An intrinsically disordered RNA-binding region provides local target selectivity and is essential for LARP6 function

In addition to structured RNA-binding domains (RBDs), most RNA-binding proteins (RBPs) contain intrinsically disordered regions (IDRs), which are thought to possess additional RNA-binding activities. Despite their prevalence, the specific RNA-binding functions of IDRs in RBPs have remained largely uncharacterised. Here we examined the ordered and disordered RNA-binding activities of LARP6, an RBP known for its diverse RNA-binding repertoire. Using mass spectrometry-based mapping of RNA-protein interaction sites, we showed that both the La-module RBD and the two IDRs of LARP6 directly interact with RNA in living cells. Mutagenesis coupled with individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) revealed the La-module to be indispensable for LARP6 binding to RNA. Deletion of the IDRs did not diminish the RNA-binding capability of LARP6, but instead broadened its interaction footprints on the target RNAs, and impaired LARP6 function in promoting cancer cell viability and invasion. In vitro biophysical analysis corroborated the iCLIP-based findings, demonstrating that rather than independently binding to RNA, IDRs can modulate the RNA-binding patterns of the tethered RBD. Based on these findings, we propose a previously unknown role for IDRs in fine-tuning RNA-RBD interactions through modulating local RNA-binding selectivity, resulting in highly specific RNA-protein interaction patterns that are critical for RBP functions.