A novel class of alternative 3?-terminal exons is involved in cell-cycle regulation by topoisomerase inhibitors

Alternative 3’-terminal exons, which use intronic polyadenylation sites, are generally unconserved and lowly expressed, while the main gene products end in the last exon of genes. In this study, we discover a class of human genes, where the last exon appeared recently during evolution, and the major gene product uses an alternative 3’-terminal exon corresponding to the ancestral last exon of the gene. This novel class of alternative 3’-terminal exons are down-regulated on a large scale by doxorubicin, a cytostatic drug targeting topoisomerase II, and play a role in cell cycle regulation, including centromere-kinetochore assembly. The RNA-binding protein, HuR/ELAVL1 is a major regulator of this specific set of alternative 3’-terminal exons. HuR binding to the alternative 3’-terminal exon in the pre-messenger RNA promotes its splicing, and is reduced by topoisomerase inhibitors. These findings provide new insights into the evolution, function and molecular regulation of alternative 3’-terminal exons. 6 samples of MCF7 cells exposed to different treatments were analyzed: 3 x control_6 hours; 3 x doxorubicin_6 hours.