No abstract

Summary The heterogeneous nature of mammalian PRC1 complexes has hindered our understanding of their biological functions. Here, we present a comprehensive proteomic and genomic analysis that uncovered six major groups of PRC1 complexes each containing a distinct PCGF subunit, a RING1A/B ubiquitin ligase, and a unique set of associated polypeptides. These PRC1 complexes differ in their genomic localization and only a small subset co-localize with H3K27me3. Further biochemical dissection revealed that the six PCGF-RING1A/B combinations form multiple complexes through association with RYBP or its homolog YAF2, which prevents the incorporation of other canonical PRC1 subunits such as CBX, PHC and SCM. Although both RYBP/YAF2- and CBX/PHC/SCM-containing complexes compact chromatin, only RYBP stimulates the activity of RING1B toward H2AK119ub1, suggesting a central role in PRC1 function. Knockdown of RYBP in ES cells compromised their ability to form embryoid bodies, likely because of defects in cell proliferation and maintenance of H2AK119ub1 level.

Enhancer of Zeste [E(z)] is a Polycomb

Summary Polycomb Group (PcG) proteins play an essential role in the epigenetic maintenance of repressive chromatin states. The gene silencing activity of the Polycomb Repressive Complex 2 (PRC2) depends on its ability to tri-methylate lysine 27 of histone H3 (H3K27) via the catalytic SET domain of the EZH2 subunit, and at least two other subunits of the complex: Suz12 and Eed. We show that the C-terminal domain of Eed specifically binds to histone tails carrying tri-methyl lysine residues associated with repressive chromatin marks and that this leads to the allosteric activation of the methyltransferase activity of PRC2. Mutations in Eed that prevent it from recognising repressive trimethyl-lysine marks abolish activation of PRC2 in vitro and, in Drosophila, reduces global methylation and disrupts development. These findings suggest a model for the propagation of the H3K27me3 mark that accounts for the maintenance of repressive chromatin domains and for the transmission of a histone modification from mother to daughter cells.

Histone lysine methylation is a central modification to mark functionally distinct chromatin regions. In particular, H3-K9 trimethylation has emerged as a hallmark of pericentric heterochromatin in mammals. Here we show that H4-K20 trimethylation is also focally enriched at pericentric heterochromatin. Intriguingly, H3-K9 trimethylation by the Suv39h HMTases is required for the induction of H4-K20 trimethylation, although the H4 Lys 20 position is not an intrinsic substrate for these enzymes. By using a candidate approach, we identified Suv4-20h1 and Suv4-20h2 as two novel SET domain HMTases that localize to pericentric heterochromatin and specifically act as nucleosomal H4-K20 trimethylating enzymes. Interaction of the Suv4-20h enzymes with HP1 isoforms suggests a sequential mechanism to establish H3-K9 and H4-K20 trimethylation at pericentric heterochromatin. Heterochromatic H4-K20 trimethylation is evolutionarily conserved, and in Drosophila, the Suv4-20 homolog is a novel PEV modifier to regulate position-effect variegation. Together, our data indicate a function for H4-K20 trimethylation in gene silencing and further suggest H3-K9 and H4-K20 trimethylation as important components of a repressive pathway that can index pericentric heterochromatin.[Keywords: Histone code; histone H4 Lys 20; mono-, di-, trimethylation; Suv4-20h HMTases; heterochromatin; combinatorial histone methyl marks] Supplemental material is available at http://www.genesdev.org.

No abstract

ATP-dependent nucleosome remodeling and core histone acetylation and deacetylation represent mechanisms to alter nucleosome structure. NuRD is a multisubunit complex containing nucleosome remodeling and histone deacetylase activities. The histone deacetylases HDAC1 and HDAC2 and the histone binding proteins RbAp48 and RbAp46 form a core complex shared between NuRD and Sin3-histone deacetylase complexes. The histone deacetylase activity of the core complex is severely compromised. A novel polypeptide highly related to the metastasis-associated protein 1, MTA2, and the methyl-CpG-binding domain-containing protein, MBD3, were found to be subunits of the NuRD complex. MTA2 modulates the enzymatic activity of the histone deacetylase core complex. MBD3 mediates the association of MTA2 with the core histone deacetylase complex. MBD3 does not directly bind methylated DNA but is highly related to MBD2, a polypeptide that binds to methylated DNA and has been reported to possess demethylase activity. MBD2 interacts with the NuRD complex and directs the complex to methylated DNA. NuRD may provide a means of gene silencing by DNA methylation. Packaging of DNA into chromatin allows the cell to store its genetic information efficiently and has an important role in regulating gene expression (Workman and Kingston 1998). Dynamic changes in chromatin structure can facilitate or prevent the access of the transcription machinery to nucleosomal DNA, leading to transcription regulation. Recent studies have revealed two mechanisms by which chromatin structure can be altered. One mechanism involves multisubunit protein complexes that use the energy derived from ATP hydrolysis to alter the structure of, or 'remodel', nucleosomes (for review, see Tsukiyama and Wu 1997;Kadonaga 1998;Varga-Weisz and Becker 1998;Travers 1999). The other mechanism involves covalent modification of nucleosomes, in particular acetylation of the core histone tails and methylation of DNA (for review, see Grunstein 1997;Struhl 1998;.Since the discovery of histone acetylation by Allfrey et al. (1964), a general correlation between histone acetylation and gene activity has been established (Hebbes et al. 1988). The enzymes that catalyze histone acetylation and deacetylation have been identified (Brownell et al. 1996;Taunton et al. 1996). Several transcriptional coactivators have histone acetyltransferase (HAT) activity, whereas several transcriptional corepressors have histone deacetylase activity (for review, see Grunstein 1997; Kuo and Allis 1998; Struhl 1998). In addition, mutagenesis studies with Gcn5 and Rpd3, the prototypical histone acetyltransferase and deacetylase, respectively, confirmed the long-speculated role of histone acetylation and deacetylation in transcription regulation (Kadosh and Struhl 1998a;Wang et al. 1998). Moreover, Rpd3/Sin3-dependent repression has been shown to be directly associated with the deacetylation of lysine 5 of histone H4 in the promoters of UME6-regulated genes (Kadosh and Struhl 1998b;Rundlett et al. 1998). However, how cor...

The FACT (facilitates chromatin transcription) complex is required for transcript elongation through nucleosomes by RNA polymerase II (Pol II) in vitro. Here, we show that FACT facilitates Pol II-driven transcription by destabilizing nucleosomal structure so that one histone H2A-H2B dimer is removed during enzyme passage. We also demonstrate that FACT possesses intrinsic histone chaperone activity and can deposit core histones onto DNA. Importantly, FACT activity requires both of its constituent subunits and is dependent on the highly acidic C terminus of its larger subunit, Spt16. These findings define the mechanism by which Pol II can transcribe through chromatin without disrupting its epigenetic status.