Gene Body CG and CHG Methylation and Suppression of Centromeric CHH Methylation are Mediated by DECREASE IN DNA METHYLATION1 in Rice.
Gene Body CG and CHG Methylation and Suppression of Centromeric CHH Methylation are Mediated by DECREASE IN DNA METHYLATION1 in Rice.
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DOI：
10.1016/j.molp.2015.08.002
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发表时间：
2015-10
期刊：
影响因子：
27.5
通讯作者：
H. Numa;K. Yamaguchi;S. Shigenobu;Y. Habu
中科院分区：
文献类型：
--
作者：
H. Numa;K. Yamaguchi;S. Shigenobu;Y. Habu
DECREASE IN DNA METHYLATION1 (DDM1) is a chromatin remodeling protein required for maintenance of cytosine and histone H3K9 methylation in heterochromatin regions in the genome of Arabidopsis thaliana (Gendrel et al., 2002). A ddm1 mutant also increases the rate of meiotic recombination in euchromatic but not heterochromatic regions of A. thaliana (Melamed-Bessudo and Levy, 2012), and changes the state of cytosine methylation of a gene flanked by a LINE element located in a region of euchromatin (Saze and Kakutani, 2007). These studies indicate that the function of DDM1 is not limited to heterochromatin regions and show that it also acts on euchromatic regions in the genome, although the mechanism determining its target specificity remains obscure. Toward understanding the function of DDM1 in the maintenance of global epigenetic state of the genome in higher plants, we performed a genome-wide analysis of cytosine methylation in an antisense-mediated DDM1-knockdown rice line (asDDM1) that exhibits similar characteristics to that of ddm1 in A. thaliana (Higo et al., 2012; Habu et al., 2015). Some intrinsic properties of rice genome differ greatly from those of A. thaliana, for example, the content of repeated sequences and their distribution, and therefore rice provides an opportunity to examine the effect of DDM1 deficiency on genomes with a higher content and broader distribution of repeats.In rice chromosomes, the distribution of CG and CHG methylation is highly correlated to that of repeats (Figure 1 A and Supplemental Figure 1), and there is no concentration of CHH methylation around centromeric regions, in clear contrast to A. thaliana, in which a concentration of CHH methylation around the centromere is observed in all chromosomes (Figure 1 A and Supplemental Figure 1)(Cokus et al., 2008; Lister et al., 2008; Feng et al., 2010). In asDDM1, the rates of CG and CHG methylation are reduced in all chromosomes, with stronger reductions around centromeres (Figure 1 A and Supplemental Figure 1). The overall distribution of differentially methylated regions between wild-type and asDDM1 is similar to that of repeats (Figure 1 A). Unexpectedly, sharp increases in CHH methylation were observed at the centromeric regions in all chromosomes of asDDM1 (Figure 1 A and Supplemental Figure 1); this clearly differs from ddm1 in A. thaliana, in which no regional changes in CHH methylation were observed in any chromosome region (Zemach et al., 2013). The changes in methylation in asDDM1 were validated by conventional methods (Supplemental Figure 2) and possible effects of plant regeneration on methylation changes during establishment of
