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.
Publication types
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Research Support, N.I.H., Extramural
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Research Support, Non-U.S. Gov't
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Research Support, U.S. Gov't, Non-P.H.S.
MeSH terms
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Arabidopsis / genetics*
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Arabidopsis / metabolism
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Chromosome Mapping / methods
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DNA Methylation*
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DNA Modification Methylases / genetics
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DNA Modification Methylases / metabolism
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DNA, Plant / genetics*
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DNA, Plant / metabolism
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Gene Expression Profiling / methods
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Gene Expression Regulation, Plant / genetics
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Gene Silencing / physiology
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Genes, Plant / genetics*
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Genome, Plant / genetics*
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Molecular Sequence Data
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Oligonucleotide Array Sequence Analysis / methods
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Promoter Regions, Genetic / genetics
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RNA, Small Interfering / genetics
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Transcription, Genetic / genetics
Substances
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DNA, Plant
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RNA, Small Interfering
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DNA Modification Methylases
Associated data
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GENBANK/BT025666
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GENBANK/BT025667
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GENBANK/BT025668
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GENBANK/BT025669
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GENBANK/BT025670
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GENBANK/BT025671
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GENBANK/BT025672
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GENBANK/BT025673
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GENBANK/BT025674
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GENBANK/BT025675
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GENBANK/BT025676
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GENBANK/BT025678
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GENBANK/BT025679
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GENBANK/BT025680
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GENBANK/BT025681
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GENBANK/BT025682
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GENBANK/BT025683
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GENBANK/BT025684
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GENBANK/BT025685
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GENBANK/BT025686
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GENBANK/BT025687
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GENBANK/BT025688
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GENBANK/BT025689
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GENBANK/BT025690
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GENBANK/BT025691
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GENBANK/BT025692
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GENBANK/BT025693
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GENBANK/BT025694
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GEO/GSE5074
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GEO/GSE5094