mRNA-seq of iXist-ChrXDom mESCs

X chromosome inactivation (XCI) is mediated by the non-coding RNA Xist which directs chromatin modification and gene silencing in cis. The RNA binding protein SPEN and associated corepressors have a central role in Xist-mediated gene silencing. Other silencing factors, notably the Polycomb system, have been reported to function downstream of SPEN. Making use of a SPEN separation-of-function mutation we show that SPEN and Polycomb pathways in fact function in parallel to establish gene silencing. Additionally, we find that differentiation-dependent recruitment of the chromosomal protein SmcHD1 is required for silencing many X-linked genes. Overall design: This series contains messenger RNA-seq (mRNA-seq) in uninduced iXist-ChrX-Dom cells, in which Xist on the M.m.Domesticus allele of female (XX) mESCs is under doxycyline-inducible control. These datasets were used to calculate and rank genes by initial gene expression levels (Transcripts per Million; TPM) prior to Xist induction.