Chromatin activity of IκBα mediates the exit from naïve pluripotency (Methylation array)

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 IκBα, the NF-κB inhibitor, that is crucial for differentiation in different types of somatic stem cells. Here we demonstrate that deficiency of IκBα 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 IκBα with specific binding to either NF-κB or histones, we demonstrate that regulation of pluripotency state by IκBα is independent of NF-kB but requires the chromatin-related IκBα function. Bisulphite converted DNA was hybridised to the Illumina Infinium Mouse Methylation Beadchip (MM285) array in mESCs and one early differentiation stages (EBs 96h). Per timepoint, 3xWT and IκBα 3xKO independent biological replicates were tested resulting in a total of 12 samples.