Allele-specific RNA-seq analysis of Wild Type, Stc1 -/-, Pygo1 -/-, Rlim -/- female mouse fibroblasts

The goal of this study is to examine and analyze allele-specific expression of both active and inacive X-chromosome genes using single nucleotide polymorphism in previously known X-chromosome inactivation factor (XCIF) knockout female mouse fibroblasts. The mouse intercross species femal fibroblasts also known as Patski cell line harbors a number of single nucleotide polymorphism on both active and inactive X-chromosomes, allowing us to distinguish between Xi- and Xa-linked gene expression.

This Patski cell line consists of inactive X-chromosome derived from C57BL/6 mouse strain and active X-chromosome derived from SPRET/EiJ mouse strain. To ensure the allele-specific gene expression, Xist which is exclusively expressed on inactive X-chromosome was analyzed. Our results show that a small subset of Xi-linked genes were reactivated from inactive X-chromosome, while a vast majority of Xi-linked genes were silenced.