TY - JOUR
T1 - Alternative cleavage and polyadenylation generates downstream uncapped RNA isoforms with translation potential
AU - Malka, Yuval
AU - Alkan, Ferhat
AU - Ju, Shinyeong
AU - Körner, Pierre Rene
AU - Pataskar, Abhijeet
AU - Shulman, Eldad
AU - Loayza-Puch, Fabricio
AU - Champagne, Julien
AU - Wenzel, Casper
AU - Faller, William James
AU - Elkon, Ran
AU - Lee, Cheolju
AU - Agami, Reuven
N1 - Publisher Copyright:
© 2022 The Authors
PY - 2022/10/20
Y1 - 2022/10/20
N2 - 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.
AB - 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.
KW - Bcl2
KW - CAP-independent translation
KW - Hidden Markov Model
KW - N-terminal mass spectrometry
KW - N6-methyladenosine
KW - RNA structure
KW - alternative cleavage and polyadenylation
KW - immunopeptidome
KW - mammalian transcriptome
KW - uncapped RNA
UR - http://www.scopus.com/inward/record.url?scp=85140349513&partnerID=8YFLogxK
U2 - 10.1016/j.molcel.2022.09.036
DO - 10.1016/j.molcel.2022.09.036
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C2 - 36270248
AN - SCOPUS:85140349513
SN - 1097-2765
VL - 82
SP - 3840-3855.e8
JO - Molecular Cell
JF - Molecular Cell
IS - 20
ER -