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

Here, we uncovered the expression of thousands of previously unnoticed 5’-Uncapped and Polyadenylated Transcripts (5’UPTs). We show that 5’UPTs appear downstream of APA points that occur within the coding and intronic regions of their host genes. Furthermore, 5’UPTs are marked with N6-methyladenosine (m6A) at their 5’ termini, and this modification is linked to their expression. We also demonstrate that 5’UPTs are strongly enriched in polysomal RNA fractions, suggesting protein production capacity. In addition, we examined the expression of 5’UPTs in the biological context of T cell activation, known to induce APA usage. In line with a causal link between APA and 5’UPTs, T cell activation induced 5’UPTs expression and their incorporation into heavy polysomal fractions. Our findings indicate that APA does not only generates shorter upstream mRNA isoforms, but is also responsible for the generation of downstream uncapped and polyadenylated transcripts that possess potential translational capacity. Examination of mRNA levels and cleavage across CDS within transcripts in U2OS, 293, HeLa cells and mouse T-cells (2/3 replicates each).