Hmga2 protein loss alters nuclear envelope and affects 3D chromatin structure upon the induction of pluripotent stem cell commitment [HiC]

Hmga2 KO pluripotent stem cells fail to develop into epiblast-like stem cells (EpiLCs). By using this experimental system, we studied the chromatin changes that take place upon the induction of EpiLCs and we observed that the loss of Hmga2 affects the histone mark H3K27me3, whose levels are higher in Hmga2 KO cells. However, gene expression differences between differentiating wt vs Hmga2 KO cells did not show any significant enrichments of PRC2 targets. Similarly, endogenous Hmga2 association to chromatin in stabilized epiblast stem cells did not show any clear relationships with gene expression modification observed in Hmga2 KO. Hmga2 ChIP-seq confirmed that this protein preferentially binds to the chromatin regions associated with nuclear lamina. As nuclear lamina is involved in the organization of 3D chromatin structure, we explored the possible effects of Hmga2 loss on this phenomenon. The analysis of HiC data in wt and Hmga2 KO cells allowed us to observe that inter-TAD interactions in Hmga2 KO cells are different from those observed in wt cells. These differences clearly show a peculiar compartmentalization of inter-TAD interactions in chromatin regions associated or not to nuclear lamina. Overall design: Comparative gene expression profiling analysis of RNA-seq data for Hmga2 wt and KO PSCs induced to differentiate into EpiLCs. Genome binding/occupancy profiling of Hmga2 in EpiLCs by high throughput sequencing. High-throughput chromatin conformation capture sequencing (HiC-seq) of Hmga2 wt and KO PSCs induced to differentiate into EpiLCs.