Evidence map›Paper›PMID 39368466›Full record

ArticleMolecular cell2024

The H3.3K36M oncohistone disrupts the establishment of epigenetic memory through loss of DNA methylation.

Joydeb Sinha, Jan F Nickels, Abby R Thurm, Connor H Ludwig, Bella N Archibald, Michaela M Hinks, Jun Wan, Dong Fang, Lacramioara Bintu

Abstract read
In one paragraph

Article in Molecular cell, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing 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

12 citing papers in PubMed.

  1. Review
  2. Article
  3. Review
  4. Article
  5. Epigenetic editing: from concept to clinic.Nature reviews. Drug discovery · 2026
    Review
  6. Article
  7. Many faces of mammalian NSD methyltransferases.Cellular & molecular biology letters · 2026
    Review
  8. Article
  9. Article
  10. Review
  11. Article
  12. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

9 authors.

Joydeb SinhaDepartment of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Jan F NickelsNiels Bohr Institute, University of Copenhagen, Copenhagen 2100, Denmark; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Abby R ThurmBiophysics Program, Stanford University, Stanford, CA 94305, USA.
Connor H LudwigDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Bella N ArchibaldDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Michaela M HinksDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Jun WanDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Dong FangLife Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.
Lacramioara BintuDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA. Electronic address: lbintu@stanford.edu.

Funding

Medical Scientist Training ProgramT32GM145402 · NIGMS · STANFORD UNIVERSITY · PI Katrin F. Chua · 2022 to 2026
$10.0M
Live-cell multiplex super-resolution imaging of chromatin state transitionsU01DK127419 · NIDDK · STANFORD UNIVERSITY · PI BINTU, LACRAMIOARA, BOETTIGER, ALISTAIR N. · 2020 to 2024
$5.3M
Single-cell analysis and synthetic control of mammalian chromatin dynamics and gene regulationR35GM128947 · NIGMS · STANFORD UNIVERSITY · PI Lacramioara Bintu · 2018 to 2026
$3.1M
Stanford ChEM-H Chemistry/Biology Interface Predoctoral Training ProgramT32GM139791 · NIGMS · STANFORD UNIVERSITY · PI Carolyn Bertozzi, Christine Jacobs-Wagner · 2021 to 2026
$2.4M
Molecular Pharmacology Training GrantT32GM113854 · NIGMS · STANFORD UNIVERSITY · PI MOCHLY-ROSEN, DARIA · 2015 to 2019
$1.1M
NIDDK NIH HHS U01 DK127419NIGMS NIH HHS R35 GM128947NIGMS NIH HHS T32 GM113854NIGMS NIH HHS T32 GM139791NIGMS NIH HHS T32 GM145402
6 · The paper itself

Abstract

Histone H3.3 is frequently mutated in tumors, with the lysine 36 to methionine mutation (K36M) being a hallmark of chondroblastomas. While it is known that H3.3K36M changes the epigenetic landscape, its effects on gene expression dynamics remain unclear. Here, we use a synthetic reporter to measure the effects of H3.3K36M on silencing and epigenetic memory after recruitment of the ZNF10 Krüppel-associated box (KRAB) domain, part of the largest class of human repressors and associated with H3K9me3 deposition. We find that H3.3K36M, which decreases H3K36 methylation and increases histone acetylation, leads to a decrease in epigenetic memory and promoter methylation weeks after KRAB release. We propose a model for establishment and maintenance of epigenetic memory, where the H3K36 methylation pathway is necessary to maintain histone deacetylation and convert H3K9me3 domains into DNA methylation for stable epigenetic memory. Our quantitative model can inform oncogenic mechanisms and guide development of epigenetic editing tools.

Indexed as

DNA MethylationEpigenesis, GeneticHistonesMutationAcetylationCell Line, TumorEpigenetic MemoryGene Expression Regulation, NeoplasticHumansLysinePromoter Regions, GeneticRepressor ProteinsHistonesLysineRepressor ProteinsDNA methylationepigenetic memoryH3.3K36MH3K36me2H3K36me3heterochromatinKRABNSD1oncohistoneSETD2

Identifiers

PMID39368466
PMCPMC11526022

What OpenQuestion holds

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Registered trials

None linked

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.