Escape from X Inactivation Varies in Mouse Tissues

X chromosome inactivation (xci) silences most genes on one x chromosome in female mammals,but some genes escape xci. to identify escape genes in vivo and to explore molecular mechanisms that regulate this process we analyzed the allele-specific expression and chromatin structure of x-linked genes in mouse tissues and cells with skewed xci and distinguishable alleles based on single nucleotide polymorphisms. using a binomial model to assess allelic expression,we demonstrate a continuum between complete silencing and expression from the inactive x (xi). the validity of the rna-seq approach was verified using rt-pcr with species-specific primers or sanger sequencing. both common escape genes and genes with significant differences in xci status between tissues were identified. such genes may be candidates for tissue-specific sex differences. overall,few genes (3–7%) escape xci in any of the mouse tissues examined,suggesting stringent silencing and escape controls. in contrast,an in vitro system represented by the embryonic-kidney-derived patski cell line showed a higher density of escape genes (21%),representing both kidney-specific escape genes and cell-line specific escape genes. allele-specific rna polymerase ii occupancy and dnase i hypersensitivity at the promoter of genes on the xi correlated well with levels of escape,consistent with an open chromatin structure at escape genes. allele-specific ctcf binding on the xi clustered at escape genes and was denser in brain compared to the patski cell line,possibly contributing to a more compartmentalized structure of the xi and fewer escape genes in brain compared to the cell line where larger domains of escape were observed. © 2015 berletch et al.