Differential genome-wide profiling of tandem 3'UTRs among human breast cancer and normal cells by high-throughput sequencing

Tandem 3'UTRs produced by alternative polyadenylation (APA) sites in last exon play an important role in gene expression network by impacting mRNA stability, translation and translocation in cells. Several studies investigated APA sites switching in various physiological states, nevertheless they only focused on the genes with two known APA sites or several candidate genes. Here we developed a strategy to study APA sites in genome-wide fashion with the second generation sequencing technology, which could not only identify new polyadenylation sites but also analyze the APA sites switching in all genes especially those with more than two APA sites. We used this strategy to explore the profiling of APA sites in two human breast cancer cell lines (MCF7 and MB231) and one cultured mammary epithelial cell line (MCF10A). More than half of the identified polyadenylation sites are not reported in human poly(A) databases. While MCF7 showed shortening 3'UTR, more genes in MB231 switched to distal poly(A) sites. Several gene ontology terms and pathways were enriched in the list of genes with switched APA sites, including cell cycle, apoptosis, metabolism and so on. These suggest the more complex regulation of APA sites in cancer cells than the previous thought. Several motifs were found to possibly contribute to the APA sites switching. In short, our novel unbiased method can be a powerful approach to uncover the complex mechanism of 3'UTR switching in genome-wide fashion among various physiological processes and diseases cost-effectively like this study.