Chromatin activity of IκBα mediates the exit from naïve pluripotency (ChIP-seq Histone marks)

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. We performed ChIP-seq for H3K27me3, H3K9me3, H3K4me3, H3K27ac and H3K4me1 histone marks in mESCs. Per histone mark, three independent biological replicates were tested in two conditions: 3xWT and IκBα 3xKO samples.