Quantitative Multiplexed ChIP Reveals Global Alterations that Shape Promoter Bivalency in Ground State Embryonic Stem Cells

Abstract

Summary: To understand the epigenomic foundation of naive pluripotency, we implement a quantitative multiplexed chromatin immunoprecipitation sequencing (ChIP-seq) method comparing mouse embryonic stem cells (ESCs) grown in 2i versus 2i/serum and serum conditions. MINUTE-ChIP has a large linear dynamic range for accurately quantifying relative differences in genome-wide histone modification patterns across multiple pooled samples. We find compelling evidence for a broad H3 lysine 27 trimethylation (H3K27me3) hypermethylation of the genome, while bivalent promoters stably retain high H3K27me3 levels in 2i. We show that DNA hypomethylation, as observed in 2i, is a contributor to genome-wide gain of H3K27me3, while active demethylation by JMJD3/UTX counteracts further accumulation of H3K27me3. In parallel, we find hypomethylation of H3 lysine 4 trimethylation (H3K4me3), particularly at bivalent promoters, to be a characteristic of the 2i ground state. Serum stimulates H3K4me3 independent of GSK-3b and ERK signaling, suggesting that low H3K4me3 and high H3K27me3 levels at bivalent promoters are a product of two independent mechanisms that safeguard naive pluripotency. : Kumar et al. employ an improved multiplexed quantitative ChIP-seq methodology to characterize mESC pluripotency. They reveal that bivalent promoters are retained in the 2i ground state, which is characterized by abundant H3K27me3. H3K4me3 levels are high in serum-primed state and a stable 2i/serum intermediate but strikingly reduced in ground state. Keywords: pluripotency, ground state, naive stem cell, pluripotent stem cells, bivalency, bivalent promoters, polycomb, quantiative ChIP-seq, multiplexed ChIP-seq, epigenomics