Pluto Bioinformatics

GSE56312: 2i induces widespread changes in OCT4, SOX2 and NANOG binding

Bulk RNA sequencing

Mouse embryonic stem cells (mESCs) cultured under standard serum/LIF conditions exhibit heterogeneous expression of key pluripotency transcription factors that can be overcome by the culture with two inhibitors of the MEK and GSK3 pathway, respectively. This 2i state is associated with homogenous expression of Nanog as well as global changes in expression and the epigenome. Although several studies have highlighted the resulting changes to the cellular state in 2i, little is known about the effectors that might contribute to this. To provide new mechanistic insights we have investigated the genome-wide targets of the core factors, OCT4, SOX2 and NANOG (OSN) and how they are reconfigured upon the transition to 2i. Interestingly, changes in the bound targets of OSN, as well as direct UTF1 target genes, which is the most downregulated transcription factor after just 24h in 2i, already account for nearly half of all genes that change at the transcriptional level between the two conditions. Dynamics in the histone modifications, H3K4me3 and H3K27me3, provide limited insights to the transcriptional changes in the early 2i transition, which is consistent with our EED depletion results that suggest PRC2 is dispensable for the de novo silencing of genes such as Utf1 and the continued repression of bivalent loci. Our study adds new mechanistic insights to the dramatic regulatory and phenotypic transition of mouse pluripotent stem cells in 2i. SOURCE: Michael,Johannes,ZillerMeissner Lab Harvard University