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

炎症信号在发育与细胞分化进程中发挥关键调控作用，但其与多能性信号及干细胞干性信号的协同调控机制仍未被充分阐明。我们此前的研究发现，核因子κB（NF-κB）抑制剂IκBα具备染色质调控功能，该功能对多种成体干细胞的分化过程至关重要。本研究证实，IκBα缺失会引发严重的染色质重编程缺陷，该缺陷可影响DNA甲基化、组蛋白翻译后修饰及转录调控，使小鼠胚胎干细胞（ESCs）稳定维持在多能性基态，同时阻止其退出多能性并发生分化。通过构建仅能特异性结合核因子κB或组蛋白的IκBα功能分离突变体，我们证实IκBα对多能性状态的调控不依赖于核因子κB，但需要其染色质相关功能。

实验设计：我们对小鼠胚胎干细胞（ESCs）中的H3K27me3、H3K9me3、H3K4me3、H3K27ac及H3K4me1组蛋白修饰标记开展了染色质免疫共沉淀测序（ChIP-seq）。针对每一种组蛋白修饰标记，我们在两种实验组中各设置3次独立生物学重复：野生型（3xWT）样本与IκBα三敲除（3xKO）样本。