Intron Retention Controls Localization of lncRNAs PURPL and MALAT1 to Promote Cell Proliferation and Migration

Intron retention (IR) is a form of alternative splicing in which introns that are normally removed are retained in mature transcripts. Despite emerging evidence of widespread IR in protein-coding genes and lncRNAs, the mechanisms and functional consequences underlying this process remain poorly understood. Here, we performed a genome-wide screen, to dissect the mechanisms governing IR in the lncRNA PURPL. Unexpectedly, the top hit from the screen was the essential splicing activator U2AF2, which promotes IR in PURPL through direct binding to a weak polypyrimidine tract. Retention of this intron drives nuclear localization of PURPL and enhances cell proliferation, revealing a functional role for IR. Transcriptome-wide analysis showed that while U2AF2 promotes splicing of most transcripts, consistent with its canonical role, it also promotes IR in a distinct subset of RNAs. This subset includes the nuclear speckle localized lncRNA MALAT1, whose speckle localization is impaired upon U2AF2 depletion. Using MALAT1 knockout cells reconstituted with wild-type or intron-deleted MALAT1 variants, we identified a single intron that is essential for MALAT1 nuclear speckle localization. Deletion of this intron from endogenous MALAT1 disrupted speckle localization and reduced cell migration, phenocopying the loss of MALAT1. Together, these findings uncover a previously unrecognized role for U2AF2 in promoting intron retention and establish IR as a key mechanism regulating lncRNA localization and function.