Histone gene replacement reveals a post-transcriptional role for H3K36 in maintaining metazoan transcriptome fidelity

  1. Michael P Meers
  2. Telmo Henriques
  3. Christopher A Lavender
  4. Daniel J McKay
  5. Brian D Strahl
  6. Robert J Duronio
  7. Karen Adelman
  8. A Gregory Matera  Is a corresponding author
  1. The University of North Carolina at Chapel Hill, United States
  2. Harvard Medical School, United States
  3. National Institute of Environmental Heatlth Science, United States

Abstract

Histone H3 lysine 36 methylation (H3K36me) is thought to participate in a host of co-transcriptional regulatory events. To study the function of this residue independent from the enzymes that modify it, we used a 'histone replacement' system in Drosophila to generate a non-modifiable H3K36 lysine-to-arginine (H3K36R) mutant. We observed global dysregulation of mRNA levels in H3K36R animals that correlates with the incidence of H3K36me3. Similar to previous studies, we found that mutation of H3K36 also resulted in H4 hyperacetylation. However, neither cryptic transcription initiation, nor alternative pre-mRNA splicing, contributed to the observed changes in expression, in contrast with previously reported roles for H3K36me. Interestingly, knockdown of the RNA surveillance nuclease, Xrn1, and members of the CCR4-Not deadenylase complex, restored mRNA levels for a class of downregulated, H3K36me3-rich genes. We propose a post-transcriptional role for modification of replication-dependent H3K36 in the control of metazoan gene expression.

Data availability

The following data sets were generated
The following previously published data sets were used
    1. Elgin S
    (2013) H3K36me3 abcam L3 Nuc Input expt.2225
    Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147189).
    1. Elgin S
    (2013) H3K36me3 abcam L3 Nuc Input expt.2226
    Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147190).
    1. Elgin S
    (2013) H3K36me3 abcam L3 Nuc ChIP expt.2259
    Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147191).
    1. Elgin S
    (2013) H3K36me3 abcam L3 Nuc ChIP expt.2260
    Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147192).
    1. Elgin S
    (2013) H3K36me1 L3 Nuc Input expt.2402
    Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147193).
    1. Elgin S
    (2013) H3K36me1 L3 Nuc Input expt.2404
    Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147194).
    1. Elgin S
    (2013) H3K36me1 L3 Nuc ChIP expt.2400
    Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147195).
    1. Elgin S
    (2013) H3K36me1 L3 Nuc ChIP expt.2401
    Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147196).
    1. Elgin S
    (2013) H3 antibody3 L3 Nuc Input expt.2222
    Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147289).
    1. Elgin S
    (2013) H3 antibody3 L3 Nuc Input expt.2224
    Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147290).
    1. Elgin S
    (2013) H3 antibody3 L3 Nuc ChIP expt.2241
    Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147291).
    1. Elgin S
    (2013) H3 antibody3 L3 Nuc ChIP expt.2242
    Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147292).
    1. Karpen G
    (2013) H3K36me2 W 14-16 hr OR Emb Input expt.2307
    Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147547).
    1. Karpen G
    (2013) H3K36me2 W 14-16 hr OR Emb Input expt.2308
    Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147548).
    1. Karpen G
    (2013) H3K36me2 W 14-16 hr OR Emb ChIP expt.2396
    Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147549).
    1. Karpen G
    (2013) H3K36me2 W 14-16 hr OR Emb ChIP expt.2397
    Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147550).
    1. Elgin S
    (2013) H4K16ac(M).L3 Input expt.2402
    Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1200107).
    1. Elgin S
    (2013) H4K16ac(M).L3 Input expt.2404
    Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1200108).
    1. Elgin S
    (2013) H4K16ac(M).L3 ChIP expt.2514
    Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1200109).
    1. Elgin S
    (2013) H4K16ac(M).L3 ChIP expt.2515
    Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1200110).

