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

Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, Mikkelsen TS, Presser A, Nusbaum C, Xie X, Chi AS, Adli M, Kasif S, Ptaszek LM, Cowan CA, Lander ES, Koseki H, Bernstein BE - PLoS Genet. (2008)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.

ABSTRACT
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.

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PRC1-positive bivalent domains are functionally distinct.(A) Box plot shows 25th, 50th and 75th percentile Ring1B ChIP-Seq signals for Ring1B-positive bivalent promoters, Ring1B-negative bivalent promoters, and for H3K4me3 only promoters. (B) Plot illustrates fraction of genes up-regulated (red) or down-regulated (blue) in PRC1-deficient ES cells for the indicated gene sets (see text for details on Ring1A/B dKO ES cell model). De-repression is evident for a significantly greater proportion of PRC1-positive bivalent promoters (p-value by Fisher's exact test). (C) The proportion of bivalent mouse promoters for which the human ortholog also carries H3K27me3 is indicated, contingent on Ring1B status in mouse ES cells. (D) The proportion of bivalent promoters for which H3K27me3 is retained in ES cell-derived neural progenitors (‘NPCs’), contingent on Ring1B status in mouse ES cells. (E) Gene Ontology categories over-represented in PRC1-positive or PRC1-negative bivalent gene sets.
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pgen-1000242-g003: PRC1-positive bivalent domains are functionally distinct.(A) Box plot shows 25th, 50th and 75th percentile Ring1B ChIP-Seq signals for Ring1B-positive bivalent promoters, Ring1B-negative bivalent promoters, and for H3K4me3 only promoters. (B) Plot illustrates fraction of genes up-regulated (red) or down-regulated (blue) in PRC1-deficient ES cells for the indicated gene sets (see text for details on Ring1A/B dKO ES cell model). De-repression is evident for a significantly greater proportion of PRC1-positive bivalent promoters (p-value by Fisher's exact test). (C) The proportion of bivalent mouse promoters for which the human ortholog also carries H3K27me3 is indicated, contingent on Ring1B status in mouse ES cells. (D) The proportion of bivalent promoters for which H3K27me3 is retained in ES cell-derived neural progenitors (‘NPCs’), contingent on Ring1B status in mouse ES cells. (E) Gene Ontology categories over-represented in PRC1-positive or PRC1-negative bivalent gene sets.

Mentions: We first considered whether physical targets of PRC1, as defined above, are also regulated by the complex. Since Ring1B and Ring1A are functionally redundant, we employed a conditional Ring1A/B double-knockout ES cell system in which Ring1B depletion is induced by addition of 4-hydroxy tamoxifen (OHT) [13]. We profiled expression changes after 48 hours of OHT treatment, at which time Ring1B protein levels are markedly depleted while Oct4 levels remain essentially unchanged [8],[13]. We found that 32% of PRC1-positive bivalent promoters are up-regulated by at least 50%, compared to just 5% of all genes (Figure 3B). A much smaller proportion of PRC1-negative bivalent promoters are up-regulated at this time point (16%). The difference between the two sets is statistically significant (p<10−10), and is not explained by baseline expression levels as bivalent promoters show very low activity, regardless of PRC1 status.


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

Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, Mikkelsen TS, Presser A, Nusbaum C, Xie X, Chi AS, Adli M, Kasif S, Ptaszek LM, Cowan CA, Lander ES, Koseki H, Bernstein BE - PLoS Genet. (2008)

PRC1-positive bivalent domains are functionally distinct.(A) Box plot shows 25th, 50th and 75th percentile Ring1B ChIP-Seq signals for Ring1B-positive bivalent promoters, Ring1B-negative bivalent promoters, and for H3K4me3 only promoters. (B) Plot illustrates fraction of genes up-regulated (red) or down-regulated (blue) in PRC1-deficient ES cells for the indicated gene sets (see text for details on Ring1A/B dKO ES cell model). De-repression is evident for a significantly greater proportion of PRC1-positive bivalent promoters (p-value by Fisher's exact test). (C) The proportion of bivalent mouse promoters for which the human ortholog also carries H3K27me3 is indicated, contingent on Ring1B status in mouse ES cells. (D) The proportion of bivalent promoters for which H3K27me3 is retained in ES cell-derived neural progenitors (‘NPCs’), contingent on Ring1B status in mouse ES cells. (E) Gene Ontology categories over-represented in PRC1-positive or PRC1-negative bivalent gene sets.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2567431&req=5

pgen-1000242-g003: PRC1-positive bivalent domains are functionally distinct.(A) Box plot shows 25th, 50th and 75th percentile Ring1B ChIP-Seq signals for Ring1B-positive bivalent promoters, Ring1B-negative bivalent promoters, and for H3K4me3 only promoters. (B) Plot illustrates fraction of genes up-regulated (red) or down-regulated (blue) in PRC1-deficient ES cells for the indicated gene sets (see text for details on Ring1A/B dKO ES cell model). De-repression is evident for a significantly greater proportion of PRC1-positive bivalent promoters (p-value by Fisher's exact test). (C) The proportion of bivalent mouse promoters for which the human ortholog also carries H3K27me3 is indicated, contingent on Ring1B status in mouse ES cells. (D) The proportion of bivalent promoters for which H3K27me3 is retained in ES cell-derived neural progenitors (‘NPCs’), contingent on Ring1B status in mouse ES cells. (E) Gene Ontology categories over-represented in PRC1-positive or PRC1-negative bivalent gene sets.
Mentions: We first considered whether physical targets of PRC1, as defined above, are also regulated by the complex. Since Ring1B and Ring1A are functionally redundant, we employed a conditional Ring1A/B double-knockout ES cell system in which Ring1B depletion is induced by addition of 4-hydroxy tamoxifen (OHT) [13]. We profiled expression changes after 48 hours of OHT treatment, at which time Ring1B protein levels are markedly depleted while Oct4 levels remain essentially unchanged [8],[13]. We found that 32% of PRC1-positive bivalent promoters are up-regulated by at least 50%, compared to just 5% of all genes (Figure 3B). A much smaller proportion of PRC1-negative bivalent promoters are up-regulated at this time point (16%). The difference between the two sets is statistically significant (p<10−10), and is not explained by baseline expression levels as bivalent promoters show very low activity, regardless of PRC1 status.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.

ABSTRACT
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.

Show MeSH