Single-Cell Analysis Reveals Partial Reactivation of X Chromosome instead of Chromosome-wide Dampening in Naive Human Pluripotent Stem Cells

Abstract

Recently, a unique form of X chromosome dosage compensation has been demonstrated in human preimplantation embryos, which happens through the dampening of X-linked gene expression from both X chromosomes. Subsequently, X chromosome dampening has also been demonstrated in female human pluripotent stem cells (hPSCs) during the transition from primed to naive state. However, the existence of dampened X chromosomes in both embryos and hPSCs remains controversial. Specifically, in preimplantation embryos it has been shown that there is inactivation of X chromosome instead of dampening. Here, we performed allelic analysis of X-linked genes at the single-cell level in hPSCs and found that there is partial reactivation of the inactive X chromosome instead of chromosome-wide dampening upon conversion from primed to naive state. In addition, our analysis suggests that the reduced X-linked gene expression in naive hPSCs might be the consequence of erasure of active X chromosome upregulation.

New Insights into X-Chromosome Reactivation during Reprogramming to Pluripotency

“…There is also gain of active Pol II and DNA demethylation [ 43 , 179 , 200 , 209 ]. One study reported H3K27me3 enrichment [ 200 ] and other studies reported little or no H3K27me3 enrichment under the XIST RNA foci in naive human pluripotent stem cells [ 180 , 210 ]. Finally, the transition also induces dampening of X-linked gene expression [ 200 ], reminiscent of early human embryos [ 183 ].…”

“…Moreover, H3K27me3 enrichment is not sufficient for silencing gene expression like in mouse [ 76 , 200 ]. Recently, another study proposed that dampening corresponds to erasure of XCU [ 210 ]. XIST reactivation is also preceded by a stage with XIST silencing [ 200 ].…”

Many XCI-ting routes to reach the eXACT dose

“…Several questions arise from this pioneering work in hPGCs to better understand what 'dampening' precisely relates to. First, it is important to bear in mind that conclusions about dampening are essentially based on scRNA-seq data analysis, which may lead to contradictory interpretations due to analyses pipelines 10,11 . As illustrated in Fig.…”

X upregulation is not global and extent of upregulation differs between ancestral and acquired X-linked genes

“…Down the line, several independent studies came out both in supporting and refuting Ohno's hypothesis [10][11][12][13][14][15][16][17][18][19]. Although, Ohno's hypothesis is still contested, recent studies by us and others have shown the presence of upregulated active-X chromosome (X2a) in different cell types in vivo and in vitro [20]. However, the dynamics of X-chromosome upregulation (XCU) during early development remain poorly understood.…”