Capture Hi-C in TX1072 XX?Xic and XO mESCs in the naive pluripotent state and during differentiation

Developmental genes are controlled by complex cis-regulatory landscapes that integrate multiple signals to ensure the correct spatio-temporal expression pattern. To investigate the underlying regulatory principles, we use the Xist locus as a model, which encodes the master regulator of X-chromosome inactivation. Xist is upregulated at the primed pluripotent state in a female-specific manner, thus integrating developmental cues and X-dosage information. It remains poorly understood how these signals are decoded by the ~800kb genomic region that controls Xist. While a series of repressive cis-regulatory elements have been identified, the distal enhancers that activate Xist transcription remain largely unknown. Here we use capture Hi-C to profile chromatin contacts within the X inactivation center at the onset of random X-chromosome inactivation using an endogenous cell model of the inactive (TX 1072 XX?Xic) and active (TX 1072 XO) X chromosome. Overall design: Capture Hi-C was performed in the TX1072 XX?Xic (XX line carrying a heterozygous deletion of the Xic: chrX:103182701-103955531 on the B6 allele) and TX1072 XO (X chromosome from Cast background) cell lines on a 3 megabase region surrounding the Xist gene (chrX:102238718-10521426). The data was collected in two replicates from cells in 2i+LIF medium (day 0), as well at day 2 of differentiation (via 2i+LIF-withdrawal).