A regulated PNUTS mRNA to lncRNA splice switch mediates EMT and tumor progression

The contribution of lncRNAs to tumor progression and regulatory mechanisms driving their expression are areas of intense investigation. Here, we characterize the binding of heterogeneous nuclear ribonucleoprotein E1 (hnRNP E1) to a nucleic acid structural element located in exon 12 of PNUTS (also known as PPP1R10) pre-RNA that regulates its alternative splicing. HnRNP E1 release from this structural element, following its silencing, nucleo-cytoplasmic translocation or in response to TGFβ, allows alternative splicing and generates a non-coding isoform of PNUTS. Functionally the lncRNA-PNUTS serves as a competitive sponge for miR-205 during epithelial-mesenchymal transition. In mesenchymal breast tumor cells and in breast tumor samples, the expression of lncRNA-PNUTS is elevated and correlates with levels of ZEB mRNAs. Thus, PNUTS is a bifunctional RNA encoding both PNUTS-mRNA and lncRNA-PNUTS each eliciting distinct biological functions. While PNUTS-mRNA is ubiquitously expressed, lncRNA-PNUTS appears to be tightly regulated dependent on hnRNP E1’s status and tumor context.