Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains.
In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications 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.
Ku
Manching
M
Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.
Koche
Richard P
RP
Rheinbay
Esther
E
Mendenhall
Eric M
EM
Endoh
Mitsuhiro
M
Mikkelsen
Tarjei S
TS
Presser
Aviva
A
Nusbaum
Chad
C
Xie
Xiaohui
X
Chi
Andrew S
AS
Adli
Mazhar
M
Kasif
Simon
S
Ptaszek
Leon M
LM
Cowan
Chad A
CA
Lander
Eric S
ES
Koseki
Haruhiko
H
Bernstein
Bradley E
BE
D000818:Animals; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation; D002874:Chromosome Mapping; D019295:Computational Biology; D018899:CpG Islands; D053595:Embryonic Stem Cells / Q000378:metabolism*; D044127:Epigenesis, Genetic; D016678:Genome; D015894:Genome, Human; D006657:Histones / Q000378:metabolism; D006801:Humans; D056484:Jumonji Domain-Containing Histone Demethylases; D008745:Methylation; D051379:Mice; D010089:Oxidoreductases, N-Demethylating / Q000378:metabolism; D039904:Pluripotent Stem Cells / Q000378:metabolism; D063146:Polycomb-Group Proteins; D011401:Promoter Regions, Genetic; D017434:Protein Structure, Tertiary; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism*
D002843:Chromatin; D006657:Histones; D063146:Polycomb-Group Proteins; D012097:Repressor Proteins; D056484:Jumonji Domain-Containing Histone Demethylases; C523761:Kdm6b protein, mouse; D010089:Oxidoreductases, N-Demethylating