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


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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Available from: Junshi Yazaki
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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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    ABSTRACT: In tomato (Solanum lycopersicum), high pigment mutations (hp-1 and hp-2) were mapped to genes encoding UV-damaged DNA binding protein 1 (DDB1) and de-etiolated-1 (DET1), respectively. Here we characterized a tomato methyl-CpG-binding domain protein SlMBD5 identified by yeast two-hybrid screening using SlDDB1 as a bait. Yeast two-hybrid assay demonstrated that the physical interaction of SlMBD5 with SlDDB1 is mediated by the C-termini of SlMBD5 and the β-propeller-C (BPC) of SlDDB1. Co-immunoprecipitation analyses revealed that SlMBD5 associates with SlDDB1-interacting partners including SlDET1, SlCUL4, SlRBX1a and SlRBX1b in vivo. SlMBD5 was shown to target to nucleus and dimerizes via its MBD motif. Electrophoresis mobility shift analysis suggested that the MBD of SlMBD5 specifically binds to methylated CpG dinucleotides but not to methylated CpHpG or CpHpH dinucleotides. SlMBD5 expressed in protoplast is capable of activating transcription of CG islands, whereas CUL4/DDB1 antagonizes this effect. Overexpressing SlMBD5 resulted in diverse developmental alterations including darker green fruits with increased plastid level and elevated pigmentation, as well as enhanced expression of SlGLK2, a key regulator of plastid biogenesis. Taken together, we hypothesize that the physical interaction of SlMBD5 with the CUL4-DDB1-DET1 complex component may affect its binding activity to methylated DNA and subsequently attenuate its transcription activation of downstream genes.
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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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    ABSTRACT: During meiosis, homologous chromosomes undergo crossover recombination, which is typically concentrated in narrow hot spots that are controlled by genetic and epigenetic information. Arabidopsis chromosomes are highly DNA methylated in the repetitive centromeres, which are also crossover-suppressed. Here we demonstrate that RNA-directed DNA methylation is sufficient to locally silence Arabidopsis euchromatic crossover hot spots and is associated with increased nucleosome density and H3K9me2. However, loss of CG DNA methylation maintenance in met1 triggers epigenetic crossover remodeling at the chromosome scale, with pericentromeric decreases and euchromatic increases in recombination. We used recombination mutants that alter interfering and noninterfering crossover repair pathways (fancm and zip4) to demonstrate that remodeling primarily involves redistribution of interfering crossovers. Using whole-genome bisulfite sequencing, we show that crossover remodeling is driven by loss of CG methylation within the centromeric regions. Using cytogenetics, we profiled meiotic DNA double-strand break (DSB) foci in met1 and found them unchanged relative to wild type. We propose that met1 chromosome structure is altered, causing centromere-proximal DSBs to be inhibited from maturation into interfering crossovers. These data demonstrate that DNA methylation is sufficient to silence crossover hot spots and plays a key role in establishing domains of meiotic recombination along chromosomes.
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