Xist RNA regulates remodeling of the Xi during B cell stimulation [RNA-seq]

The inactive X (Xi) is formed by a process called X-Chromosome Inactivation (XCI), with Xist upregulation, retention of Xist RNA transcripts at the Xi, chromatin re-organization, and transcriptional silencing. Female lymphocytes have ‘dynamic’ XCI maintenance where Xist RNA is transcribed but absent from the Xi in naïve lymphocytes and re-localizes after in-vitro activation. How ‘dynamic’ XCI impacts Xi dosage and nuclear organization, or where Xist RNA interacts with the Xi is unknown. Here we find maintenance of Xi dosage and global structure despite the absence of Xist RNA in naïve B-cells. However, we identified 104 escape genes and observe a gain of de-novo TADs on the Xi. Stimulation-dependent Xi remodeling co-occurs with Xist RNA re-accumulation at the Xi, and loss of Xist increases TAD remodeling and decompacts the Xi in both naïve and stimulated B-cells. Altogether, these results reveal B-cell specific Xi plasticity which could underlie female-specific mechanisms in lymphocytes.