E2F mediates enhanced alternative polyadenylation in proliferation

Here, we explored, on a transcriptome-wide scale, alternative polyadenylation events associated with cellular proliferation and neoplastic transformation. We applied a deep-sequencing technique for identification and quantification of poly(A) sites to two human cellular models, each examined under proliferative, arrested and transformed states. In both cell systems we observed global 3' UTR shortening associated with proliferation, a link that was markedly stronger than the association with transformation. Furthermore, we found that proliferation is also associated with enhanced cleavage at intronic poly(A) sites. Last, we found that the expression level of the set of genes that encode for 3'-end processing proteins is globally elevated in proliferation, and that E2F transcription factors contribute to this regulation.Our results comprehensively identify alternative polyadenylation events associated with cellular proliferation and transformation, and demonstrate that the enhanced alternative polyadenylation in proliferative conditions results not only in global 3' UTR shortening but also in enhanced premature cleavage in introns. Our results also indicate that E2F-mediated co-transcriptional regulation of 3'-end processing genes is one of the mechanisms that links enhanced alternative polyadenylation to proliferation.Cleavage and polyadenylation are required for the maturation of most mRNA transcripts [1]. The pre-mRNA is cleaved approximately 10 to 30 nucleotides downstream of the polyadenylation signal (PAS) and an untemplated poly(A) tail is added to the transcript. The canonical PAS is AAUAAA, which appears in about 50% of the cleavage sites (CSs). More than 10 PAS variants have been documented, the most prevalent of which is AUUAAA [2,3]. In addition, various upstream and downstream auxiliary elements were found to regulate the efficiency of poly(A) site usage, prominent among them U-rich and GU-rich elements downstream of the cleavage sites [2]. Recently, usin