Premature cleavage and polyadenylation in the minor intron of PTEN modulate its expression and generates a functional long non-coding RNA in breast cancer

Abstract

Minor introns constitute 0.4% of all introns in human cells, but they are unique in their ability to regulate the genes in which they are embedded such that their low splicing efficiency can be a rate limiting step in gene expression. The first intron of the tumor suppressor gene, PTEN, has been documented to be a minor intron, but very little is known about its regulation. Regulation of PTEN levels in cancer cells, especially breast cancer is tightly controlled as a very small reduction in its expression can lead to tumorigenesis. Indeed, many genetic, epigenetic, post-transcriptional and post-translational mechanisms are employed to reduce PTEN levels or activities, leading to cancer. Here, we uncover a previously unexplored mechanism for modulating PTEN expression utilizing its minor intron. The minor intron of PTEN minor intron has one of the lowest splicing efficacies in breast cancer cells, causing at least 50% of PTEN pre-mRNA to retain it, and thus not produce a functional protein. We also show that, unlike other minor introns, the retained intron in PTEN pre-mRNA is not used as a molecular switch that would be spliced out when needed but is rather processed by premature cleavage and polyadenylation into a long noncoding RNA (lncRNA) that we termed PINC. Exogenous expression of PINC caused significant alterations to cellular proliferation, including breast cancer cells that harbor a genetic mutation in the PTEN gene and do not produce a functional PTEN protein. This shows that this novel lncRNA functions independently of the encoded protein of the host gene.