Domains Rearranged Methylase 2 maintains DNA methylation at large DNA hypomethylated shores and long‐range chromatin interactions in rice

生物 DNA甲基化 表观遗传学 染色质 表观遗传学 组蛋白 遗传学 H3K4me3 组蛋白甲基化 甲基化 体育锻炼的表观遗传学 DNA 基因 发起人 基因表达
作者
Wei Zhang,Huanhuan Wang,Yuning Ma,Baibai Gao,Pengpeng Guan,Xingyu Huang,Weizhi Ouyang,Minrong Guo,Guoting Chen,Guoliang Li,Xingwang Li
出处
期刊:Plant Biotechnology Journal [Wiley]
卷期号:21 (11): 2333-2347 被引量:1
标识
DOI:10.1111/pbi.14134
摘要

DNA methylation plays an important role in gene regulation and genomic stability. However, large DNA hypomethylated regions known as DNA methylation valleys (DMVs) or canyons have also been suggested to serve unique regulatory functions, largely unknown in rice (Oryza sativa). Here, we describe the DMVs in rice seedlings, which were highly enriched with developmental and transcription regulatory genes. Further detailed analysis indicated that grand DMVs (gDMVs) might be derived from nuclear integrants of organelle DNA (NORGs). Furthermore, Domains Rearranged Methylase 2 (OsDRM2) maintained DNA methylation at short DMV (sDMV) shores. Epigenetic maps indicated that sDMVs were marked with H3K4me3 and/or H3K27me3, although the loss of DNA methylation had a negligible effect on histone modification within these regions. In addition, we constructed H3K27me3-associated interaction maps for homozygous T-DNA insertion mutant of the gene (osdrm2) and wild type (WT). From a global perspective, most (90%) compartments were stable between osdrm2 and WT plants. At a high resolution, we observed a dramatic loss of long-range chromatin loops in osdrm2, which suffered an extensive loss of non-CG (CHG and CHH, H = A, T, or C) methylation. From another viewpoint, the loss of non-CG methylation at sDMV shores in osdrm2 could disrupt H3K27me3-mediated chromatin interaction networks. Overall, our results demonstrated that DMVs are a key genomic feature in rice and are precisely regulated by epigenetic modifications, including DNA methylation and histone modifications. OsDRM2 maintained DNA methylation at sDMV shores, while OsDRM2 deficiency strongly affected three-dimensional (3D) genome architectures.
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