Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains

Manching Ku*, Richard P. Koche, Esther Rheinbay, Eric M. Mendenhall, Mitsuhiro Endoh, Tarjei S. Mikkelsen, Aviva Presser, Chad Nusbaum, Xiaohui Xie, Andrew S. Chi, Mazhar Adli, Simon Kasif, Leon M. Ptaszek, Chad A. Cowan, Eric S. Lander, Haruhiko Koseki, Bradley E. Bernstein

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

697 Scopus citations

Abstract

In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histonemodifications mark the promoters of more than 2,000 genes. To gain insight into the structure and function of bivalent domains, we mapped key histone modifications and subunits of Polycomb-repressive complexes 1 and 2 (PRC1 and PRC2) genomewide in human and mouse ES cells by chromatin immunoprecipitation, followed by ultra high-throughput sequencing. We find that bivalent domains can be segregated into two classes - the first occupied by both PRC2 and PRC1 (PRC1-positive) and the second specifically bound by PRC2 (PRC2-only). PRC1-positive bivalent domains appear functionally distinct as they more efficiently retain lysine 27 tri-methylation upon differentiation, show stringent conservation of chromatin state, and associate with an overwhelming number of developmental regulator gene promoters. We also used computational genomics to search for sequence determinants of Polycomb binding. This analysis revealed that the genomewide locations of PRC2 and PRC1 can be largely predicted from the locations, sizes, and underlying motif contents of CpG islands. We propose that large CpG islands depleted of activating motifs confer epigenetic memory by recruiting the full repertoire of Polycomb complexes in pluripotent cells.

Original languageEnglish (US)
Article numbere1000242
JournalPLoS genetics
Volume4
Issue number10
DOIs
StatePublished - Oct 2008

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Genetics(clinical)
  • Cancer Research

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