DNA甲基化在基因调控和基因组稳定性中起着重要作用。然而,称为DNA甲基化谷(DMV)或峡谷的大DNA低甲基化区域也被认为具有独特的调节功能。在水稻(水稻)中大部分未知。这里,我们描述了水稻幼苗中的DMV,它们高度富含发育和转录调节基因。进一步的详细分析表明,大DMV(gDMV)可能来自细胞器DNA(NORG)的核整合体。此外,域重排甲基化酶2(OsDRM2)在短DMV(sDMV)海岸维持DNA甲基化。表观遗传图谱表明sDMV用H3K4me3和/或H3K27me3标记,尽管DNA甲基化的丢失对这些区域内的组蛋白修饰的影响可忽略不计。此外,我们构建了该基因(osdrm2)和野生型(WT)的纯合T-DNA插入突变体的H3K27me3相关相互作用图。从全球角度来看,osdrm2和WT植物之间的大多数(90%)隔室是稳定的。在高分辨率下,我们观察到osdrm2中远程染色质环的急剧损失,其中非CG(CHG和CHH,H=A,T,或C)甲基化。从另一个角度来看,osdrm2中sDMV海岸非CG甲基化的丢失可能会破坏H3K27me3介导的染色质相互作用网络.总的来说,我们的结果表明,DMV是水稻的关键基因组特征,并且受到表观遗传修饰的精确调控,包括DNA甲基化和组蛋白修饰。OsDRM2在sDMV海岸维持DNA甲基化,而OsDRM2缺乏强烈影响三维(3D)基因组结构。
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.