Establishment of 3D chromatin structure after fertilization and the metabolic switch at the morula-to-blastocyst transition require CTCF [Hi-C]

The eukaryotic genome is tightly packed inside the nucleus, where it is organized in 3D at different scales. This structure is driven and maintained by different chromatin states and by architectural factors that bind DNA, such as the multi-zinc finger protein CTCF. Zygotic genome structure is established de novo after fertilization, but the impact of such structure on genome function during the first stages of mammalian development is still unclear. Here, we show that deletion of the Ctcf gene in mouse embryos impairs the correct establishment of chromatin structure, but initial lineage decisions take place and embryos are viable until the late blastocyst stage. Furthermore, we observe that maternal CTCF is not necessary for development. Transcriptomic analyses of mutant embryos show that the changes in metabolic and protein homeostasis programs that occur during the progression from the morula to the blastocyst depend on CTCF. Yet, these changes in gene expression do not correlate with disruption of chromatin structure, but mainly with proximal binding of CTCF to the promoter region of genes downregulated in mutants. Our results show that CTCF regulates both 3D genome organization and transcription during mouse preimplantation development, but mostly as independent processes. Hi-C experiments on biological replicates of single embryos at the blastocyst stage.

真核基因组紧密包裹于细胞核内，并以不同尺度的三维（3D）结构进行组织。该结构由多种染色质状态以及结合DNA的结构因子所驱动并维持，例如多锌指蛋白CTCF。合子基因组结构在受精后从头建立，但该结构在哺乳动物发育早期阶段对基因组功能的影响仍不明确。本研究发现，在小鼠胚胎中敲除Ctcf基因会破坏染色质结构的正常建立，但胚胎的初始谱系分化仍可正常进行，且可存活至晚期囊胚阶段。此外，本研究观察到母体来源的CTCF对胚胎发育并非必需。对突变胚胎的转录组分析显示，从桑椹胚发育至囊胚过程中发生的代谢与蛋白质稳态程序变化，依赖于CTCF的调控。然而，这些基因表达的变化与染色质结构的破坏并无关联，而主要与CTCF在突变体中下调基因的启动子区域的近端结合有关。本研究结果表明，CTCF在小鼠植入前发育过程中同时调控三维基因组组织与基因转录，但二者的调控大多相互独立。本研究还对囊胚期单个胚胎的生物学重复样本进行了Hi-C实验。