Chromatin activity of I?Ba mediates the exit from naïve pluripotency (RNA-Seq)

Inflammatory signals are key in development and cell differentiation but their orchestration with pluripotency and stemness signals is poorly understood. Our previous work identified a chromatin function of I?Ba, the NF-?B inhibitor, that is crucial for differentiation in different types of somatic stem cells. Here we demonstrate that deficiency of I?Ba imposes a profound chromatin rewiring defect that impacts on DNA methylation, histone post-translational modifications and transcriptional regulation, stabilizing mouse embryonic stem cells (ESCs) in a ground state of pluripotency while preventing them from pluripotency exit and differentiation. By engineering separation-of-function mutants of I?Ba with specific binding to either NF-?B or histones, we demonstrate that regulation of pluripotency state by I?Ba is independent of NF-kB but requires the chromatin-related I?Ba function. Overall design: We performed bulk RNAseq analysis in mESCs and two early differentiation stages (EBs 48h and EBs 96h). Per timepoint, 3xWT and I?Ba 3xKO independent biological replicates were tested resulting in a total of 18 samples.