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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    • "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.
    Genes & Development 10/2015; 29(20):2183-2202. DOI:10.1101/gad.270876.115 · 10.80 Impact Factor
    • "the sepa - rate or combined exposure to MSB and NaCl occurred almost exclusively in CHH and CHG contexts within the two analysed DNA regions ( Supplementary Figs . 2 and 3 ) . It has been proposed that the dynamic methylation of cytosines in CHH and CHG sites plays an important role in regulating the expression of structural genes in Arabidopsis ( Zhang et al . , 2006 ) . This is because certain mutations that impair methyl - transferase activities and cause a hypomethylation state in the non - CG context ( drm1drm2cmt3 triple mutant ) lead to the activation of many genes scattered throughout the genome . It is widely accepted that cytosine methylation negatively affects gene expression through the r"
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    ABSTRACT: Plants are able to develop numerous defence strategies to face stress. Amongst these, higher plants are capable of demonstrating stress imprint, a mechanism related with the phenomenon of priming. This is usually defined as genetic or biochemical modifications induced by a first stress exposure that leads to enhanced resistance to a later stress. Menadione sodium bisulphite (MSB), a water-soluble addition compound of vitamin K3, was first studied as a plant growth regulator and has been later widely shown to function as plant defence activator against several pathogens in a number of plant species. We recently reported that treating Arabidopsis seeds with MSB primes salt tolerance by inducing an early acclimation to salt stress. Here we describe the analysis of the effect of MSB on cytosine methylation in a salt stress background demonstrating that one of the mechanisms underlying this early acclimation to salt stress is an epigenetic mark. Specifically, MSB leads to a hypomethylation state at the promoter region of genes involved in the biosynthesis (P5CS1) and degradation (ERD5) of proline, affecting mainly CHG and CHH sites(where H is any nucleotide except G). The epigenetic changes detected are correlated with the observed expression patterns of P5CS1 (upregulation) and ERD5 (downregulation) genes and the increase in proline accumulation.
    Environmental and Experimental Botany 07/2015; 120:20-30. · 3.36 Impact Factor
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    • "Epigenetics is a change in gene expression through chromatin modifications without base sequence alteration (Law and Jacobsen 2010), which facilitates recruitment of the RNA polymerase II transcriptional machinery to the promoter. This frequently occurs during somatic cell differentiation, in which the clonal expansion of a single cell leads to a diversity of cell types (Zhang et al. 2006). Such a cellular inheritance is common during ontogeny but is usually erased before gametes are produced (Reik and Walter 2001). "

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