Evidence map›Paper›PMID 40716115›Full record

ArticleProtein science : a publication of the Protein Society2025

An intrinsically disordered region of Ubp10 regulates its binding and activity on ubiquitinated histone substrates.

Anneliese M Faustino, Melesse Nune, Raquel Merino-Urteaga, Edgar Manriquez-Sandoval, Matthew Poyton, Taekjip Ha, Cynthia Wolberger, Stephen D Fried

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Protein science : a publication of the Protein Society, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Anneliese M FaustinoDepartment of Chemistry, Johns Hopkins University, Baltimore, Maryland, USA.ORCID 0000-0003-1743-9186
Melesse NuneDepartment of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.ORCID 0000-0002-3385-3320
Raquel Merino-UrteagaDepartment of Biology, Johns Hopkins University, Baltimore, Maryland, USA.ORCID 0009-0002-9367-0435
Edgar Manriquez-SandovalT. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA.ORCID 0000-0001-7284-1237
Matthew PoytonDepartment of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
Taekjip HaDepartment of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.ORCID 0000-0003-2195-6258
Cynthia WolbergerDepartment of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.ORCID 0000-0001-8578-2969
Stephen D FriedDepartment of Chemistry, Johns Hopkins University, Baltimore, Maryland, USA.ORCID 0000-0003-2494-2193

Funding

PROGRAM IN MOLECULAR BIOPHYSICST32GM008403 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI BARRICK, DOUGLAS E. · 1990 to 2019
$13.5M
Mechanistic studies of chromatin modification in transcription regulationR35GM130393 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI Cynthia Wolberger · 2019 to 2026
$7.3M
Single Molecule Studies of Nucleic Acids RemodelingR35GM122569 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI Taekjip Ha · 2017 to 2026
$3.5M
Watching Proteins Fold (or Misfold) in vivo with Mass SpectrometryDP2GM140926 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI FRIED, STEPHEN DAVID · 2020 to 2020
$2.3M
Characterizing SWR1-mediated Histone Exchange at the Single Molecule LevelF32GM128299 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI POYTON, MATTHEW F. · 2018 to 2020
$192k
Ada Sinz Hill fellowshipAlfred P. Sloan FoundationCamille and Henry Dreyfus FoundationHoward Hughes Medical InstituteNational Science Foundation MCB2045844NIGMS NIH HHS DP2 GM140926NIGMS NIH HHS DP2-GM140926NIGMS NIH HHS F32 GM128299NIGMS NIH HHS R35 GM122569NIGMS NIH HHS R35-GM122569NIGMS NIH HHS R35 GM130393NIGMS NIH HHS R35-GM130393NIGMS NIH HHS T32 GM008403NSF Graduate Research FellowshipSloan Foundation
6 · The paper itself

Abstract

Monoubiquitinated histone H2B at K123 in yeast (K120 in humans) is a transient modification that is both attached and removed during transcription. H2B is ubiquitinated in yeast by the E2/E3 pair, Rad6/Bre1, and deubiquitinated by two enzymes, Ubp8 and Ubp10. Previous studies had shown that Ubp10 has higher activity on ubiquitinated H2A/H2B dimers than on intact nucleosomes, but that activity on nucleosomes is higher in the presence of the histone chaperone, FACT. By contrast, the Ubp8 complex has equal activity on both histone substrates and is unaffected by FACT. We report here the results of single-molecule FRET experiments showing that FACT unwraps DNA and evicts ubiquitinated H2A/H2B dimers, the preferred substrate of Ubp10. To explore the basis for the differing activity of Ubp10 on ubiquitinated H2A/H2B dimers and nucleosomes, we employed crosslinking mass spectrometry combined with structural modeling. These studies revealed that Ubp10 forms a different set of interactions with H2A/H2B in free versus nucleosomal states. Acidic stretches within the N-terminal intrinsically disordered region (IDR) of Ubp10 interact extensively with H2A/H2B heterodimers, whereas this portion of Ubp10 interacts more with the tails of histones H3 and H4 in the nucleosome. The importance of these interactions for affinity is consistent with binding studies showing the IDR is necessary for substrate interactions. Structural modeling using the crosslinks as constraints suggests that the complex formed by Ubp10 with free H2A/H2B dimers could not be formed within a nucleosome due to steric clash with the DNA, H3, and H4, thereby explaining its low activity on ubiquitinated nucleosomes.

Indexed as

HistonesIntrinsically Disordered ProteinsSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsModels, MolecularNucleosomesProtein BindingUbiquitinationUbiquitin ThiolesteraseHistonesIntrinsically Disordered ProteinsNucleosomesSaccharomyces cerevisiae ProteinsUbiquitin ThiolesteraseUBP10 protein, S cerevisiaecrosslinking mass spectrometrydeubiqutinaseFACTsingle‐molecule FRETubiquitinated histoneUbp10

Identifiers

PMID40716115
PMCPMC12679948

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.