Chromosome Compartments on the Inactive X Guide TAD Formation Independently of Transcription during X-Reactivation

To investigate the dynamics of X-chromosome reactivation, we differentiated mouse embryonic stem cells (ESCs) into neural precursor cells (NPCs) and later reprogrammed them into induced pluripotent stem cells (iPSCs). During the conversions of NPCs into iPSC, we assessed the kinetics of X-chromosome reactivation. We generated allele-specific RNA-seq datasets to assess gene reactivation dynamics, employed ATAC-seq to investigate chromatin opening dynamics and performed in situ Hi-C to explore dynamics of chromosome structure. Allele-specific total RNA-seq, ATAC-seq and in situ Hi-C in ESC, NPCs derived from ESCs and multiple iPSC samples at different stages of X-chromosome reactivation.