ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2
- Memorial Sloan Kettering Cancer Center, United States
- Weill Cornell Medicine, United States
Abstract
Mechanisms regulating mammalian meiotic progression are poorly understood. Here we identify mouse YTHDC2 as a critical component. A screen yielded a sterile mutant, 'ketu', caused by a Ythdc2 missense mutation. Mutant germ cells enter meiosis but proceed prematurely to aberrant metaphase and apoptosis, and display defects in transitioning from spermatogonial to meiotic gene expression programs. ketu phenocopies mutants lacking MEIOC, a YTHDC2 partner. Consistent with roles in post-transcriptional regulation, YTHDC2 is cytoplasmic, has 3′→5′ RNA helicase activity in vitro, and has similarity within its YTH domain to an N6-methyladenosine recognition pocket. Orthologs are present throughout metazoans, but are diverged in nematodes and, more dramatically, Drosophilidae, where Bgcn is descended from a Ythdc2 gene duplication. We also uncover similarity between MEIOC and Bam, a Bgcn partner unique to schizophoran flies. We propose that regulation of gene expression by YTHDC2-MEIOC is an evolutionarily ancient strategy for controlling the germline transition into meiosis.
Data availability
-
ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE108044).
-
YTHDC2 regulates spermatogenesis through promoting the translation of N6-methyladenosine-modified RNAPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE98085).
-
Cellular source and mechanisms of high transcriptome complexity in the mammalian testis (RNA-Seq cells)Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE43717).
Article and author information
Author details
Christopher D Lima
Funding
Howard Hughes Medical Institute
- M Rhyan Puno
- Christopher D Lima
- Scott Keeney
National Aeronautics and Space Administration (NNX14AH50G 15-15Omni2-0063)
- Cem Meydan
- Christopher E Mason
Bill and Melinda Gates Foundation (OPP1151054)
- Cem Meydan
- Christopher E Mason
Cycle for Survival
- Nathalie Lailler
Marie-Josée and Henry R. Kravis Center for Molecular Oncology
- Nathalie Lailler
Eunice Kennedy Shriver National Institute of Child Health and Human Development (R37 HD035455)
- Kathryn V Anderson
Human Frontier Science Program
- Devanshi Jain
National Cancer Institute (P30 CA008748)
- Nathalie Lailler
National Institute of General Medical Sciences (R35 GM118080)
- M Rhyan Puno
- Christopher D Lima
Starr Cancer Consortium (I9-A9-071)
- Cem Meydan
- Christopher E Mason
Bert L and N Kuggie Vallee Foundation
- Cem Meydan
- Christopher E Mason
WorldQuant Foundation
- Cem Meydan
- Christopher E Mason
Pershing Square Sohn Cancer Research Alliance
- Cem Meydan
- Christopher E Mason
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: This study was performed in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. All experiments conformed to regulatory standards and were approved by the Memorial Sloan Kettering Cancer Center (MSKCC) Institutional Animal Care and Use Committee under protocol #01-03-007.
Reviewing Editor
- Bernard de Massy, Institute of Human Genetics, CNRS UPR 1142, France
Publication history
- Received: August 1, 2017
- Accepted: January 22, 2018
- Accepted Manuscript published: January 23, 2018 (version 1)
- Version of Record published: March 1, 2018 (version 2)
Copyright
© 2018, Jain 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
-
- 3,187
- Page views
-
- 597
- Downloads
-
- 96
- Citations
Article citation count generated by polling the highest count across the following sources: Scopus, Crossref, PubMed Central.
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)
ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2
eLife 7:e30919.
https://doi.org/10.7554/eLife.30919
Further reading
-
- Chromosomes and Gene Expression
- Genetics and Genomics
Alternative polyadenylation yields many mRNA isoforms whose 3' termini occur disproportionately in clusters within 3' UTRs. Previously, we showed that profiles of poly(A) site usage are regulated by the rate of transcriptional elongation by RNA polymerase (Pol) II (Geisberg et., 2020). Pol II derivatives with slow elongation rates confer an upstream-shifted poly(A) profile, whereas fast Pol II strains confer a downstream-shifted poly(A) profile. Within yeast isoform clusters, these shifts occur steadily from one isoform to the next across nucleotide distances. In contrast, the shift between clusters from the last isoform of one cluster to the first isoform of the next - is much less pronounced, even over large distances. GC content in a region 13-30 nt downstream from isoform clusters correlates with their sensitivity to Pol II elongation rate. In human cells, the upstream shift caused by a slow Pol II mutant also occurs continuously at the nucleotide level within clusters, but not between them. Pol II occupancy increases just downstream of the most speed-sensitive poly(A) sites, suggesting a linkage between reduced elongation rate and cluster formation. These observations suggest that 1) Pol II elongation speed affects the nucleotide-level dwell time allowing polyadenylation to occur, 2) poly(A) site clusters are linked to the local elongation rate and hence do not arise simply by intrinsically imprecise cleavage and polyadenylation of the RNA substrate, 3) DNA sequence elements can affect Pol II elongation and poly(A) profiles, and 4) the cleavage/polyadenylation and Pol II elongation complexes are spatially, and perhaps physically, coupled so that polyadenylation occurs rapidly upon emergence of the nascent RNA from the Pol II elongation complex.
-
- Chromosomes and Gene Expression
- Structural Biology and Molecular Biophysics
Transcription factors (TFs) are classically attributed a modular construction, containing well-structured sequence-specific DNA-binding domains (DBDs) paired with disordered activation domains (ADs) responsible for protein-protein interactions targeting co-factors or the core transcription initiation machinery. However, this simple division of labor model struggles to explain why TFs with identical DNA-binding sequence specificity determined in vitro exhibit distinct binding profiles in vivo. The family of hypoxia-inducible factors (HIFs) offer a stark example: aberrantly expressed in several cancer types, HIF-1α and HIF-2α subunit isoforms recognize the same DNA motif in vitro – the hypoxia response element (HRE) – but only share a subset of their target genes in vivo, while eliciting contrasting effects on cancer development and progression under certain circumstances. To probe the mechanisms mediating isoform-specific gene regulation, we used live-cell single particle tracking (SPT) to investigate HIF nuclear dynamics and how they change upon genetic perturbation or drug treatment. We found that HIF-α subunits and their dimerization partner HIF-1β exhibit distinct diffusion and binding characteristics that are exquisitely sensitive to concentration and subunit stoichiometry. Using domain-swap variants, mutations, and a HIF-2α specific inhibitor, we found that although the DBD and dimerization domains are important, another main determinant of chromatin binding and diffusion behavior is the AD-containing intrinsically disordered region (IDR). Using Cut&Run and RNA-seq as orthogonal genomic approaches, we also confirmed IDR-dependent binding and activation of a specific subset of HIF target genes. These findings reveal a previously unappreciated role of IDRs in regulating the TF search and binding process that contribute to functional target site selectivity on chromatin.
