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, Oct 05, 2015
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    • "There must be an uncoupling between/among the smRNAs, DNA methylation, and H3K9me2 at some stage of RdDM to initiate the pathway. Genome-wide DNA methylation profiling and smRNA sequencing showed that methylated DNA (both CG and non-CG) regions are not always associated with smRNA clusters (Zhang et al., 2006; Lister et al., 2008). In a previous study using promoter sequence-targeting RNAs to trigger TGS of endogenes , we found that DNA methylation levels and silencing efficiency was not tightly correlated with smRNA levels (Deng et al., 2014). "
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    ABSTRACT: Transposable elements (TEs) and repetitive sequences are ubiquitously present in eukaryotic genomes which are in general epigenetically silenced by DNA methylation and/or histone 3 lysine 9 methylation (H3K9me). RNA-directed DNA methylation (RdDM) is the major pathway that initiates de novo DNA methylation in Arabidopsis and sets up a self-reinforcing silencing loop between DNA methylation and H3K9me. However, a key issue is the requirement of a basal level transcript from the target loci to initiate the RNA-based silencing. How the heterochromatic silenced loci are transcribed remains largely unknown. Here, we show that JMJ24, a JmjC-domain containing protein counteracts H3K9me to promote basal level transcription of endogenous silenced loci in Arabidopsis. JMJ24 functionally resembles the fission yeast JmjC protein Epe1. The transcript promoted by JMJ24, is at least in part, processed to small RNA to initiate the RdDM. Genome-wide transcriptome profiling indicates that transcript levels of TEs are more likely regulated by JMJ24, compared to protein-coding genes. Our data suggest that JMJ24 plays a conserved role in promoting basal level transcription of endogenous silenced loci to reinforce the silencing. We also provide evidence of a physical association between JMJ24 and RNA-dependent RNA polymerase 2 (RDR2), which represents an evolved property of the RNA silencing pathway. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    The Plant Journal 06/2015; 83(5). DOI:10.1111/tpj.12924 · 5.97 Impact Factor
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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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    ABSTRACT: Along with its essential role in the maintenance of genome integrity, DNA methylation takes part in regulation of genes which are important for plant development and stress response. In plants, DNA methylation process can be directed by small RNAs in process known as RNA-directed DNA methylation (RdDM) involving two plant-specific RNA polymerases – PolIV and PolV. The aim of the present study was to investigate the effect of heat stress on the expression of genes encoding key players in DNA methylation – DNA methyltransferase (MET1, CMT3, and DRM2), the largest subunits of PoIIV and PolV (NRPD1 and NRPE1 respectively) and the DNA demethylase ROS1. We also examined the high-temperature effect on two protein-coding genes – At3g50770 and At5g43260 whose promoters contain transposon insertions and are affected by DNA-methylation, as well as on the AtSN1, a SINE-like retrotransposon. To assess the involvement of PolIV and PolV in heat stress response, the promoter methylation status and transcript levels of these genes were compared between wild type and double mutant lacking NRPD1 and NRPE1. The results demonstrate coordinated up-regulation of the DRM2, NRPD1 and NRPE1 in response to high temperature and suggest that PolIV and/or PolV might be required for the induction of DRM2 expression under heat stress. The ROS1 expression was confirmed to be suppressed in the mutant lacking active PolIV and PolV that might be a consequence of abolished DNA methylation. The increased expression of At3g50770 in response to elevated temperature correlated with reduced promoter DNA methylation, while the stress response of At5g43260 did not show inverse correlation between promoter methylation and gene expression. Our results also imply that PolIV and/or PolV could regulate gene expression under stress conditions not only through RdDM but also by acting in other regulatory processes.
    Plant Physiology and Biochemistry 02/2015; 87. DOI:10.1016/j.plaphy.2014.12.022 · 2.76 Impact Factor
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    • "Mapped reads account for only 9.7% and 11.6% of male and female sequencing reads, respectively . Among the mapped reads, it was found that 74.1% of total sequence reads mapped to intergenic sequences, similar methylation patterns to the results observed in A. thaliana and Oryza sativa (Zhang et al., 2006; Li et al., 2012). "
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    ABSTRACT: Previous studies showed sex-specific DNA methylation and expression of candidate genes in bisexual flowers of andromonoecious poplar, but the regulatory relationship between methylation and microRNAs (miRNAs) remains unclear. To investigate whether the methylation of miRNA genes regulates gene expression in bisexual flower development, the methylome, microRNA, and transcriptome were examined in female and male flowers of andromonoecious poplar. 27 636 methylated coding genes and 113 methylated miRNA genes were identified. In the coding genes, 64.5% of the methylated reads mapped to the gene body region; by contrast, 60.7% of methylated reads in miRNA genes mainly mapped in the 5' and 3' flanking regions. CHH methylation showed the highest methylation levels and CHG showed the lowest methylation levels. Correlation analysis showed a significant, negative, strand-specific correlation of methylation and miRNA gene expression (r=0.79, P <0.05). The methylated miRNA genes included eight long miRNAs (lmiRNAs) of 24 nucleotides and 11 miRNAs related to flower development. miRNA172b might play an important role in the regulation of bisexual flower development-related gene expression in andromonoecious poplar, via modification of methylation. Gynomonoecious, female, and male poplars were used to validate the methylation patterns of the miRNA172b gene, implying that hyper-methylation in andromonoecious and gynomonoecious poplar might function as an important regulator in bisexual flower development. Our data provide a useful resource for the study of flower development in poplar and improve our understanding of the effect of epigenetic regulation on genes other than protein-coding genes. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email:
    Journal of Experimental Botany 01/2015; 66(7). DOI:10.1093/jxb/eru531 · 5.53 Impact Factor
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