mRNA initiation and termination are spatially coordinated
Transcriptional initiation and termination decisions drive messenger RNA (mRNA) isoform diversity but the relationship between them remains poorly understood. By systematically profiling joint usage of transcription start and end sites, we observed that mRNA using upstream starts preferentially use upstream end sites and that the usage of downstream sites is similarly coupled. Our results suggest a positional initiation termination axis (PITA), in which usage of alternative terminal sites are coupled based on their genomic order. PITA is enriched in longer genes with distinct chromatin features. We find that mRNA 5' start choice directly influences 3' ends depending on RNA polymerase II trafficking speed. Our results indicate that spatial organization and transcriptional dynamics couple transcription initiation and mRNA 3' end decisions to define mRNA isoform expression.
Authors
- Valeria C. Sanabria (ORCID: https://orcid.org/0000-0002-3138-2393)
- Athma A. Pai (ORCID: https://orcid.org/0000-0002-7995-9948)
- Sergey V. Venev (ORCID: https://orcid.org/0000-0002-1507-7460)
- Christine L. Carroll (ORCID: https://orcid.org/0009-0005-9992-6296)
- Job Dekker (ORCID: https://orcid.org/0000-0001-5631-0698)
- Maritere Urióstegui-Arcos (ORCID: https://orcid.org/0000-0002-5077-1714)
- Ezequiel Calvo-Roitberg (ORCID: https://orcid.org/0000-0002-2431-515X)
- Ana Fiszbein (ORCID: https://orcid.org/0000-0002-4190-5901)
- Joseph Paquette (ORCID: https://orcid.org/0009-0004-8536-8951)
- Steven T. Mick (ORCID: https://orcid.org/0000-0002-7781-7831)
- Gyeungyun Kim (ORCID: https://orcid.org/0000-0003-4382-503X)
Institutions
- Boston University (US)
- Howard Hughes Medical Institute (US)
- University of Massachusetts Chan Medical School (US)
- University of Massachusetts Boston (US)
Publication Details
- Journal
- Science
- Published
- 2025-10-09
- DOI
- https://doi.org/10.1126/science.ado8279
- Citations
- 7
- Primary Topic
- RNA Research and Splicing
- Type
- article
- Field-Weighted Citation Impact
- 5.64