X-Chromosome Dosage Modulates Multiple Molecular and Cellular Properties of Mouse Pluripotent Stem Cells Independently of Global DNA Methylation Levels

Abstract

Summary: Reprogramming female mouse somatic cells into induced pluripotent stem cells (iPSCs) leads to X-chromosome reactivation. The extent to which increased X-chromosome dosage (X-dosage) in female iPSCs compared with male iPSCs leads to differences in the properties of iPSCs is still unclear. We show that chromatin accessibility in mouse iPSCs is modulated by X-dosage. Specific sets of transcriptional regulator motifs are enriched in chromatin with increased accessibility in XX or XY iPSCs. The transcriptome, growth and pluripotency exit are also modulated by X-dosage in iPSCs. To understand how increased X-dosage modulates the properties of mouse pluripotent stem cells, we used heterozygous deletions of the X-linked gene Dusp9. We show that X-dosage regulates the transcriptome, open chromatin landscape, growth, and pluripotency exit largely independently of global DNA methylation. Our results provide insights into how gene dosage modulates the epigenetic and genetic mechanisms that regulate cell identity. : Female mouse pluripotent stem cells have two active X chromosomes while male cells have only one. Using genome-wide transcription and open chromatin analyses, Pasque and colleagues show that female and male iPSCs adopt differences in transcription, open chromatin landscape, and cellular growth. These differences can be uncoupled from global DNA hypomethylation in female ESCs through Dusp9 heterozygous deletion. Keywords: X-chromosome reactivation, mouse pluripotent stem cells, pluripotency, DNA methylation, chromatin accessibility, X-chromosome inactivation, X dosage, iPS cells, dosage compensation