Alternative Cleavage and Polyadenylation Generates Downstream Uncapped RNA Isoforms with Translation Potential

Overview

Journal Mol Cell

Publisher Cell Press

Specialty Cell Biology

Date 2022 Oct 21

PMID 36270248

Authors

Yuval Malka

Ferhat Alkan

Shinyeong Ju

Pierre-Rene Korner

Abhijeet Pataskar

Eldad Shulman

Fabricio Loayza-Puch

Julien Champagne

Casper Wenzel

William James Faller

Ran Elkon

Cheolju Lee

Reuven Agami

Affiliations

Soon will be listed here.

Abstract

The use of alternative promoters, splicing, and cleavage and polyadenylation (APA) generates mRNA isoforms that expand the diversity and complexity of the transcriptome. Here, we uncovered thousands of previously undescribed 5' uncapped and polyadenylated transcripts (5' UPTs). We show that these transcripts resist exonucleases due to a highly structured RNA and N6-methyladenosine modification at their 5' termini. 5' UPTs appear downstream of APA sites within their host genes and are induced upon APA activation. Strong enrichment in polysomal RNA fractions indicates 5' UPT translational potential. Indeed, APA promotes downstream translation initiation, non-canonical protein output, and consistent changes to peptide presentation at the cell surface. Lastly, we demonstrate the biological importance of 5' UPTs using Bcl2, a prominent anti-apoptotic gene whose entire coding sequence is a 5' UPT generated from 5' UTR-embedded APA sites. Thus, APA is not only accountable for terminating transcripts, but also for generating downstream uncapped RNAs with translation potential and biological impact.

Citing Articles

A short ncRNA modulates gene expression and affects stress response and parasite differentiation in .

Quilles Jr J, Espada C, Orsine L, Defina T, Almeida L, Holetz F Front Cell Infect Microbiol. 2025; 15:1513908.

PMID: 39981380 PMC: 11841412. DOI: 10.3389/fcimb.2025.1513908.

ALKBH5 suppresses gastric cancer tumorigenesis and metastasis by inhibiting the translation of uncapped WRAP53 RNA isoforms in an m6A-dependent manner.

Zheng Z, Lin F, Zhao B, Chen G, Wei C, Chen X Mol Cancer. 2025; 24(1):19.

PMID: 39815301 PMC: 11734446. DOI: 10.1186/s12943-024-02223-4.

Fateful Decisions of Where to Cut the Line: Pathology Associated with Aberrant 3' End Processing and Transcription Termination.

Grzechnik P, Mischo H J Mol Biol. 2024; 437(1):168802.

PMID: 39321865 PMC: 11870849. DOI: 10.1016/j.jmb.2024.168802.

Post-transcriptional dynamics and RNA homeostasis in autophagy and cancer.

Kolapalli S, Nielsen T, Frankel L Cell Death Differ. 2023; 32(1):27-36.

PMID: 37558732 PMC: 11742036. DOI: 10.1038/s41418-023-01201-5.

Transcriptome sequencing suggests that pre-mRNA splicing counteracts widespread intronic cleavage and polyadenylation.

Vlasenok M, Margasyuk S, Pervouchine D NAR Genom Bioinform. 2023; 5(2):lqad051.

PMID: 37260513 PMC: 10227441. DOI: 10.1093/nargab/lqad051.

References

Nam J, Rissland O, Koppstein D, Abreu-Goodger C, Jan C, Agarwal V . Global analyses of the effect of different cellular contexts on microRNA targeting. Mol Cell. 2014; 53(6):1031-1043. PMC: 4062300. DOI: 10.1016/j.molcel.2014.02.013. View

Mercer T, Wilhelm D, Dinger M, Solda G, Korbie D, Glazov E . Expression of distinct RNAs from 3' untranslated regions. Nucleic Acids Res. 2010; 39(6):2393-403. PMC: 3064787. DOI: 10.1093/nar/gkq1158. View

Liu B, Merriman D, Choi S, Schumacher M, Plangger R, Kreutz C . A potentially abundant junctional RNA motif stabilized by mA and Mg. Nat Commun. 2018; 9(1):2761. PMC: 6050335. DOI: 10.1038/s41467-018-05243-z. View

Elkon R, Ugalde A, Agami R . Alternative cleavage and polyadenylation: extent, regulation and function. Nat Rev Genet. 2013; 14(7):496-506. DOI: 10.1038/nrg3482. View

