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TitleRead-write mechanisms of H2A ubiquitination by Polycomb repressive complex 1.
Journal, issue, pagesNature, Vol. 636, Issue 8043, Page 755-761, Year 2024
Publish dateNov 13, 2024
AuthorsVictoria Godínez López / Marco Igor Valencia-Sánchez / Stephen Abini-Agbomson / Jonathan F Thomas / Rachel Lee / Pablo De Ioannes / Brian A Sosa / Jean-Paul Armache / Karim-Jean Armache /
PubMed AbstractEpigenetic inheritance of silent chromatin domains is fundamental to cellular memory during embryogenesis, but it must overcome the dilution of repressive histone modifications during DNA replication. ...Epigenetic inheritance of silent chromatin domains is fundamental to cellular memory during embryogenesis, but it must overcome the dilution of repressive histone modifications during DNA replication. One such modification, histone H2A lysine 119 monoubiquitination (H2AK119Ub), needs to be re-established by the Polycomb repressive complex 1 (PRC1) E3 ligase to restore the silent Polycomb domain. However, the exact mechanism behind this restoration remains unknown. Here, combining cryo-electron microscopy (cryo-EM) and functional approaches, we characterize the read-write mechanism of the non-canonical PRC1-containing RYBP (ncPRC1). This mechanism, which functions as a positive-feedback loop in epigenetic regulation, emphasizes the pivotal role of ncPRC1 in restoring H2AK119Ub. We observe an asymmetrical binding of ncPRC1 to H2AK119Ub nucleosomes, guided in part by the N-terminal zinc-finger domain of RYBP binding to residual H2AK119Ub on nascent chromatin. This recognition positions the RING domains of RING1B and BMI1 on the unmodified nucleosome side, enabling recruitment of the E2 enzyme to ubiquitinate H2AK119 within the same nucleosome (intra-nucleosome read-write) or across nucleosomes (inter-nucleosome read-write). Collectively, our findings provide key structural and mechanistic insights into the dynamic interplay of epigenetic regulation, highlighting the significance of ncPRC1 in H2AK119Ub restoration to sustain repressive chromatin domains.
External linksNature / PubMed:39537923
MethodsEM (single particle)
Resolution2.8 - 11.81 Å
Structure data

46728

9dby

EMDB-46728, PDB-9dby:
ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-46729: Map with best defined NZF RYBP of ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-46730: Map with best defined RING1B/BMI1 of ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Method: EM (single particle) / Resolution: 3.01 Å

EMDB-46731: Composite map of ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-46732: Overall map of ncPRC1RYBP bound to doubly modified H2AK119Ub nucleosome
Method: EM (single particle) / Resolution: 3.41 Å

EMDB-46733: ncPRC1RYBP bound to symmetric H2AK119Ub dinucleosome
Method: EM (single particle) / Resolution: 11.81 Å

EMDB-46734: Map focused on RYBP/Ub of ncPRC1RYBP bound to symmetric H2AK119Ub dinucleosome
Method: EM (single particle) / Resolution: 4.24 Å

EMDB-46735: Map focused on RING1B/BMI1 of ncPRC1RYBP bound to symmetric H2AK119Ub dinucleosome
Method: EM (single particle) / Resolution: 4.69 Å

EMDB-46736: Overall map of ncPRC1RYBP bound to asymmetric H2AK119Ub dinucleosome
Method: EM (single particle) / Resolution: 7.91 Å

EMDB-46737: Map focused on RYBP/Ub of ncPRC1RYBP bound to asymmetric H2AK119Ub dinucleosome
Method: EM (single particle) / Resolution: 6.19 Å

EMDB-46738: Map focused on RING1B/BMI1 of ncPRC1RYBP bound to asymmetric H2AK119Ub dinucleosome
Method: EM (single particle) / Resolution: 3.61 Å

46771

9dde

EMDB-46771, PDB-9dde:
ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome
Method: EM (single particle) / Resolution: 3.2 Å

46822

9dg3

EMDB-46822, PDB-9dg3:
ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome
Method: EM (single particle) / Resolution: 3.46 Å

46823

9dgg

EMDB-46823, PDB-9dgg:
ncPRC1RYBP bound to unmodified nucleosome
Method: EM (single particle) / Resolution: 2.98 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • homo sapiens (human)
  • xenopus laevis (African clawed frog)
  • synthetic construct (others)
KeywordsGENE REGULATION/DNA / DNA complex protein / hydrolase / structural protein / GENE REGULATION / GENE REGULATION-DNA complex / NUCLEAR PROTEIN/DNA / NUCLEAR PROTEIN-DNA complex

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