name: de Bustos
- first_name: Renata F.
  full_name: Ditt, Renata F.
  last_name: Ditt
- first_name: Jorja G.
  full_name: Henikoff, Jorja G.
  last_name: Henikoff
- first_name: Anders M.
  full_name: Lindroth, Anders M.
  last_name: Lindroth
- first_name: Jeffrey
  full_name: Delrow, Jeffrey
  last_name: Delrow
- first_name: Tom
  full_name: Boyle, Tom
  last_name: Boyle
- first_name: Samson
  full_name: Kwong, Samson
  last_name: Kwong
- first_name: Terri D.
  full_name: Bryson, Terri D.
  last_name: Bryson
- first_name: Steven E.
  full_name: Jacobsen, Steven E.
  last_name: Jacobsen
- first_name: Steven
  full_name: Henikoff, Steven
  last_name: Henikoff
citation:
  ama: Tran RK, Zilberman D, de Bustos C, et al. Chromatin and siRNA pathways cooperate
    to maintain DNA methylation of small transposable elements in Arabidopsis. <i>Genome
    Biology</i>. 2005;6(11). doi:<a href="https://doi.org/10.1186/gb-2005-6-11-r90">10.1186/gb-2005-6-11-r90</a>
  apa: Tran, R. K., Zilberman, D., de Bustos, C., Ditt, R. F., Henikoff, J. G., Lindroth,
    A. M., … Henikoff, S. (2005). Chromatin and siRNA pathways cooperate to maintain
    DNA methylation of small transposable elements in Arabidopsis. <i>Genome Biology</i>.
    Springer Nature. <a href="https://doi.org/10.1186/gb-2005-6-11-r90">https://doi.org/10.1186/gb-2005-6-11-r90</a>
  chicago: Tran, Robert K., Daniel Zilberman, Cecilia de Bustos, Renata F. Ditt, Jorja
    G. Henikoff, Anders M. Lindroth, Jeffrey Delrow, et al. “Chromatin and SiRNA Pathways
    Cooperate to Maintain DNA Methylation of Small Transposable Elements in Arabidopsis.”
    <i>Genome Biology</i>. Springer Nature, 2005. <a href="https://doi.org/10.1186/gb-2005-6-11-r90">https://doi.org/10.1186/gb-2005-6-11-r90</a>.
  ieee: R. K. Tran <i>et al.</i>, “Chromatin and siRNA pathways cooperate to maintain
    DNA methylation of small transposable elements in Arabidopsis,” <i>Genome Biology</i>,
    vol. 6, no. 11. Springer Nature, 2005.
  ista: Tran RK, Zilberman D, de Bustos C, Ditt RF, Henikoff JG, Lindroth AM, Delrow
    J, Boyle T, Kwong S, Bryson TD, Jacobsen SE, Henikoff S. 2005. Chromatin and siRNA
    pathways cooperate to maintain DNA methylation of small transposable elements
    in Arabidopsis. Genome Biology. 6(11), R90.
  mla: Tran, Robert K., et al. “Chromatin and SiRNA Pathways Cooperate to Maintain
    DNA Methylation of Small Transposable Elements in Arabidopsis.” <i>Genome Biology</i>,
    vol. 6, no. 11, R90, Springer Nature, 2005, doi:<a href="https://doi.org/10.1186/gb-2005-6-11-r90">10.1186/gb-2005-6-11-r90</a>.
  short: R.K. Tran, D. Zilberman, C. de Bustos, R.F. Ditt, J.G. Henikoff, A.M. Lindroth,
    J. Delrow, T. Boyle, S. Kwong, T.D. Bryson, S.E. Jacobsen, S. Henikoff, Genome
    Biology 6 (2005).
date_created: 2021-06-07T13:12:41Z
date_published: 2005-10-19T00:00:00Z
date_updated: 2021-12-14T09:09:41Z
day: '19'
department:
- _id: DaZi
doi: 10.1186/gb-2005-6-11-r90
extern: '1'
external_id:
  pmid:
  - '16277745'
intvolume: '         6'
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1186/gb-2005-6-11-r90
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
  eissn:
  - 1465-6906
  issn:
  - 1474-760X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromatin and siRNA pathways cooperate to maintain DNA methylation of small
  transposable elements in Arabidopsis
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 6
year: '2005'
...
---
_id: '9511'
abstract:
- lang: eng
  text: Recent progress in understanding the silencing of transposable elements in
    the model plant Arabidopsis has revealed an interplay between DNA methylation,
    histone methylation and small interfering RNAs. DNA and histone methylation are
    not always sufficient to maintain silencing, and RNA-based reinforcement can be
    needed to maintain as well as initiate it.
article_number: '249'
article_processing_charge: No
article_type: review
author:
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
- first_name: Steven
  full_name: Henikoff, Steven
  last_name: Henikoff
citation:
  ama: 'Zilberman D, Henikoff S. Silencing of transposons in plant genomes: kick them
    when they’re down. <i>Genome Biology</i>. 2004;5(12). doi:<a href="https://doi.org/10.1186/gb-2004-5-12-249">10.1186/gb-2004-5-12-249</a>'
  apa: 'Zilberman, D., &#38; Henikoff, S. (2004). Silencing of transposons in plant
    genomes: kick them when they’re down. <i>Genome Biology</i>. Springer Nature.
    <a href="https://doi.org/10.1186/gb-2004-5-12-249">https://doi.org/10.1186/gb-2004-5-12-249</a>'
  chicago: 'Zilberman, Daniel, and Steven Henikoff. “Silencing of Transposons in Plant
    Genomes: Kick Them When They’re Down.” <i>Genome Biology</i>. Springer Nature,
    2004. <a href="https://doi.org/10.1186/gb-2004-5-12-249">https://doi.org/10.1186/gb-2004-5-12-249</a>.'
  ieee: 'D. Zilberman and S. Henikoff, “Silencing of transposons in plant genomes:
    kick them when they’re down,” <i>Genome Biology</i>, vol. 5, no. 12. Springer
    Nature, 2004.'
  ista: 'Zilberman D, Henikoff S. 2004. Silencing of transposons in plant genomes:
    kick them when they’re down. Genome Biology. 5(12), 249.'
  mla: 'Zilberman, Daniel, and Steven Henikoff. “Silencing of Transposons in Plant
    Genomes: Kick Them When They’re Down.” <i>Genome Biology</i>, vol. 5, no. 12,
    249, Springer Nature, 2004, doi:<a href="https://doi.org/10.1186/gb-2004-5-12-249">10.1186/gb-2004-5-12-249</a>.'
  short: D. Zilberman, S. Henikoff, Genome Biology 5 (2004).
date_created: 2021-06-07T12:58:06Z
date_published: 2004-11-16T00:00:00Z
date_updated: 2021-12-14T08:44:24Z
day: '16'
department:
- _id: DaZi
doi: 10.1186/gb-2004-5-12-249
extern: '1'
external_id:
  pmid:
  - '15575975'
intvolume: '         5'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1186/gb-2004-5-12-249
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
  eissn:
  - 1465-6906
  issn:
  - 1474-760X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Silencing of transposons in plant genomes: kick them when they''re down'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 5
year: '2004'
...