1. Chromosomes and Gene Expression
Download icon

Surprising phenotypic diversity of cancer-associated mutations of Gly 34 in the histone H3 tail

  1. Brandon R Lowe
  2. Rajesh K Yadav
  3. Ryan A Henry
  4. Patrick Schreiner
  5. Atsushi Matsuda
  6. Alfonso G Fernandez
  7. David Finkelstein
  8. Margaret Campbell
  9. Satish Kallappagoudar
  10. Carolyn M Jablonowski
  11. Andrew J Andrews
  12. Yasushi Hiraoka
  13. Janet F Partridge  Is a corresponding author
  1. St Jude Children's Research Hospital, United States
  2. Fox Chase Cancer Center, United States
  3. National Institute of Information and Communications Technology, Japan
  4. Osaka University, Japan
Research Advance
  • Cited 1
  • Views 870
  • Annotations
Cite this article as: eLife 2021;10:e65369 doi: 10.7554/eLife.65369

Abstract

Sequencing of cancer genomes has identified recurrent somatic mutations in histones, termed oncohistones, which are frequently poorly understood. Previously we showed that fission yeast expressing only the H3.3G34R mutant identified in aggressive pediatric glioma had reduced H3K36 trimethylation and acetylation, increased genomic instability and replicative stress, and defective homology-dependent DNA damage repair (Yadav et al., 2017). Here we show that surprisingly distinct phenotypes result from G34V (also in glioma) and G34W (giant cell tumors of bone) mutations, differentially affecting H3K36 modifications, subtelomeric silencing, genomic stability, sensitivity to irradiation, alkylating agents, hydroxyurea and influencing DNA repair. In cancer, only one of thirty alleles encoding H3 is mutated. Whilst co-expression of wild-type H3 rescues most G34 mutant phenotypes, G34R causes dominant hydroxyurea sensitivity and homologous recombination defects, and dominant subtelomeric silencing. Together, these studies demonstrate the complexity associated with different substitutions at even a single residue in H3 and highlight the utility of genetically tractable systems for their analysis.

Data availability

RNAseq data have been deposited in GEO under accession code GSE162572.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Brandon R Lowe

    Department of Pathology, St Jude Children's Research Hospital, Memphis, United States
    Competing interests
    The authors declare that no competing interests exist.

  2. Rajesh K Yadav

    Pathology, St Jude Children's Research Hospital, Memphis, United States
    Competing interests
    The authors declare that no competing interests exist.

  3. Ryan A Henry

    Cancer Biology, Fox Chase Cancer Center, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.

  4. Patrick Schreiner

    Center for Applied Bioinformatics, Dept. of Bioinformatics, St Jude Children's Research Hospital, Memphis, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5391-2642

  5. Atsushi Matsuda

    Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Japan
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0510-213X

  6. Alfonso G Fernandez

    Pathology, St Jude Children's Research Hospital, Memphis, United States
    Competing interests
    The authors declare that no competing interests exist.

  7. David Finkelstein

    Computational Biology, St Jude Children's Research Hospital, Memphis, United States
    Competing interests
    The authors declare that no competing interests exist.

  8. Margaret Campbell

    Pathology, St Jude Children's Research Hospital, Memphis, United States
    Competing interests
    The authors declare that no competing interests exist.

  9. Satish Kallappagoudar

    Pathology, St Jude Children's Research Hospital, Memphis, United States
    Competing interests
    The authors declare that no competing interests exist.

  10. Carolyn M Jablonowski

    Pathology, St Jude Children's Research Hospital, Memphis, United States
    Competing interests
    The authors declare that no competing interests exist.

  11. Andrew J Andrews

    Cancer Biology, Fox Chase Cancer Center, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.

  12. Yasushi Hiraoka

    Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9407-8228

  13. Janet F Partridge

    Pathology, St Jude Children's Research Hospital, Memphis, United States
    For correspondence
    janet.partridge@stjude.org
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1102-6305

Funding

St. Baldrick's Foundation (Research grant with generous support from the Henry Cermak fund for Pediatric Cancer Research.)

