The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking

Abstract

Epithelial-mesenchymal transition (EMT) plays important roles in tumour progression and is orchestrated by dynamic changes in gene expression. While it is well established that post-transcriptional regulation plays a significant role in EMT, the extent of alternative polyadenylation (APA) during EMT has not yet been explored. Using 3 end anchored RNA sequencing, we mapped the alternative polyadenylation landscape (APA) following TGF-{beta}-mediated induction of EMT in human mammary epithelial cells and found APA generally causes 3UTR lengthening during this cell state transition. Analysis of the RNA-binding protein Quaking (QKI), a splicing factor induced during EMT, revealed enrichment of its binding adjacent to cleavage and polyadenylation sites within 3UTRs. Following QKI knockdown, APA of many transcripts are altered to produce predominantly shorter 3UTRs associated with reduced gene expression. Among these, QKI binds to its own cleavage site to produce a transcript with a longer 3UTR. These findings reveal extensive changes in APA occur during EMT and identify a novel function for QKI in this process.