STARR-seq in 1.8 XX and XO mESCs 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 STARR-seq to profile enhancer activity within the X inactivation center at the onset of random X-chromosome inactivation. Overall design: STARR-seq was performed in the 1.8 XX and 1.8 XO cell lines using the BAC clones of the RPCI-23 Female (C57BL/6J) Mouse BAC Library (RP23-106C4, RP23-11P22, RP23-423B1, RP23-273N4, RP23-71K8) as the input DNA source. The data was collected in 3 replicates from cells in 2i+LIF medium (day 0), as well at day 2 of differentiation (via 2i+LIF-withdrawal).