Non-canonical Function of the Splicing Activator U2AF2 in Promoting Intron Retention in the Lncrnas PURPL and MALAT1

Intron retention (IR) is a form of alternative splicing in which an intron that is typically spliced out is retained in the mature RNA. Despite emerging evidence of widespread IR in protein-coding genes and lncRNAs, the underlying molecular mechanisms remain unclear. Here, we developed a genome-wide screen termed CRASP-seq, to investigate the mechanisms underlying IR in the lncRNA PURPL. Unexpectedly, the top hit was the essential splicing activator U2AF2 that promoted IR in PURPL by directly binding to a weak polypyrimidine tract. U2AF2 promoted IR in additional transcripts, including the nuclear speckle-localized MALAT1 whose localization to nuclear speckles was disrupted upon U2AF2 depletion. Importantly, retention of a specific endogenous MALAT1 intron was critical for its nuclear speckle localization and promoting cell migration. These findings uncover a non-canonical function of U2AF2 in promoting IR and reveal how IR contributes to the subcellular localization and functions of PURPL and MALAT1 .