Alternative splicing modulation mediated by G-quadruplex structures in MALAT1 lncRNA

MALAT1, an abundant lncRNA specifically localized to nuclear speckles, regulates alternative-splicing. The molecular basis of its role in alternative splicing remains poorly understood. Here, we report three conserved, thermodynamically stable, parallel RNA G quadruplexes present in the 3 prime regions of MALAT1 which regulates this function. Using rG4 domain-specific RNA-pull-down followed by mass spectrometry, RNA immunoprecipitation, and imaging, we demonstrate the rG4 dependent localization of Nucleolin and Nucleophosmin to nuclear speckles. Specific G to A mutations that abolish RNA G quadruplex structures, results in the localization loss of both the proteins from speckles. Functionally, disruption of rG4 in MALAT1 phenocopies NCL knockdown resulting in altered pre mRNA splicing of endogenous genes. These results reveal a central role of RNA G quadruplexes within the 3 prime regions of the MALAT1 orchestrating Alternative Splicing.