Chromatin RNA-seq of Xist-mediated silencing upon YY1 degradation in iXist-ChrX YY1-FKBP12-T7 mESCs
X chromosome inactivation (XCI) in mammals is mediated by Xist RNA which functions in cis to silence genes on a single X chromosome in XX female cells, thereby equalising levels of X-linked gene expression relative to XY males. XCI progresses over a period of several days, with some X-linked genes silencing faster than others. Chromosomal location of a gene is an important determinant of silencing rate, but uncharacterised gene-intrinsic features also mediate resistance or susceptibility to silencing. In this study, we examine mouse embryonic stem cell lines with an inducible Xist allele (iXist-ChrX mESCs) and integrate allele-specific data of gene silencing and decreasing inactive X (Xi) chromatin accessibility over time-courses of Xist induction with cellular differentiation. Our analysis reveals that motifs bound by the transcription factor YY1 are associated with persistently accessible regulatory elements, including many promoters and enhancers of slow-silencing genes. We further show that YY1 is evicted relatively slowly from target sites on Xi, and that silencing of X-linked genes is increased upon YY1 degradation. Together our results suggest that YY1 acts as barrier to Xist-mediated silencing until late stages of the XCI process. Overall design: This series contains data from Chromatin RNA-seq experiments performed in iXist-ChrX YY1-FKBP12-3xT7 mESCs. Two clones (aF1 and cC3) were analysed as biological replicates. Clone aF1 derives from the iXist-ChrX-Dom line so harbours inducible Xist on the Domesticus/129/Sv allele and X-linked genes preceding the Xist locus (0-103Mb) are amenable to allelic silencing analysis. Clone cC3 derives from the iXist-ChrX-Cast line so has inducible Xist on the Castaneous allele and all X-linked genes can be analysed. Silencing is assayed at 0, 2 and 6 days of Xist induction, with and without treatment with 100nM dTAG-13 52 hours before sample collection. Hence, in the day 2 timepoints YY1 degradation occurs 4 hours prior to Xist induction, whereas in the day 6 timepoint YY1 is degraded at a stage where silencing has initiated and progressed substantially but is not fully complete.