Article and author information

Author details

  1. Michael P Meers

    Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, United States
    Competing interests
    No competing interests declared.
  2. Telmo Henriques

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
    Competing interests
    No competing interests declared.
  3. Christopher A Lavender

    Integrative Bioinformatics Support Group, National Institute of Environmental Heatlth Science, Research Triangle Park, United States
    Competing interests
    No competing interests declared.
  4. Daniel J McKay

    Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, United States
    Competing interests
    No competing interests declared.
  5. Brian D Strahl

    Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, United States
    Competing interests
    No competing interests declared.
  6. Robert J Duronio

    Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, United States
    Competing interests
    No competing interests declared.
  7. Karen Adelman

    Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Heatlth Science, Boston, United States
    Competing interests
    Karen Adelman, Reviewing editor, eLife.
  8. A Gregory Matera

    Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, United States
    For correspondence
    matera@unc.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6406-0630

Funding

National Institutes of Health (For use of Harvard TRiP lines,R01-GM084947)

  • Michael P Meers
  • A Gregory Matera

National Cancer Institute (Ruth L. Kirschstein Predoctoral Fellowship,F31-CA177088)

  • Michael P Meers

Office of the Director (Epigenomics Roadmap Project,R01-DA036897)

  • Brian D Strahl
  • Robert J Duronio
  • A Gregory Matera

National Institute of Environmental Health Sciences (Intramural Research Program,Z01-ES101987)

  • Karen Adelman

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

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Metrics

  • 3,905
    views
  • 838
    downloads
  • 50
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

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)

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

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

  1. Michael P Meers
  2. Telmo Henriques
  3. Christopher A Lavender
  4. Daniel J McKay
  5. Brian D Strahl
  6. Robert J Duronio
  7. Karen Adelman
  8. A Gregory Matera
(2017)
Histone gene replacement reveals a post-transcriptional role for H3K36 in maintaining metazoan transcriptome fidelity
eLife 6:e23249.
https://doi.org/10.7554/eLife.23249

Share this article

https://doi.org/10.7554/eLife.23249

Further reading

    1. Chromosomes and Gene Expression
    2. Evolutionary Biology
    Gülnihal Kavaklioglu, Alexandra Podhornik ... Christian Seiser
    Research Article

    Repression of retrotransposition is crucial for the successful fitness of a mammalian organism. The domesticated transposon protein L1TD1, derived from LINE-1 (L1) ORF1p, is an RNA-binding protein that is expressed only in some cancers and early embryogenesis. In human embryonic stem cells, it is found to be essential for maintaining pluripotency. In cancer, L1TD1 expression is highly correlative with malignancy progression and as such considered a potential prognostic factor for tumors. However, its molecular role in cancer remains largely unknown. Our findings reveal that DNA hypomethylation induces the expression of L1TD1 in HAP1 human tumor cells. L1TD1 depletion significantly modulates both the proteome and transcriptome and thereby reduces cell viability. Notably, L1TD1 associates with L1 transcripts and interacts with L1 ORF1p protein, thereby facilitating L1 retrotransposition. Our data suggest that L1TD1 collaborates with its ancestral L1 ORF1p as an RNA chaperone, ensuring the efficient retrotransposition of L1 retrotransposons, rather than directly impacting the abundance of L1TD1 targets. In this way, L1TD1 might have an important role not only during early development but also in tumorigenesis.

    1. Chromosomes and Gene Expression
    Shihui Chen, Carolyn Marie Phillips
    Research Article

    RNA interference (RNAi) is a conserved pathway that utilizes Argonaute proteins and their associated small RNAs to exert gene regulatory function on complementary transcripts. While the majority of germline-expressed RNAi proteins reside in perinuclear germ granules, it is unknown whether and how RNAi pathways are spatially organized in other cell types. Here, we find that the small RNA biogenesis machinery is spatially and temporally organized during Caenorhabditis elegans embryogenesis. Specifically, the RNAi factor, SIMR-1, forms visible concentrates during mid-embryogenesis that contain an RNA-dependent RNA polymerase, a poly-UG polymerase, and the unloaded nuclear Argonaute protein, NRDE-3. Curiously, coincident with the appearance of the SIMR granules, the small RNAs bound to NRDE-3 switch from predominantly CSR-class 22G-RNAs to ERGO-dependent 22G-RNAs. NRDE-3 binds ERGO-dependent 22G-RNAs in the somatic cells of larvae and adults to silence ERGO-target genes; here we further demonstrate that NRDE-3-bound, CSR-class 22G-RNAs repress transcription in oocytes. Thus, our study defines two separable roles for NRDE-3, targeting germline-expressed genes during oogenesis to promote global transcriptional repression, and switching during embryogenesis to repress recently duplicated genes and retrotransposons in somatic cells, highlighting the plasticity of Argonaute proteins and the need for more precise temporal characterization of Argonaute-small RNA interactions.