Contiguous Erosion of the Inactive X in Human Pluripotency Concludes With Global DNA Hypomethylation

Female human pluripotent stem cells (hPSCs) are prone to undergoing X chromosome erosion (XCE), a progressive loss of key epigenetic features on the inactive X that initiates with repression of XIST, the long non-coding RNA required for X inactivation. As a result, previously silenced genes on the eroding X (Xe) reactivate, some of which are thought to provide selective advantages. To-date, the sporadic and progressive nature of XCE has largely obscured its scale, dynamics, and key transition events. To address this knowledge gap, we performed an integrated analysis of DNA methylation (DNAme), chromatin accessibility, and gene expression across hundreds of hPSC samples. Differential methylation across the Xe enables ordering female hPSCs across a trajectory of XCE from initiation to terminal stages. Our results identify a crucial cis-regulatory element for XIST expression, trace contiguously growing domains of reactivation to a few euchromatic origins on the Xi, and indicate that the late-stage Xe impairs DNAme genome-wide. Surprisingly, from this altered epigenetic landscape emerge select features of naïve pluripotency, suggesting its link to X chromosome dosage may be partially conserved in human embryonic development. Bisulfite-converted DNA from the 22 samples were hybridised to the Illumina Infinium methylEPIC (850K) Human Methylation BeadChip.

女性人类多能干细胞（human pluripotent stem cells, hPSCs）极易发生X染色体侵蚀（X chromosome erosion, XCE）——这是一类发生于失活X染色体上的关键表观遗传特征逐步丢失的过程，其起始事件为XIST（X染色体失活所必需的长链非编码RNA）的表达抑制。随之而来的是，原本处于沉默状态的侵蚀X染色体（eroding X, Xe）上的基因发生重新激活，其中部分基因被认为可赋予细胞生长选择优势。迄今为止，XCE的散发性与进行性特征极大地阻碍了学界对其发生规模、动态变化过程及关键过渡事件的认知。为填补这一研究空白，我们对数百例hPSC样本开展了DNA甲基化（DNA methylation, DNAme）、染色质可及性与基因表达的整合分析。基于Xe染色体上的差异甲基化特征，我们可将女性hPSC按照XCE的发生轨迹进行排序，覆盖从起始阶段到终末阶段的完整进程。本研究鉴定出一个调控XIST表达的关键顺式调控元件（cis-regulatory element）；追踪发现重新激活的染色质域呈现连续扩展的特征，其起源于失活X染色体（inactive X, Xi）上的少数常染色质位点；同时证实晚期阶段的Xe可导致全基因组范围内的DNA甲基化异常。令人意外的是，这种发生改变的表观遗传景观会呈现出初始多能性（naïve pluripotency）的部分特征，提示X染色体剂量相关的调控机制在人类胚胎发育中存在部分保守性。本研究中的22例样本的亚硫酸氢盐转化DNA被用于杂交至Illumina Infinium methylEPIC（850K）人类甲基化微珠芯片。