Article

Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis

Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA.
Cell (Impact Factor: 32.24). 10/2006; 126(6):1189-201. DOI: 10.1016/j.cell.2006.08.003
Source: PubMed

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.

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    • "DNA methylation of TEs and repeats inactivates their transcription and is an evolutionary mechanism of defense against selfish DNA. Gene-body methylation was found to correlate with high expression levels (Tran et al., 2005; Zemach et al., 2010; Zhang et al., 2006) or, alternatively, DNA methylation can define exons boundaries or regulate alternative splicing, because it has been observed that exons are more highly methylated than introns (Feng et al., 2010; Laurent et al., 2010). DNA methylation occurs in three different sequence contexts: CG, CNG (where N is any base) and asymmetric CHH (where H ¼ A, T, or C), and is catalyzed by DNA methyltransferase enzymes (DNMT). "

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    • "In plants, the cytosines in heterochromatic regions are heavily methylated (Zhang et al., 2006). Furthermore, the genomewide profiling of DNA methylation in Arabidopsis found the methylation in a gene's transcribed region to be correlated with a high level of expression, whereas promoter-methylated genes showed a greater degree of tissue-specific expression (Zhang et al., 2006). There are five MBD proteins in humans: MeCP2, MBD1, MBD2, MBD3 and MBD4 (Dhasarathy & Wade, 2008). "
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    • "In contrast, crossovers are largely suppressed in repeat-rich heterochromatic regions in plant genomes (Copenhaver et al. 1999; Wei et al. 2009; Mayer et al. 2012; The Tomato Genome Consortium 2012; Yelina et al. 2012; Choulet et al. 2014; Rodgers-Melnick et al. 2015). Plant heterochromatin is densely epigenetically modified with DNA cytosine methylation and histone H3K9me2 methylation, which contribute to suppressed RNA polymerase II (Pol II) transcription, late DNA replication , cytological condensation, and higher-order structural organization (Fransz et al. 2002; Soppe et al. 2002; Zhang et al. 2006; Mathieu et al. 2007; Lister et al. 2008; Lee et al. 2010; Feng et al. 2014). DNA methylation occurs in CG, CHG, and CHH sequence contexts (where H = A, T, or C) in plant genomes (Law and Jacobsen 2010). "
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