NFYA alternative cleavage and polyadenylation in cancer

The majority of human genes can undergo alternative cleavage and polyadenylation resulting in the expression of distinct transcript isoforms and in a different microRNA-mediated regulation under certain conditions and states. In this context, we aim at studying the microRNA regulation of NFYA with a special focus on the 3’UTR repertoire. NFYA exists in two splicing isoforms and encodes for the regulatory subunit of the nuclear transcription factor Y, which is known to control key transcriptional changes in pathways broadly deregulated in cancer cells. The poor correlation between NF-YA protein and mRNA expression suggests that post-transcriptional regulation may be as relevant as other mechanisms to control NF-YA activity in different cancer types. In this regard, our preliminary bioinformatic analyses identified more than one potential alternative polyadenylation sites resulting in four possible 3’UTRs. Among these, only two exist in current annotations, though the 3’UTR that we found to be the mostly used in both normal and tumor tissues/cells is not yet annotated. Furthermore, such analyses did not highlight any association between a certain NFYA splicing isoform and a specific 3’UTR. Instead, we found an increased NF-YA protein/mRNA ratio when the usage of shortest 3’UTR is higher. In addition, different exon composition and/or different 3’UTR lengths may affect the structural conformation of the transcript, possibly resulting in changes in the accessibility of microRNA binding sites, thus ultimately altering post-transcriptional regulation. Bioinformatic and functional studies are ongoing to assess the differential usage of all potential alternative polyadenylation sites in different conditions/states. Moreover, the effect of different NFYA 3’UTRs on the transcript stability and protein level as well as the biological implications in the cancer context are under study by employing different strategies to alter the 3’UTR usage endogenously or exogenously. Therefore, our goal is to characterize the alternative cleavage and polyadenylation of NFYA in the cancer context from a functional and biological point of view.