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PMID: 16949657 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis.

Cell ·Vol. 126 ·No. 6 ·2006-09-22 ·Pages 1189-201

Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR

Abstract

Cytosine methylation is important for transposon silencing and epigenetic regulation of endogenous genes, although the extent to which this DNA modification functions to regulate the genome is still unknown. Here we report the first comprehensive DNA methylation map of an entire genome, at 35 base pair resolution, using the flowering plant Arabidopsis thaliana as a model. We find that pericentromeric heterochromatin, repetitive sequences, and regions producing small interfering RNAs are heavily methylated. Unexpectedly, over one-third of expressed genes contain methylation within transcribed regions, whereas only approximately 5% of genes show methylation within promoter regions. Interestingly, genes methylated in transcribed regions are highly expressed and constitutively active, whereas promoter-methylated genes show a greater degree of tissue-specific expression. Whole-genome tiling-array transcriptional profiling of DNA methyltransferase null mutants identified hundreds of genes and intergenic noncoding RNAs with altered expression levels, many of which may be epigenetically controlled by DNA methylation.

MeSH Terms
Arabidopsis/genetics,metabolism Chromosome Mapping/methods DNA Methylation DNA Modification Methylases/genetics,metabolism DNA, Plant/genetics,metabolism Gene Expression Profiling/methods Gene Expression Regulation, Plant/genetics Gene Silencing/physiology Genes, Plant/genetics Genome, Plant/genetics Molecular Sequence Data Oligonucleotide Array Sequence Analysis/methods Promoter Regions, Genetic/genetics RNA, Small Interfering/genetics Transcription, Genetic/genetics
Chemicals
DNA, Plant RNA, Small Interfering DNA Modification Methylases
Authors & Affiliations
11 authors, click to expand affiliations / ORCID
Zhang Xiaoyu
Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA.
Yazaki Junshi
Sundaresan Ambika
Cokus Shawn
Chan Simon W-L
Chen Huaming
Henderson Ian R
Shinn Paul
Pellegrini Matteo
Jacobsen Steve E
Ecker Joseph R
Article Info
Journal
Cell
Abbr.
Cell
ISSN
0092-8674
DOI
10.1016/j.cell.2006.08.003
Published
2006-09-22
Epub
2006-00-31
Pages
1189-201
Language
English
Region
United States
NLM ID
0413066
Subset
IM
Grants
NIGMS NIH HHS · GM60398 · United States
NHGRI NIH HHS · HG003523 · United States
NIGMS NIH HHS · T32 GM08666 · United States
Databases
GENBANK
BT025666, BT025667, BT025668, BT025669, BT025670, BT025671, BT025672, BT025673, BT025674, BT025675, BT025676, BT025677, BT025678, BT025679, BT025680, BT025681, BT025682, BT025683, BT025684, BT025685, BT025686, BT025687, BT025688, BT025689, BT025690, BT025691, BT025692, BT025693, BT025694
GEO
GSE5074, GSE5094
Corrections
CommentIn
PMID: 16990127
External Links
PubMed source DOI: 10.1016/j.cell.2006.08.003 View journal details
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