Requirement for cleavage factor II(m) in the control of alternative polyadenylation in breast cancer cells

Alternative polyadenylation (APA) determines stability, localization and translation potential of the majority of mRNA in eukaryotic cells. The heterodimeric mammalian cleavage factor II (CF II(m)) is required for pre-mRNA 3′ end cleavage and is composed of the RNA kinase hClp1 and the termination factor hPcf11; the latter protein binds to RNA and the RNA polymerase II carboxy-terminal domain. Here, we used siRNA mediated knockdown and poly(A) targeted RNA sequencing to analyze the role of CF II(m) in gene expression and APA in estrogen receptor positive MCF7 breast cancer cells. Identified gene ontology terms link CF II(m) function to regulation of growth factor activity, protein heterodimerization and the cell cycle. An overlapping requirement for hClp1 and hPcf11 suggested that CF II(m) protein complex was involved in the selection of proximal poly(A) sites. In addition to APA shifts within 3′ untranslated regions (3′-UTRs), we observed shifts from promoter proximal regions to the 3′-UTR facilitating synthesis of full-length mRNAs. Moreover, we show that several truncated mRNAs that resulted from APA within introns in MCF7 cells cosedimented with ribosomal components in an EDTA sensitive manner suggesting that those are translated into protein. We propose that CF II(m) contributes to the regulation of mRNA function in breast cancer.