NFYA alternative cleavage and polyadenylation in cancer

Most human genes undergo alternative cleavage and polyadenylation (APA) regulating 3’UTR length and accessibility, thus affecting mRNA stability and protein level by altering microRNA and RNA-binding protein (RBP) activity. NFYA encodes for the regulatory subunit of the nuclear transcription factor Y, which controls key transcriptional changes in pathways broadly deregulated in cancer. NFYA is overexpressed in human tumors and the poor correlation between NF-YA protein and mRNA suggests that APA may be as relevant as other mechanisms to control NF-YA activity in cancer. Concerning this, our bioinformatic analyses identified multiple APA sites resulting in four possible NFYA 3’UTRs, not yet correctly annotated. We observed that tumor and immortalized cells mainly use shorter 3’UTRs compared with normal cells, which prevalently use longer ones. In this regard, we found an increased NF-YA protein/mRNA ratio to be associated with higher usage of shorter 3’UTRs. Regarding the molecular aspects, a preliminary screening of RBPs highlighted ELAVL1, known to stabilize polyA transcripts, which binds to a conserved site of NFYA 3’UTR and stabilizes longer NFYA 3’UTR isoforms. Moreover, the effect of different NFYA 3’UTRs on transcript stability, protein level, and microRNA and RBP binding is under study employing different strategies to alter NFYA 3’UTR usage endogenously or exogenously. Notably, the emerging application of antisense oligonucleotides in the clinics opens the possibility to target/mask polyadenylation signals, microRNA or RBP binding sites to therapeutically manipulate the effects of APA in cancer. Overall, our studies intend to functionally characterize the alternative cleavage and polyadenylation of NFYA in cancer.