Xist upstream deletion impairs topological contacts of Xist locus and affects Xist coating/expression and autosomal gene expression [ChIP-Seq]

In this study, we have investigated the role of Xist upstream region located near the Xist-TAD boundary in maintenance of imprinted X-chromosome inactivation in extraembryonic endoderm stem cells (XEN). We found that deletion of Xist upstream region(~6Kb) leads to the alterations of Xist intra-TAD contacts and upregulate Xist expression. Moreover, it impaired the interactions of the Xist locus across X-chromosomes and autosomes. Moreover, Xist upstream deletion resulted dispersal of Xist coating and loss of accumulation of diffrent repressive chromatin marks on the inactive-X. Surprisingly there was no effect on inactive-X gene silencing, however, it affeted the autosomal gene expression. We performed RNA-seq in WT XEN clones and Xist upstream deleted XEN cell clones (two biological replicates for each deletion) to investigated the effect of Xist upstream deletion in XEN cells. We also performed ChIP-seq and 4C experiments in WT XEN and Xist deleted XEN cells.