Widespread 3′UTR capped RNAs derive from G-rich regions in proximity to AGO2 binding sites
The 3' untranslated region (3'UTR) plays a crucial role in determining mRNA stability, localisation, translation and degradation. Cap analysis of gene expression (CAGE), a method for the detection of capped 5' ends of mRNAs, additionally reveals a large number of apparently 5' capped RNAs derived from locations within the body of the transcript, including 3'UTRs. Here, we provide direct evidence that these 3'UTR-derived RNAs are indeed capped and widespread in mammalian cells. By using a combination of AGO2 enhanced individual nucleotide resolution UV crosslinking and immunoprecipitation (eiCLIP) and CAGE following siRNA treatment, we find that these 3'UTR-derived RNAs likely originate from AGO2-binding sites, and most often occur at locations with G-rich motifs bound by the RNA-binding protein UPF1. High-resolution imaging and long-read sequencing analysis validate several 3'UTR-derived RNAs, showcase their variable abundance and show that they may not co-localise with the parental mRNAs. Taken together, we provide new insights into the origin and prevalence of 3'UTR-derived RNAs, show the utility of CAGE-seq for their genome-wide detection and provide a rich dataset for exploring new biology of a poorly understood new class of RNAs.
Authors
- Nejc Haberman (ORCID: https://orcid.org/0000-0001-9247-4139)
- Kayoko Yasuzawa (ORCID: https://orcid.org/0000-0002-1362-3093)
- Andrew M Jobbins (ORCID: https://orcid.org/0000-0002-9174-1503)
- Holly Digby (ORCID: https://orcid.org/0000-0003-1360-9686)
- Rebecca Cheung
- Hazuki Takahashi (ORCID: https://orcid.org/0000-0001-7315-7349)
- Christopher R. Sibley (ORCID: https://orcid.org/0000-0002-8286-4683)
- Boris Lenhard (ORCID: https://orcid.org/0000-0002-1114-1509)
- Callum Parr (ORCID: https://orcid.org/0000-0002-4454-5577)
- Santiago Vernia (ORCID: https://orcid.org/0000-0001-6728-5555)
- Aida Martínez-Sánchez (ORCID: https://orcid.org/0000-0001-5142-2527)
- Takeya Kasukawa (ORCID: https://orcid.org/0000-0001-5085-0802)
- Piero Carninci (ORCID: https://orcid.org/0000-0001-7202-7243)
- Jernej Ule (ORCID: https://orcid.org/0000-0002-2452-4277)
- Anob M. Chakrabarti (ORCID: https://orcid.org/0000-0002-6841-5718)
- Rupert Faraway (ORCID: https://orcid.org/0000-0002-1217-795X)
- Chi Wai Yip (ORCID: https://orcid.org/0000-0003-3327-5695)
- Masaki Kato (ORCID: https://orcid.org/0000-0001-8091-8476)
Institutions
- Allen Institute for Brain Science (US)
- King's College London (GB)
- The Francis Crick Institute (GB)
- Human Technopole (IT)
- Institute of Clinical Research (US)
- UK Dementia Research Institute (GB)
- Instituto de Biomedicina de Valencia (ES)
- RIKEN Center for Integrative Medical Sciences (JP)
- MRC London Institute of Medical Sciences (GB)
- University College London (GB)
- Imperial College London (GB)
- University of Edinburgh (GB)
Publication Details
- Journal
- BMC Biology
- Published
- 2024-11-07
- DOI
- https://doi.org/10.1186/s12915-024-02032-7
- Citations
- 6
- Primary Topic
- RNA modifications and cancer
- Type
- article
- Field-Weighted Citation Impact
- 1.40
Funders
- Wellcome Trust
- Francis Crick Institute
- Cancer Research UK
- Imperial College London
- Ministry of Education, Culture, Sports, Science and Technology
- Medical Research Council
- RIKEN