Internal ribosome entry sites enhance translation in <i>trans</i> in antisense non-coding SINEUP and circular RNAs
Sequences in the 5'-untranslated regions of cellular and viral mRNAs can function as internal ribosome entry sites (IRESs), driving cis-acting translation of the downstream protein-coding open reading frame. Here we demonstrate that RNA sequences with either newly identified or well-characterized IRES activity can also induce trans-acting translation of an independent mRNA species through an antisense sequence. SINEUPs are antisense long non-coding RNAs that enhance the translation of overlapping sense mRNAs in trans by employing two critical domains: the invSINEB2 sequence, which up-regulates translation (effector domain), and an antisense region providing target specificity (binding domain). First, we show that the invSINEB2 from the natural SINEUP AS Uchl1 RNA acts as an IRES when functioning in cis. Next, we establish that known viral and cellular sequences with IRES activity can operate in trans as an effector domain in synthetic SINEUPs. To identify natural IRES-containing non-coding RNAs with transactivity, we found that the non-coding hsa_circ_0 085 533 (circMyc), transcribed from the c-myc locus, enhances protein expression of PX Domain Containing Serine/Threonine Kinase Like (PXK) by promoting mRNA association with polysomes through antisense sequences. These results suggest that SINEUPs and some circular RNAs are trans-acting IRESs, expanding the repertoire of molecular mechanisms to regulate translation.
Authors
- Angelita Simonetti (ORCID: https://orcid.org/0000-0001-7983-4945)
- S. Zucchelli (ORCID: https://orcid.org/0000-0003-4556-2990)
- Mattia D’Agostino (ORCID: https://orcid.org/0000-0002-1711-6996)
- Stefano Gustincich (ORCID: https://orcid.org/0000-0002-2749-2514)
- Andrea Armirotti (ORCID: https://orcid.org/0000-0002-3766-8755)
- Pierre Lau (ORCID: https://orcid.org/0000-0002-7367-364X)
- Abraham Tettey‐Matey (ORCID: https://orcid.org/0000-0001-9260-0940)
- Valerio Di Carlo (ORCID: https://orcid.org/0000-0002-5099-0685)
- Federica Maniscalco (ORCID: https://orcid.org/0000-0002-9757-6043)
- Margherita Scarpato
- Carlotta Bon (ORCID: https://orcid.org/0000-0002-7443-4659)
- Devid Damiani (ORCID: https://orcid.org/0000-0003-2962-6296)
- Sabrina D’Agostino (ORCID: https://orcid.org/0000-0002-4858-8873)
- Denisa Smělá (ORCID: https://orcid.org/0000-0003-0368-2409)
- Omar Peruzzo
- Stefano Espinoza (ORCID: https://orcid.org/0000-0002-3048-4822)
- Massimiliano Volpe (ORCID: https://orcid.org/0000-0003-4184-5264)
- Federico Ansaloni (ORCID: https://orcid.org/0000-0002-6344-4931)
- Clarissa Braccia (ORCID: https://orcid.org/0000-0002-6343-9614)
- Claudio Santoro (ORCID: https://orcid.org/0000-0002-4552-9624)
- Gian Gaetano Tartaglia
- Bianca Pierattini (ORCID: https://orcid.org/0000-0001-5023-7629)
- Gloria Ros (ORCID: https://orcid.org/0000-0003-2214-5254)
- Laura Broglia (ORCID: https://orcid.org/0000-0003-2099-7373)
- Piero Carninci (ORCID: https://orcid.org/0000-0001-7202-7243)
- Francesca Persichetti (ORCID: https://orcid.org/0000-0002-9804-644X)
- Luca Pandolfini (ORCID: https://orcid.org/0000-0003-1444-8167)
- Remo Sanges (ORCID: https://orcid.org/0000-0002-5047-9713)
- Elías Bechara (ORCID: https://orcid.org/0000-0003-2551-4991)
Institutions
- Università degli Studi del Piemonte Orientale “Amedeo Avogadro” (IT)
- Scuola Internazionale Superiore di Studi Avanzati (IT)
- Italian Institute of Technology (IT)
- Human Technopole (IT)
- Architecture et Réactivité de l'arN (FR)
- RIKEN Center for Integrative Medical Sciences (JP)
Publication Details
- Journal
- Nucleic Acids Research
- Published
- 2025-08-03
- DOI
- https://doi.org/10.1093/nar/gkaf788
- Citations
- 4
- Primary Topic
- Circular RNAs in diseases
- Type
- article
- Field-Weighted Citation Impact
- 3.22
Funders
- Ministero dell’Istruzione, dell’Università e della Ricerca