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Cited by 593Epigenetics and DNA MethylationGenomics and Chromatin DynamicsPlant Molecular Biology Research

Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks

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Zilberman, Daniel, Coleman-Derr, Devin, Ballinger, Tracy, Henikoff, Steven·2008·Nature
DOI 10.1038/nature07324PMC PMC2877514
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Abstract

Eukaryotic chromatin is separated into functional domains differentiated by post-translational histone modifications, histone variants and DNA methylation. Methylation is associated with repression of transcriptional initiation in plants and animals, and is frequently found in transposable elements. Proper methylation patterns are crucial for eukaryotic development, and aberrant methylation-induced silencing of tumour suppressor genes is a common feature of human cancer. In contrast to methylation, the histone variant H2A.Z is preferentially deposited by the Swr1 ATPase complex near 5' ends of genes where it promotes transcriptional competence. How DNA methylation and H2A.Z influence transcription remains largely unknown. Here we show that in the plant Arabidopsis thaliana regions of DNA methylation are quantitatively deficient in H2A.Z. Exclusion of H2A.Z is seen at sites of DNA methylation in the bodies of actively transcribed genes and in methylated transposons. Mutation of the MET1 DNA methyltransferase, which causes both losses and gains of DNA methylation, engenders opposite changes (gains and losses) in H2A.Z deposition, whereas mutation of the PIE1 subunit of the Swr1 complex that deposits H2A.Z leads to genome-wide hypermethylation. Our findings indicate that DNA methylation can influence chromatin structure and effect gene silencing by excluding H2A.Z, and that H2A.Z protects genes from DNA methylation.

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Cited by

Sorted by citations

Authors
Zilberman, D., Coleman-Derr, D., Ballinger, T., & Henikoff, S.
Affiliations
  • University of California, Berkeley (US)
  • Howard Hughes Medical Institute (US)
Corresponding author
  • Zilberman, Daniel
  • Henikoff, Steven
ORCID
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2008-09-24
Volume
456
Issue
7218
Pages
125-129
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/nature07324
PMC
PMC2877514
OpenAlex
W2022587035
Cited by
593
References
1
Citations by year
2026: 19 · 2025: 22 · 2024: 24 · 2023: 27 · 2022: 24 · 2021: 20 · 2020: 37 · 2019: 28 · 2018: 25 · 2017: 33 · 2016: 28 · 2015: 42 · 2014: 42 · 2013: 45 · 2012: 39
FWCI
18.81
Type
journal article
Language
en
Open access
Licence
www.springer.com/tdm (tdm)
Locations
  • Nature (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
Funders
Howard Hughes Medical Institute
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
Keywords
histone H2A.Z, DNA methylation, chromatin structure, gene silencing, SWR1 complex, transposable elements, Arabidopsis thaliana, histone variants, transcriptional repression, chromatin organization
MeSH terms
Chromatin, DNA (Cytosine-5-)-Methyltransferases, Histones, Mutation, Transcription Factors, Transcription, Genetic, Arabidopsis, Gene Expression Regulation, Plant, DNA Methylation, Gene Silencing, Arabidopsis Proteins

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