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PMID: 23071449 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Deposition of histone variant H2A.Z within gene bodies regulates responsive genes.

PLoS genetics ·Vol. 8 ·No. 10 ·2012-00-00 ·Pages e1002988

Coleman-Derr D, Zilberman D

Abstract

The regulation of eukaryotic chromatin relies on interactions between many epigenetic factors, including histone modifications, DNA methylation, and the incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic histone variants that is enriched at the transcriptional start sites of genes, has been implicated in a variety of chromosomal processes. Recently, we reported a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic hallmark of heterochromatin that has also been found in the bodies of active genes in plants and animals. Here, we investigate the basis of this anticorrelation using a novel h2a.z loss-of-function line in Arabidopsis thaliana. Through genome-wide bisulfite sequencing, we demonstrate that loss of H2A.Z in Arabidopsis has only a minor effect on the level or profile of DNA methylation in genes, and we propose that the global anticorrelation between DNA methylation and H2A.Z is primarily caused by the exclusion of H2A.Z from methylated DNA. RNA sequencing and genomic mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at the TSS, is correlated with lower transcription levels and higher measures of gene responsiveness. Loss of H2A.Z causes misregulation of many genes that are disproportionately associated with response to environmental and developmental stimuli. We propose that H2A.Z deposition in gene bodies promotes variability in levels and patterns of gene expression, and that a major function of genic DNA methylation is to exclude H2A.Z from constitutively expressed genes.

MeSH Terms
Arabidopsis/genetics,metabolism Arabidopsis Proteins/genetics,metabolism Cluster Analysis DNA Methylation Epigenesis, Genetic Gene Expression Profiling Gene Expression Regulation, Plant Histones/genetics,metabolism Mutation Phenotype Plants, Genetically Modified Transcription Factors/genetics,metabolism
Chemicals
Arabidopsis Proteins H2A.Z protein, Arabidopsis Histones PIE1 protein, Arabidopsis Transcription Factors
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Coleman-Derr Devin
Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA.
Zilberman Daniel
Conflict of Interest

The authors have declared that no competing interests exist.

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Article Info
Journal
PLoS genetics
Abbr.
PLoS Genet
ISSN
1553-7404
DOI
10.1371/journal.pgen.1002988
Published
2012-00-00
Epub
2012-00-11
Pages
e1002988
Language
English
Region
United States
NLM ID
101239074
PMCID
PMC3469445
Subset
IM
External Links
PubMed source DOI: 10.1371/journal.pgen.1002988 PMC Full Text View journal details
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