Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency

Yaser Atlasi, Wout Megchelenbrink, Tianran Peng, Ehsan Habibi, Onkar Joshi, Shuang Yin Wang, Cheng Wang, Colin Logie, Ina Poser, Hendrik Marks, Hendrik G. Stunnenberg

Research output: Contribution to journalArticlepeer-review

39 Citations (Scopus)

Abstract

The mechanisms underlying enhancer activation and the extent to which enhancer–promoter rewiring contributes to spatiotemporal gene expression are not well understood. Using integrative and time-resolved analyses we show that the extensive transcriptome and epigenome resetting during the conversion between ‘serum’ and ‘2i’ states of mouse embryonic stem cells (ESCs) takes place with minimal enhancer–promoter rewiring that becomes more evident in primed-state pluripotency. Instead, differential gene expression is strongly linked to enhancer activation via H3K27ac. Conditional depletion of transcription factors and allele-specific enhancer analysis reveal an essential role for Esrrb in H3K27 acetylation and activation of 2i-specific enhancers. Restoration of a polymorphic ESRRB motif using CRISPR–Cas9 in a hybrid ESC line restores ESRRB binding and enhancer H3K27ac in an allele-specific manner but has no effect on chromatin interactions. Our study shows that enhancer activation in serum- and 2i-ESCs is largely driven by transcription factor binding and epigenetic marking in a hardwired network of chromatin interactions.

Original languageEnglish
Pages (from-to)568-578
Number of pages11
JournalNature Cell Biology
Volume21
Issue number5
DOIs
Publication statusPublished - 1 May 2019
Externally publishedYes

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