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Cell Rep. 2019 Sep 17;28(12):3274-3284.e5. doi: 10.1016/j.celrep.2019.08.046.

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

Author information

1
Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden; Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, 17177 Stockholm, Sweden.
2
Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden; Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, 17177 Stockholm, Sweden. Electronic address: simon.elsasser@scilifelab.se.

Abstract

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.

KEYWORDS:

bivalency; bivalent promoters; epigenomics; ground state; multiplexed ChIP-seq; naive stem cell; pluripotency; pluripotent stem cells; polycomb; quantiative ChIP-seq

PMID:
31533047
DOI:
10.1016/j.celrep.2019.08.046
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