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TitleUbiquitinated histone H2B as gatekeeper of the nucleosome acidic patch.
Journal, issue, pagesNucleic Acids Res, Vol. 52, Issue 16, Page 9978-9995, Year 2024
Publish dateSep 9, 2024
AuthorsChad W Hicks / Sanim Rahman / Susan L Gloor / James K Fields / Natalia Ledo Husby / Anup Vaidya / Keith E Maier / Michael Morgan / Michael-Christopher Keogh / Cynthia Wolberger /
PubMed AbstractMonoubiquitination of histones H2B-K120 (H2BK120ub) and H2A-K119 (H2AK119ub) play opposing roles in regulating transcription and chromatin compaction. H2BK120ub is a hallmark of actively transcribed ...Monoubiquitination of histones H2B-K120 (H2BK120ub) and H2A-K119 (H2AK119ub) play opposing roles in regulating transcription and chromatin compaction. H2BK120ub is a hallmark of actively transcribed euchromatin, while H2AK119ub is highly enriched in transcriptionally repressed heterochromatin. Whereas H2BK120ub is known to stimulate the binding or activity of various chromatin-modifying enzymes, this post-translational modification (PTM) also interferes with the binding of several proteins to the nucleosome H2A/H2B acidic patch via an unknown mechanism. Here, we report cryoEM structures of an H2BK120ub nucleosome showing that ubiquitin adopts discrete positions that occlude the acidic patch. Molecular dynamics simulations show that ubiquitin remains stably positioned over this nucleosome region. By contrast, our cryoEM structures of H2AK119ub nucleosomes show ubiquitin adopting discrete positions that minimally occlude the acidic patch. Consistent with these observations, H2BK120ub, but not H2AK119ub, abrogates nucleosome interactions with acidic patch-binding proteins RCC1 and LANA, and single-domain antibodies specific to this region. Our results suggest a mechanism by which H2BK120ub serves as a gatekeeper to the acidic patch and point to distinct roles for histone H2AK119 and H2BK120 ubiquitination in regulating protein binding to nucleosomes.
External linksNucleic Acids Res / PubMed:39149911 / PubMed Central
MethodsEM (single particle)
Resolution2.93 - 3.47 Å
Structure data

29767

8g6g

EMDB-29767, PDB-8g6g:
H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 5
Method: EM (single particle) / Resolution: 2.93 Å

29769

8g6h

EMDB-29769, PDB-8g6h:
H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 6
Method: EM (single particle) / Resolution: 3.06 Å

29778

8g6q

EMDB-29778, PDB-8g6q:
H2AK119ub-modified nucleosome ubiquitin position 1
Method: EM (single particle) / Resolution: 3.41 Å

29781

8g6s

EMDB-29781, PDB-8g6s:
H2AK119ub-modified nucleosome ubiquitin position 2
Method: EM (single particle) / Resolution: 3.47 Å

42898

8v25

EMDB-42898, PDB-8v25:
H2BK120ub-modified nucleosome ubiquitin position 1
Method: EM (single particle) / Resolution: 3.32 Å

42899

8v26

EMDB-42899, PDB-8v26:
H2BK120ub-modified nucleosome ubiquitin position 2
Method: EM (single particle) / Resolution: 3.33 Å

42900

8v27

EMDB-42900, PDB-8v27:
H2BK120ub-modified nucleosome ubiquitin position 3
Method: EM (single particle) / Resolution: 3.34 Å

42901

8v28

EMDB-42901, PDB-8v28:
H2BK120ub-modified nucleosome ubiquitin position 4
Method: EM (single particle) / Resolution: 3.36 Å

Source
  • xenopus laevis (African clawed frog)
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsDNA BINDING PROTEIN/DNA / nucleosome / ubiquitin / histone / chromatin / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex

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