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Use of an intronic polyadenylation site in breast cancer

Köksal Bıçakcı, Gözd
Alternative polyadenylation is an important mRNA processing step in which the length and/or the sequence of 3’UTR of mRNAs are altered. This change in 3’UTRs may have significant effects on mRNA stability, localization and translational efficiency. One of the APA types, called intronic polyadenylation (IPA), occurs on intronic sites rather than 3’UTRs. Recent evidence shows that almost 20% of human genes have a poly(A) site in at least one intron. In fact, some introns even may have more than one poly(A) site. Since generation of IPA isoforms could potentially have serious consequences on both protein levels and function, the significance of intronic APA and its occurrence is of interest. Here, we describe such an IPA site in a eukaryotic initiation factor 2B-3 (EIF2B3). Using in silico, and in vitro tools, we studied this IPA site usage in response to estrogen in ER+ breast cancer cells. We confirmed expression of EIF2B3 IPA isoform in MCF7, ER+ breast cancer cells, as well as other breast cancer cell lines and patient samples. We confirmed the usage of this intronic poly(A) site by 3’RACE, cloning and sequencing. Moreover, we showed the expression of a protein from this IPA isoform. Overall, we provide confirmatory data on an in-silico prediction of an IPA case in breast cancers. Future experiments will show the consequence of this IPA event and provide insight into similar IPA events that may happen in cancer cells.