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

Abstract

SUMMARY 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.

New Insights into X-Chromosome Reactivation during Reprogramming to Pluripotency

“…Therefore, it is possible that 3D chromatin organization could help prime genes for reactivation, but this must be experimentally tested. Recently, work in human ESCs (hESCs) found that early reactivated genes during XCR in hESCs, known as erosion of XCI (See Section 12 ) also starts at genes with shorter genomic distance to escapee genes [ 161 ]. Collectively, these results indicate a possible conserved link between chromatin organization and the stability and reversibility of gene silencing on the Xi, and may also be linked to the mechanisms regulating variable escape from XCI [ 162 , 163 ].…”

“…Erosion of XCI influences the differentiation potential of hPSCs [ 44 ]. More recently, XCR by erosion of XCI was shown to start at genes with a shorter genomic distance to escapee genes [ 161 ]. These results are in line with the shorter genomic distance of early reactivated genes during mouse iPSC reprogramming [ 48 , 49 ].…”