Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome

Abstract

The Polycomb group of epigenetic enzymes represses expression of developmentally regulated genes in higher eukaryotes. This group includes the Polycomb repressive complex 1 (PRC1), which ubiquitylates nucleosomal histone H2A Lys119 using its E3 ubiquitin ligase subunits, Ring1B and Bmi1, together with an E2 ubiquitin-conjugating enzyme, UbcH5c. However, the molecular mechanism of nucleosome substrate recognition by PRC1 or other chromatin enzymes is unclear. Here we present the crystal structure of the Ring1B/Bmi1/UbcH5c E3-E2 complex (the PRC1 ubiquitylation module) bound to its nucleosome core particle substrate. The structure shows how a chromatin enzyme achieves substrate specificity by interacting with multiple nucleosome surfaces spatially distinct from the site of catalysis. Our structure further reveals an unexpected role for the ubiquitin E2 enzyme in substrate recognition, and provides insight into how the related histone H2A E3 ligase, BRCA1, interacts with and ubiquitylates the nucleosome.

The Polycomb Repressive Complex 1 Protein BMI1 Is Required for Constitutive Heterochromatin Formation and Silencing in Mammalian Somatic Cells

“…The observation that BMI1 and BRCA1 proteins accumulation is mutually independent and that BMI1 levels are increased in BRCA1-deficient cells (and reciprocally) also suggests that both protein complexes possibly bind to very close substrates to catalyze H2A monoubiquitinylation. Structural analyses have indeed revealed a high degree of conservation between the nucleosome-binding loop of BRCA1 and the corresponding domain of RING1B (78). Notably, the reduced neuronal chromocenter number and size phenotype observed in Bmi1-null neurons is about identical to that reported for mouse cortical neurons conditionally deficient for BRCA1, thus further supporting our findings (22).…”

X-ray structure of the MMTV-A nucleosome core

“…Unfortunately, there are no structures of pioneer factors bound to a nucleosome, and the existing structures of nucleosome corebinding proteins bound to a NCP are nonspecific complexes that make little contact with NCP DNA (20,22,30). The recent structure of the prototype foamy virus integrase bound to NCP shows that this enzyme makes substantial contact with SHL ±3.5, but the low resolution does not permit a deeper analysis (31).…”

Structure of the PRC2 complex and application to drug discovery

“…Once thought of as a unique complex, it is now clear that human PRC1 exists as a modular subset of complexes with distinct functions and gene targets [8] . All PRC1 complexes contain a common core -the RING-type E3 ubiquitin ligase composed of Ring1B (also known as RNF2) or Ring1A, and Bmi1 (also known as PCGF4) or one of six Polycomb group RING finger (PCGF) subunits, as well as additional subunits that define canonical PRC1 (CBX and PHC subunits) and noncanonical PRC1 (RYBP/YAP2) [8,9] . The subunit com-position affects both PRC1 recruitment to target genes and the catalytic activity of the complex [8,9] .…”

“…All PRC1 complexes contain a common core -the RING-type E3 ubiquitin ligase composed of Ring1B (also known as RNF2) or Ring1A, and Bmi1 (also known as PCGF4) or one of six Polycomb group RING finger (PCGF) subunits, as well as additional subunits that define canonical PRC1 (CBX and PHC subunits) and noncanonical PRC1 (RYBP/YAP2) [8,9] . The subunit com-position affects both PRC1 recruitment to target genes and the catalytic activity of the complex [8,9] . PRC2 catalyzes the methylation of histone H3 lysine 27 (H3K27) through its EZH2 subunit, a modification thought to mediate transcriptional silencing through chromatin compaction [1,10] .…”

“…PRC1 catalyzes the monoubiquitylation of histone H2A Lys 119 [1,8] . Once thought of as a unique complex, it is now clear that human PRC1 exists as a modular subset of complexes with distinct functions and gene targets [8] .…”