Roost C, Lynch S, Batista P, Qu K, Chang H, Kool E . Structure and thermodynamics of N6-methyladenosine in RNA: a spring-loaded base modification. J Am Chem Soc. 2015; 137(5):2107-15. PMC: 4405242. DOI: 10.1021/ja513080v. View

Russ B, Olshanksy M, Smallwood H, Li J, Denton A, Prier J . Distinct epigenetic signatures delineate transcriptional programs during virus-specific CD8(+) T cell differentiation. Immunity. 2014; 41(5):853-65. PMC: 4479393. DOI: 10.1016/j.immuni.2014.11.001. View

Chernyakov I, Whipple J, Kotelawala L, Grayhack E, Phizicky E . Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5'-3' exonucleases Rat1 and Xrn1. Genes Dev. 2008; 22(10):1369-80. PMC: 2377191. DOI: 10.1101/gad.1654308. View

Shatsky I, Terenin I, Smirnova V, Andreev D . Cap-Independent Translation: What's in a Name?. Trends Biochem Sci. 2018; 43(11):882-895. DOI: 10.1016/j.tibs.2018.04.011. View

Lee S, Singh I, Tisdale S, Abdel-Wahab O, Leslie C, Mayr C . Widespread intronic polyadenylation inactivates tumour suppressor genes in leukaemia. Nature. 2018; 561(7721):127-131. PMC: 6527314. DOI: 10.1038/s41586-018-0465-8. View

10.

Ren Y, Sun C, Sun Y, Tan H, Wu Y, Cui B . PPAR gamma protects cardiomyocytes against oxidative stress and apoptosis via Bcl-2 upregulation. Vascul Pharmacol. 2009; 51(2-3):169-74. DOI: 10.1016/j.vph.2009.06.004. View

11.

Anders S, Pyl P, Huber W . HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2014; 31(2):166-9. PMC: 4287950. DOI: 10.1093/bioinformatics/btu638. View

12.

Vidigal J, Ventura A . Rapid and efficient one-step generation of paired gRNA CRISPR-Cas9 libraries. Nat Commun. 2015; 6:8083. PMC: 4544769. DOI: 10.1038/ncomms9083. View

13.

Pan R, Hogdal L, Benito J, Bucci D, Han L, Borthakur G . Selective BCL-2 inhibition by ABT-199 causes on-target cell death in acute myeloid leukemia. Cancer Discov. 2013; 4(3):362-75. PMC: 3975047. DOI: 10.1158/2159-8290.CD-13-0609. View

14.

Masamha C, Xia Z, Yang J, Albrecht T, Li M, Shyu A . CFIm25 links alternative polyadenylation to glioblastoma tumour suppression. Nature. 2014; 510(7505):412-6. PMC: 4128630. DOI: 10.1038/nature13261. View

15.

Xuan J, Sun W, Lin P, Zhou K, Liu S, Zheng L . RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data. Nucleic Acids Res. 2017; 46(D1):D327-D334. PMC: 5753293. DOI: 10.1093/nar/gkx934. View

16.

Gruber A, Zavolan M . Alternative cleavage and polyadenylation in health and disease. Nat Rev Genet. 2019; 20(10):599-614. DOI: 10.1038/s41576-019-0145-z. View

17.

Zheng G, Qin Y, Clark W, Dai Q, Yi C, He C . Efficient and quantitative high-throughput tRNA sequencing. Nat Methods. 2015; 12(9):835-837. PMC: 4624326. DOI: 10.1038/nmeth.3478. View

18.

Lorenz R, Bernhart S, Honer Zu Siederdissen C, Tafer H, Flamm C, Stadler P . ViennaRNA Package 2.0. Algorithms Mol Biol. 2011; 6:26. PMC: 3319429. DOI: 10.1186/1748-7188-6-26. View

19.

Wan C, Li P, Spolski R, Oh J, Andraski A, Du N . IL-21-mediated non-canonical pathway for IL-1β production in conventional dendritic cells. Nat Commun. 2015; 6:7988. PMC: 4555999. DOI: 10.1038/ncomms8988. View

20.

Kasowitz S, Ma J, Anderson S, Leu N, Xu Y, Gregory B . Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development. PLoS Genet. 2018; 14(5):e1007412. PMC: 5991768. DOI: 10.1371/journal.pgen.1007412. View