Selective reactivation of human X-linked genes in female fibroblasts reprogrammed by cell fusion

In female mammals, one of the two X chromosomes is silenced as pluripotent cells differentiate. This process, termed X-inactivation, is random and results in mosaic expression of many X-linked genes in female tissues. Although X-inactivation can be reversed in vitro by reprogramming, the extent varies according to species, operator and conditions. Here, we have reprogrammed cloned female human fibroblasts by fusing them with mouse ESCs and examined the kinetics of X-linked gene re-expression. Allele-specific RNA sequencing analysis was used to determine the expression from the inactive X chromosome. This study revealed that a subset of loci within domains prone to escape X-inactivation, or that showed variable expression between somatic clones, were consistently reactivated upon pluripotent reprogramming. This suggests that stochastic events may be stabilised by reprogramming, and conversely, that variable expression is predictive for Xi genes susceptible to re-activation. Overall design: We performed RNA-sequencing of two human fibroblast clones derived from TERT-immortalised NHDF17914 (Lonza) and expressing reciprocal X chromosomes (i.e. clone 12 and 34) before and at 0, 4 and 6 days after fusion with mouse ESC (E14Tg2a:puroR). Two biological replicates were sequenced for each clone.