  • Janet F Partridge

National Cancer Institute (Cancer Center support grant (NCI CCSG 2 P30 CA21765))

  • Rajesh K Yadav
  • Janet F Partridge

American Lebanese Syrian Associated Charities

  • Brandon R Lowe
  • Rajesh K Yadav
  • Patrick Schreiner
  • Alfonso G Fernandez
  • David Finkelstein
  • Margaret Campbell
  • Satish Kallappagoudar
  • Carolyn M Jablonowski
  • Janet F Partridge

National Institutes of Health (NIH GM102503)

  • Andrew J Andrews

Fox Chase Cancer Center (Board of Associates Fellowship)

  • Ryan A Henry

Japan Society for the Promotion of Science (Kakheni grant JP19H03202 and JP20H05894)

  • Atsushi Matsuda

Japan Society for the Promotion of Science (Kakheni grants JP18H05533 and JP20H00454)

  • Yasushi Hiraoka

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Jerry L Workman, Stowers Institute for Medical Research, United States

Publication history

  1. Received: December 2, 2020
  2. Accepted: January 30, 2021
  3. Accepted Manuscript published: February 1, 2021 (version 1)
  4. Version of Record published: February 9, 2021 (version 2)

Copyright

© 2021, Lowe et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 870
    Page views
  • 181
    Downloads
  • 1
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Categories and tags

Research organism

Further reading

    1. Chromosomes and Gene Expression

    Histone H3G34R mutation causes replication stress, homologous recombination defects and genomic instability in S. pombe

    Rajesh K Yadav et al.
    Research Article

    Recurrent somatic mutations of H3F3A in aggressive pediatric high-grade gliomas generate K27M or G34R/V mutant histone H3.3. H3.3-G34R/V mutants are common in tumors with mutations in p53 and ATRX, an H3.3-specific chromatin remodeler. To gain insight into the role of H3-G34R, we generated fission yeast that express only the mutant histone H3. H3-G34R specifically reduces H3K36 tri-methylation and H3K36 acetylation, and mutants show partial transcriptional overlap with set2 deletions. H3-G34R mutants exhibit genomic instability and increased replication stress, including slowed replication fork restart, although DNA replication checkpoints are functional. H3-G34R mutants are defective for DNA damage repair by homologous recombination (HR), and have altered HR protein dynamics in both damaged and untreated cells. These data suggest H3-G34R slows resolution of HR-mediated repair and that unresolved replication intermediates impair chromosome segregation. This analysis of H3-G34R mutant fission yeast provides mechanistic insight into how G34R mutation may promote genomic instability in glioma.

    1. Chromosomes and Gene Expression

    SUV39 SET domains mediate crosstalk of heterochromatic histone marks

    Alessandro Stirpe et al.
    Research Article

    The SUV39 class of methyltransferase enzymes deposits histone H3 lysine 9 di- and trimethylation (H3K9me2/3), the hallmark of constitutive heterochromatin. How these enzymes are regulated to mark specific genomic regions as heterochromatic is poorly understood. Clr4 is the sole H3K9me2/3 methyltransferase in the fission yeast Schizosaccharomyces pombe, and recent evidence suggests that ubiquitination of lysine 14 on histone H3 (H3K14ub) plays a key role in H3K9 methylation. However, the molecular mechanism of this regulation and its role in heterochromatin formation remain to be determined. Our structure-function approach shows that the H3K14ub substrate binds specifically and tightly to the catalytic domain of Clr4, and thereby stimulates the enzyme by over 250-fold. Mutations that disrupt this mechanism lead to a loss of H3K9me2/3 and abolish heterochromatin silencing similar to clr4 deletion. Comparison with mammalian SET domain proteins suggests that the Clr4 SET domain harbors a conserved sensor for H3K14ub, which mediates licensing of heterochromatin formation.

    1. Chromosomes and Gene Expression
    2. Microbiology and Infectious Disease

    A nascent polypeptide sequence modulates DnaA translation elongation in response to nutrient availability

    Michele Felletti et al.
    Research Article

    The ability to regulate DNA replication initiation in response to changing nutrient conditions is an important feature of most cell types. In bacteria, DNA replication is triggered by the initiator protein DnaA, which has long been suggested to respond to nutritional changes; nevertheless, the underlying mechanisms remain poorly understood. Here, we report a novel mechanism that adjusts DnaA synthesis in response to nutrient availability in Caulobacter crescentus. By performing a detailed biochemical and genetic analysis of the dnaA mRNA, we identified a sequence downstream of the dnaA start codon that inhibits DnaA translation elongation upon carbon exhaustion. Our data show that the corresponding peptide sequence, but not the mRNA secondary structure or the codon choice, is critical for this response, suggesting that specific amino acids in the growing DnaA nascent chain tune translational efficiency. Our study provides new insights into DnaA regulation and highlights the importance of translation elongation as a regulatory target. We propose that translation regulation by nascent chain sequences, like the one described, might constitute a general strategy for modulating the synthesis rate of specific proteins under changing conditions.