A versatile toolbox for determining IRES activity in cells and embryonic tissues
Widespread control of gene expression through translation has emerged as a key level of spatiotemporal regulation of protein expression. A prominent mechanism by which ribosomes can confer gene regulation is via internal ribosomal entry sites (IRESes), whose functions have however, remained difficult to rigorously characterize. Here we present a set of technologies in embryos and cells, including IRES-mediated translation of circular RNA (circRNA) reporters, single-molecule messenger (m)RNA isoform imaging, PacBio long-read sequencing, and isoform-sensitive mRNA quantification along polysome profiles as a new toolbox for understanding IRES regulation. Using these techniques, we investigate a broad range of cellular IRES RNA elements including Hox IRESes. We show IRES-dependent translation in circRNAs, as well as the relative expression, localization, and translation of an IRES-containing mRNA isoform in specific embryonic tissues. We thereby provide a new resource of technologies to elucidate the roles of versatile IRES elements in gene regulation and embryonic development.
Authors
- Naomi R. Genuth (ORCID: https://orcid.org/0000-0003-2240-1318)
- Martin Haimann
- Philipp Koch
- Teodorus Theo Susanto
- Kathrin Leppek (ORCID: https://orcid.org/0000-0002-8012-8076)
- Maria Barna (ORCID: https://orcid.org/0000-0002-6843-4396)
- Alena Khmelinskaia (ORCID: https://orcid.org/0000-0003-1584-9800)
- Gun Woo Byeon (ORCID: https://orcid.org/0000-0001-5022-4342)
- Saurabh Dey (ORCID: https://orcid.org/0000-0003-1432-3823)
- Zijian Zhang
Institutions
- Howard Hughes Medical Institute (US)
- University of Bonn (DE)
- University of Washington (US)
- University Hospital Bonn (DE)
- Life & Brain (Germany) (DE)
- Genome Institute of Singapore (SG)
- Ludwig-Maximilians-Universität München (DE)
- University of California, Berkeley (US)
- Stanford University (US)
Publication Details
- Journal
- The EMBO Journal
- Published
- 2025-03-13
- DOI
- https://doi.org/10.1038/s44318-025-00404-5
- Citations
- 7
- Primary Topic
- RNA modifications and cancer
- Type
- article
- Field-Weighted Citation Impact
- 5.64
Funders
- National Science Foundation
- University of California, Santa Cruz
- Helsingin Yliopisto
- University of Washington
- Agency for Science, Technology and Research
- Deutsche Forschungsgemeinschaft
- Rheinische Friedrich-Wilhelms-Universität Bonn
- National Institutes of Health
- University of California, San Francisco
- National Institute of Allergy and Infectious Diseases