Alternative cleavage and polyadenylation generates downstream uncapped RNA isoforms with translation potential

Yuval Malka*, Ferhat Alkan, Shinyeong Ju, Pierre Rene Körner, Abhijeet Pataskar, Eldad Shulman, Fabricio Loayza-Puch, Julien Champagne, Casper Wenzel, William James Faller, Ran Elkon, Cheolju Lee, Reuven Agami*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

7 Scopus citations


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.

Original languageEnglish
Pages (from-to)3840-3855.e8
JournalMolecular Cell
Issue number20
StatePublished - 20 Oct 2022


FundersFunder number
NUDT21KD cells
Netherlands Cancer Institute
RNA-seq5,930, NUDT21KD, S20–S21, 2E, 6,537
TAAANUDT21, 6.3 × 10−677, INTS11KD
European Research CouncilEMBO ALTF 796-2018, EEG- CEC / EU 832844
National Research Foundation of Korea2020R1A2C2003685
KWF Kankerbestrijding11574, 13647


    • Bcl2
    • CAP-independent translation
    • Hidden Markov Model
    • N-terminal mass spectrometry
    • N6-methyladenosine
    • RNA structure
    • alternative cleavage and polyadenylation
    • immunopeptidome
    • mammalian transcriptome
    • uncapped RNA


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