Histone gene replacement reveals a post-transcriptional role for H3K36 in maintaining metazoan transcriptome fidelity
- The University of North Carolina at Chapel Hill, United States
- Harvard Medical School, United States
- National Institute of Environmental Heatlth Science, United States
- Harvard University, 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
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Histone gene replacement reveals a post-transcriptional role for H3K36 in maintaining metazoan transcriptome fidelityPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE96922).
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H3K36me3 abcam L3 Nuc Input expt.2225Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147189).
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H3K36me3 abcam L3 Nuc Input expt.2226Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147190).
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H3K36me3 abcam L3 Nuc ChIP expt.2259Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147191).
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H3K36me3 abcam L3 Nuc ChIP expt.2260Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147192).
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H3K36me1 L3 Nuc Input expt.2402Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147193).
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H3K36me1 L3 Nuc Input expt.2404Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147194).
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H3K36me1 L3 Nuc ChIP expt.2400Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147195).
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H3K36me1 L3 Nuc ChIP expt.2401Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147196).
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H3 antibody3 L3 Nuc Input expt.2222Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147289).
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H3 antibody3 L3 Nuc Input expt.2224Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147290).
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H3 antibody3 L3 Nuc ChIP expt.2241Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147291).
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H3 antibody3 L3 Nuc ChIP expt.2242Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147292).
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H3K36me2 W 14-16 hr OR Emb Input expt.2307Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147547).
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H3K36me2 W 14-16 hr OR Emb Input expt.2308Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147548).
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H3K36me2 W 14-16 hr OR Emb ChIP expt.2396Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147549).
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H3K36me2 W 14-16 hr OR Emb ChIP expt.2397Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147550).
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H4K16ac(M).L3 Input expt.2402Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1200107).
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H4K16ac(M).L3 Input expt.2404Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1200108).
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H4K16ac(M).L3 ChIP expt.2514Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1200109).
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H4K16ac(M).L3 ChIP expt.2515Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1200110).
Article and author information
Author details
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.
Reviewing Editor
- Elisa Izaurralde, Max Planck Institute for Developmental Biology, Germany
Version history
- Received: November 12, 2016
- Accepted: March 23, 2017
- Accepted Manuscript published: March 27, 2017 (version 1)
- Accepted Manuscript updated: April 7, 2017 (version 2)
- Version of Record published: April 25, 2017 (version 3)
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.
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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
Further reading
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Heat stress is a major threat to global crop production, and understanding its impact on plant fertility is crucial for developing climate-resilient crops. Despite the known negative effects of heat stress on plant reproduction, the underlying molecular mechanisms remain poorly understood. Here, we investigated the impact of elevated temperature on centromere structure and chromosome segregation during meiosis in Arabidopsis thaliana. Consistent with previous studies, heat stress leads to a decline in fertility and micronuclei formation in pollen mother cells. Our results reveal that elevated temperature causes a decrease in the amount of centromeric histone and the kinetochore protein BMF1 at meiotic centromeres with increasing temperature. Furthermore, we show that heat stress increases the duration of meiotic divisions and prolongs the activity of the spindle assembly checkpoint during meiosis I, indicating an impaired efficiency of the kinetochore attachments to spindle microtubules. Our analysis of mutants with reduced levels of centromeric histone suggests that weakened centromeres sensitize plants to elevated temperature, resulting in meiotic defects and reduced fertility even at moderate temperatures. These results indicate that the structure and functionality of meiotic centromeres in Arabidopsis are highly sensitive to heat stress, and suggest that centromeres and kinetochores may represent a critical bottleneck in plant adaptation to increasing temperatures.
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- Chromosomes and Gene Expression
Splicing is the stepwise molecular process by which introns are removed from pre-mRNA and exons are joined together to form mature mRNA sequences. The ordering and spatial distribution of these steps remain controversial, with opposing models suggesting splicing occurs either during or after transcription. We used single-molecule RNA FISH, expansion microscopy, and live-cell imaging to reveal the spatiotemporal distribution of nascent transcripts in mammalian cells. At super-resolution levels, we found that pre-mRNA formed clouds around the transcription site. These clouds indicate the existence of a transcription-site-proximal zone through which RNA move more slowly than in the nucleoplasm. Full-length pre-mRNA undergo continuous splicing as they move through this zone following transcription, suggesting a model in which splicing can occur post-transcriptionally but still within the proximity of the transcription site, thus seeming co-transcriptional by most assays. These results may unify conflicting reports of co-transcriptional versus post-transcriptional splicing.
