The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking
Daniel P. Neumann,
Katherine A. Pillman,
B. Kate Dredge,
Andrew G. Bert,
Caroline A. Phillips,
Rachael Lumb,
Yesha Ramani,
Cameron P. Bracken,
Brett G. Hollier,
Luke A. Selth,
Traude H. Beilharz,
Gregory J. Goodall,
Philip A. Gregory
Affiliations
Daniel P. Neumann
Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
Katherine A. Pillman
Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
B. Kate Dredge
Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
Andrew G. Bert
Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
Caroline A. Phillips
Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
Rachael Lumb
Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
Yesha Ramani
Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
Cameron P. Bracken
Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
Brett G. Hollier
Australian Prostate Cancer Research Centre - Queensland, Centre for Genomics and Personalised Health, Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
Luke A. Selth
Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
Traude H. Beilharz
Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
Gregory J. Goodall
Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
Philip A. Gregory
Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
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 (APA) landscape following Transforming Growth Factor (TGF)-β-mediated induction of EMT in human mammary epithelial cells and found APA generally causes 3’UTR lengthening during this cell state transition. Investigation of potential mediators of APA indicated the RNA-binding protein Quaking (QKI), a splicing factor induced during EMT, regulates a subset of events including the length of its own transcript. Analysis of QKI crosslinked immunoprecipitation (CLIP)-sequencing data identified the binding of QKI within 3’ untranslated regions (UTRs) was enriched near cleavage and polyadenylation sites. Following QKI knockdown, APA of many transcripts is altered to produce predominantly shorter 3’UTRs associated with reduced gene expression. These findings reveal the changes in APA that occur during EMT and identify a potential role for QKI in this process.
