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）是一种高度保守的转录沉默型表观遗传标记。携带H3K9me2修饰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技术所定义的B区室具有高度共定位性。然而，H3K9me2在三维基因组组织中发挥的功能仍未明确。本研究通过抑制或敲除5种H3K9甲基转移酶（H3K9 methyltransferases, MTases）——G9a、GLP、SETDB1、SUV39H1及SUV39H2，分析了小鼠胚胎干细胞（mouse embryonic stem cells, mESCs）中全基因组范围内的H3K9me2分布、转录组及三维基因组组织。尽管5种甲基转移酶均可调控H3K9me2的水平，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区室的H3K9me2主要由G9a/GLP及SETDB1调控，而B区室的H3K9me2则受全部5种甲基转移酶共同调控。此外，H3K9me2水平的降低与区室状态向更活跃的状态转变及转录激活过程相伴相关。总体实验设计：检测H3K9甲基转移酶缺陷型小鼠胚胎干细胞（mESCs）与诱导型小鼠胚胎成纤维细胞（induced mouse embryonic fibroblasts, iMEFs）中的H3K9me2、H3K9me3、转录组及三维基因组组织。