Contiguous erosion of the inactive X in human pluripotency concludes with global DNA hypomethylation. 2021

Prakhar Bansal, and Darcy T Ahern, and Yuvabharath Kondaveeti, and Catherine W Qiu, and Stefan F Pinter
Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA; Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA.

Female human pluripotent stem cells (hPSCs) routinely undergo inactive X (Xi) erosion. This progressive loss of key repressive features follows the loss of XIST expression, the long non-coding RNA driving X inactivation, and causes reactivation of silenced genes across the eroding X (Xe). To date, the sporadic and progressive nature of erosion has obscured its scale, dynamics, and key transition events. To address this problem, we perform an integrated analysis of DNA methylation (DNAme), chromatin accessibility, and gene expression across hundreds of hPSC samples. Differential DNAme orders female hPSCs across a trajectory from initiation to terminal Xi erosion. Our results identify a cis-regulatory element crucial for XIST expression, trace contiguously growing reactivated domains to a few euchromatic origins, and indicate that the late-stage Xe impairs DNAme genome-wide. Surprisingly, from this altered regulatory landscape emerge select features of naive pluripotency, suggesting that its link to X dosage may be partially conserved in human embryonic development.

UI MeSH Term Description Entries
D002454 Cell Differentiation Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs. Differentiation, Cell,Cell Differentiations,Differentiations, Cell
D005260 Female Females
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D049951 X Chromosome Inactivation A dosage compensation process occurring at an early embryonic stage in mammalian development whereby, at random, one X CHROMOSOME of the pair is repressed in the somatic cells of females. X Inactivation,Lyon Hypothesis,Lyonization,X-Inactivation,Chromosome Inactivation, X,Hypothesis, Lyon,Inactivation, X,Inactivation, X Chromosome,X Inactivations
D019175 DNA Methylation Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor. DNA Methylations,Methylation, DNA,Methylations, DNA
D039904 Pluripotent Stem Cells Cells that can give rise to cells of the three different GERM LAYERS. Stem Cells, Pluripotent,Pluripotent Stem Cell,Stem Cell, Pluripotent

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