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

MALAT1, an abundant lncRNA specifically localized to nuclear speckles, regulates alternative-splicing (AS). The molecular basis of its role in AS remains poorly understood. Here, we report three conserved, thermodynamically stable, parallel RNA-G-quadruplexes (rG4s) present in the 3 prime region of MALAT1 which regulates this function. Using rG4 domain-specific RNA-pull-down followed by mass-spectrometry, RNA-immuno-precipitation, and imaging, we demonstrate the rG4 dependent localization of Nucleolin (NCL) and Nucleophosmin (NPM) to nuclear speckles. Specific G-to-A mutations that abolish rG4 structures, result in the localization loss of both the proteins from speckles. Functionally, mutation of rG4 structures and NCL knockdown had distinct as well as overlapping effects on the expression of genes. A variety of alterations in the splicing pattern of specific pre-mRNAs in the rG4 mutant suggests an important role for MALAT1 rG4s in orchestrating AS.