The Transcriptional and Epigenomic Foundations of Ground State Pluripotency

Hendrik Marks,Tüzer Kalkan,Roberta Menafra,Sergey Denissov,Kenneth Jones,Helmut Hofemeister,Jennifer Nichols,Andrea Kranz,A Francis Stewart,Austin Smith,Hendrik G Stunnenberg

doi:10.1016/j.cell.2012.03.026

Abstract

SummaryMouse embryonic stem (ES) cells grown in serum exhibit greater heterogeneity in morphology and expression of pluripotency factors than ES cells cultured in defined medium with inhibitors of two kinases (Mek and GSK3), a condition known as “2i” postulated to establish a naive ground state. We show that the transcriptome and epigenome profiles of serum- and 2i-grown ES cells are distinct. 2i-treated cells exhibit lower expression of lineage-affiliated genes, reduced prevalence at promoters of the repressive histone modification H3K27me3, and fewer bivalent domains, which are thought to mark genes poised for either up- or downregulation. Nonetheless, serum- and 2i-grown ES cells have similar differentiation potential. Precocious transcription of developmental genes in 2i is restrained by RNA polymerase II promoter-proximal pausing. These findings suggest that transcriptional potentiation and a permissive chromatin context characterize the ground state and that exit from it may not require a metastable intermediate or multilineage priming.

Highlights

Mouse embryonic stem (ES) cells are characterized by the potency to generate all somatic and germline lineages in vitro and in chimaeric embryos (Smith, 2001)
Each cell line is functionally pluripotent as demonstrated by competence to generate high-contribution chimaeras with germline transmission
This comparison showed that 1,489 genes have more than 2-fold higher transcript abundance in 2i (p value < 0.2), whereas 1,947 genes exhibit more than 2-fold higher expression in serum (Figure 1A)

Summary

SUMMARY

Mouse embryonic stem (ES) cells grown in serum exhibit greater heterogeneity in morphology and expression of pluripotency factors than ES cells cultured in defined medium with inhibitors of two kinases (Mek and GSK3), a condition known as ‘‘2i’’ postulated to establish a naive ground state. 2itreated cells exhibit lower expression of lineageaffiliated genes, reduced prevalence at promoters of the repressive histone modification H3K27me, and fewer bivalent domains, which are thought to mark genes poised for either up- or downregulation. Precocious transcription of developmental genes in 2i is restrained by RNA polymerase II promoter-proximal pausing. These findings suggest that transcriptional potentiation and a permissive chromatin context characterize the ground state and that exit from it may not require a metastable intermediate or multilineage priming

INTRODUCTION

RESULTS

DISCUSSION

EXPERIMENTAL PROCEDURES