SmcHD1 underlies the formation of H3K9me3 blocks on the inactive X chromosome in mice [RNA-seq]

Stable silencing of the inactive X chromosome (Xi) in female mammals is crucial for the development of embryos and their postnatal health. SmcHD1 is essential for stable silencing of the Xi, and its functional deficiency results in derepression of many X-inactivated genes. Although SmcHD1 has been suggested to play an important role in the formation of higher-order chromatin structure of the Xi, the underlying mechanism is largely unknown. Here, we explore the epigenetic state of the Xi in SmcHD1-deficient epiblast stem cells and mouse embryonic fibroblasts in comparison with their wild-type counterparts. The results suggest that SmcHD1 underlies the formation of H3K9me3-enriched blocks on the Xi, which, although the importance of H3K9me3 has been largely overlooked in mice, play a crucial role in the establishment of the stably silenced state. We propose that the H3K9me3 blocks formed on the Xi facilitate robust heterochromatin formation in combination with H3K27me3, and that the substantial loss of H3K9me3 caused by SmcHD1 deficiency leads to aberrant distribution of H3K27me3 on the Xi and derepression of X-inactivated genes. Overall design: Allele-specific RNA-seq analysis of epiblast stem cells (EpiSCs) prepared from female fetuses deficient for SmcHD1

雌性哺乳动物体内失活X染色体（inactive X chromosome, Xi）的稳定沉默，对于胚胎发育及其产后健康至关重要。SmcHD1是实现Xi稳定沉默的必需因子，其功能缺陷会导致大量X失活基因发生去阻遏。尽管已有研究提示SmcHD1在Xi的高阶染色质结构形成中发挥重要作用，但其具体调控机制仍未明确。本研究通过对比SmcHD1缺陷型外胚层干细胞（epiblast stem cells, EpiSCs）、小鼠胚胎成纤维细胞及其野生型对照细胞中的Xi表观遗传状态，开展相关研究。研究结果显示，SmcHD1是Xi上富集H3K9me3的结构域形成的关键基础；尽管H3K9me3在小鼠中的重要性长期被忽视，但其对于Xi稳定沉默状态的建立具有不可或缺的作用。本研究提出，Xi上形成的H3K9me3结构域可与H3K27me3协同，促进高效异染色质形成；而SmcHD1缺陷引发的H3K9me3大量缺失，会导致Xi上H3K27me3的分布异常，并最终造成X失活基因的去阻遏。总体实验设计：对源自SmcHD1缺陷雌性胎儿的外胚层干细胞（epiblast stem cells, EpiSCs）开展等位基因特异性RNA测序分析。