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

doi:10.1080/15476286.2023.2294222

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

RNA Biol. 2024 Jan;21(1):1-11. doi: 10.1080/15476286.2023.2294222. Epub 2023 Dec 19.

Authors

Daniel P Neumann¹, Katherine A Pillman¹, B Kate Dredge¹, Andrew G Bert¹, Caroline A Phillips¹, Rachael Lumb¹, Yesha Ramani¹, Cameron P Bracken^{1

2}, Brett G Hollier³, Luke A Selth^{2

4}, Traude H Beilharz⁵, Gregory J Goodall^{1

2}, Philip A Gregory^{1

2}

Affiliations

¹ Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia.
² Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia.
³ 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.
⁴ Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia.
⁵ Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia.

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 (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.

Keywords: 3’ untranslated region (3’UTR); Crosslinked immunopreciptation (CLIP) sequencing; Quaking; RNA binding protein (RBP); alternative polyadenylation; epithelial-mesenchymal transition.

MeSH terms

3' Untranslated Regions
Base Sequence
Epithelial-Mesenchymal Transition / genetics
Gene Expression Regulation*
Humans
Polyadenylation*
RNA-Binding Proteins / genetics

Substances

RNA-Binding Proteins
3' Untranslated Regions

Grants and funding

The work was supported by the Australian Research Council [FT180100049]; Cancer Council South Australia [Principal Cancer Research Fellowship]; National Breast Cancer Foundation [IIRS-18-147]; National Health and Medical Research Council [1128479, 1164669, 1118170]; National Health and Medical Research Council [1128479,1164669].