Widespread 3′UTR capped RNAs derive from G-rich regions in proximity to AGO2 binding sites
Abstract 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 d...
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2024-11-01
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| Online Access: | https://doi.org/10.1186/s12915-024-02032-7 |
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| author | Nejc Haberman Holly Digby Rupert Faraway Rebecca Cheung Anob M. Chakrabarti Andrew M. Jobbins Callum Parr Kayoko Yasuzawa Takeya Kasukawa Chi Wai Yip Masaki Kato Hazuki Takahashi Piero Carninci Santiago Vernia Jernej Ule Christopher R. Sibley Aida Martinez-Sanchez Boris Lenhard |
| author_facet | Nejc Haberman Holly Digby Rupert Faraway Rebecca Cheung Anob M. Chakrabarti Andrew M. Jobbins Callum Parr Kayoko Yasuzawa Takeya Kasukawa Chi Wai Yip Masaki Kato Hazuki Takahashi Piero Carninci Santiago Vernia Jernej Ule Christopher R. Sibley Aida Martinez-Sanchez Boris Lenhard |
| author_sort | Nejc Haberman |
| collection | DOAJ |
| description | Abstract 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. Graphical Abstract Schematic representation of the proposed model where 3′UTR-derived RNAs originate from G-rich regions enriched in AGO2 and UPF1 binding sites. |
| format | Article |
| id | doaj-art-ad037dcdd70a4cf1aefd83bb7b5773ce |
| institution | DOAJ |
| issn | 1741-7007 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Biology |
| spelling | doaj-art-ad037dcdd70a4cf1aefd83bb7b5773ce2025-08-20T02:50:08ZengBMCBMC Biology1741-70072024-11-0122112310.1186/s12915-024-02032-7Widespread 3′UTR capped RNAs derive from G-rich regions in proximity to AGO2 binding sitesNejc Haberman0Holly Digby1Rupert Faraway2Rebecca Cheung3Anob M. Chakrabarti4Andrew M. Jobbins5Callum Parr6Kayoko Yasuzawa7Takeya Kasukawa8Chi Wai Yip9Masaki Kato10Hazuki Takahashi11Piero Carninci12Santiago Vernia13Jernej Ule14Christopher R. Sibley15Aida Martinez-Sanchez16Boris Lenhard17MRC Laboratory of Medical SciencesUK Dementia Research Institute at King’s College LondonUK Dementia Research Institute at King’s College LondonSection of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College LondonUCL Respiratory, Division of Medicine, University College LondonMRC Laboratory of Medical SciencesRIKEN Center for Integrative Medical SciencesRIKEN Center for Integrative Medical SciencesRIKEN Center for Integrative Medical SciencesRIKEN Center for Integrative Medical SciencesRIKEN Center for Integrative Medical SciencesRIKEN Center for Integrative Medical SciencesRIKEN Center for Integrative Medical SciencesMRC Laboratory of Medical SciencesUK Dementia Research Institute at King’s College LondonInstitute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of EdinburghSection of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College LondonMRC Laboratory of Medical SciencesAbstract 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. Graphical Abstract Schematic representation of the proposed model where 3′UTR-derived RNAs originate from G-rich regions enriched in AGO2 and UPF1 binding sites.https://doi.org/10.1186/s12915-024-02032-73′UTRCAGECappingAGO2UPF13′UTR-derived RNA |
| spellingShingle | Nejc Haberman Holly Digby Rupert Faraway Rebecca Cheung Anob M. Chakrabarti Andrew M. Jobbins Callum Parr Kayoko Yasuzawa Takeya Kasukawa Chi Wai Yip Masaki Kato Hazuki Takahashi Piero Carninci Santiago Vernia Jernej Ule Christopher R. Sibley Aida Martinez-Sanchez Boris Lenhard Widespread 3′UTR capped RNAs derive from G-rich regions in proximity to AGO2 binding sites BMC Biology 3′UTR CAGE Capping AGO2 UPF1 3′UTR-derived RNA |
| title | Widespread 3′UTR capped RNAs derive from G-rich regions in proximity to AGO2 binding sites |
| title_full | Widespread 3′UTR capped RNAs derive from G-rich regions in proximity to AGO2 binding sites |
| title_fullStr | Widespread 3′UTR capped RNAs derive from G-rich regions in proximity to AGO2 binding sites |
| title_full_unstemmed | Widespread 3′UTR capped RNAs derive from G-rich regions in proximity to AGO2 binding sites |
| title_short | Widespread 3′UTR capped RNAs derive from G-rich regions in proximity to AGO2 binding sites |
| title_sort | widespread 3 utr capped rnas derive from g rich regions in proximity to ago2 binding sites |
| topic | 3′UTR CAGE Capping AGO2 UPF1 3′UTR-derived RNA |
| url | https://doi.org/10.1186/s12915-024-02032-7 |
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