Regulation of 3D genome organization, transcription and histone H3K9me2 by histone H3K9 methyltransferases [ChIP-Seq]. Regulation of 3D genome organization, transcription and histone H3K9me2 by histone H3K9 methyltransferases [ChIP-Seq]

Histone H3 lysine 9 dimethylation (H3K9me2) is a highly conserved silencing epigenetic mark. Chromatin marked with H3K9me2 forms large domains in mammalian cells and overlaps well with lamina-associated domains and the B compartment defined by Hi-C. However, the role of H3K9me2 in 3-dimensional (3D) genome organization remains unclear. We investigated genome-wide H3K9me2 distribution, transcriptome, and 3D genome organization in mouse embryonic stem cells following the inhibition or depletion of five H3K9 methyltransferases (MTases): G9a, GLP, SETDB1, SUV39H1, and SUV39H2. H3K9me2 was regulated by all five MTases; however, H3K9me2 and transcription in the A and B compartments were regulated by different MTases. H3K9me2 in A compartments was primarily regulated by G9a/GLP and SETDB1, while H3K9me2 in the B compartments was regulated by all five MTases. Furthermore, decreased H3K9me2 correlated with changes to the more active compartmental state that accompanied transcriptional activation. Overall design: Examination of H3K9me2, H3K9me3, transcriptome and 3D genome organization in H3K9 methyltransferase deficient mESCs and iMEFs

组蛋白H3赖氨酸9二甲基化（Histone H3 lysine 9 dimethylation, H3K9me2）是一种高度保守的沉默型表观遗传标记。被H3K9me2标记的染色质在哺乳动物细胞中形成大型结构域，且与核纤层关联结构域（lamina-associated domains）及Hi-C技术定义的B区室高度重合。然而，H3K9me2在三维（3D）基因组组织中的作用仍不明确。
我们针对小鼠胚胎干细胞（mouse embryonic stem cells, mESCs），在抑制或敲除五种H3K9甲基转移酶（methyltransferases, MTases）——G9a、GLP、SETDB1、SUV39H1及SUV39H2——后，对全基因组范围的H3K9me2分布、转录组以及三维基因组组织展开了研究。
H3K9me2可被这五种甲基转移酶共同调控；但A、B区室中的H3K9me2与转录分别由不同的甲基转移酶调控。A区室中的H3K9me2主要由G9a/GLP及SETDB1调控，而B区室中的H3K9me2则受全部五种甲基转移酶的调控。此外，H3K9me2水平降低与更具活性的区室状态改变相关，该改变伴随转录激活过程。
总体设计：检测H3K9甲基转移酶缺陷型小鼠胚胎干细胞（mESCs）及永生化小鼠胚胎成纤维细胞（immortalized mouse embryonic fibroblasts, iMEFs）中的H3K9me2、H3K9me3、转录组及三维基因组组织。