Histone gene replacement reveals a post-transcriptional role for H3K36 in maintaining metazoan transcriptome fidelity
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
-
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).
-
H3K36me3 abcam L3 Nuc Input expt.2225Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147189).
-
H3K36me3 abcam L3 Nuc Input expt.2226Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147190).
-
H3K36me3 abcam L3 Nuc ChIP expt.2259Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147191).
-
H3K36me3 abcam L3 Nuc ChIP expt.2260Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147192).
-
H3K36me1 L3 Nuc Input expt.2402Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147193).
-
H3K36me1 L3 Nuc Input expt.2404Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147194).
-
H3K36me1 L3 Nuc ChIP expt.2400Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147195).
-
H3K36me1 L3 Nuc ChIP expt.2401Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147196).
-
H3 antibody3 L3 Nuc Input expt.2222Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147289).
-
H3 antibody3 L3 Nuc Input expt.2224Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147290).
-
H3 antibody3 L3 Nuc ChIP expt.2241Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147291).
-
H3 antibody3 L3 Nuc ChIP expt.2242Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147292).
-
H3K36me2 W 14-16 hr OR Emb Input expt.2307Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147547).
-
H3K36me2 W 14-16 hr OR Emb Input expt.2308Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147548).
-
H3K36me2 W 14-16 hr OR Emb ChIP expt.2396Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147549).
-
H3K36me2 W 14-16 hr OR Emb ChIP expt.2397Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1147550).
-
H4K16ac(M).L3 Input expt.2402Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1200107).
-
H4K16ac(M).L3 Input expt.2404Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1200108).
-
H4K16ac(M).L3 ChIP expt.2514Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSM1200109).
-
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.
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
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)
Further reading
-
- Chromosomes and Gene Expression
- Evolutionary Biology
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.
-
- Chromosomes and Gene Expression
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.