RNA G-quadruplexes mediate cooperativity in HNRNPH binding and splicing regulation

Authors:
Preprint
Publisher website
Google Scholar
Abstract
Alternative splicing, regulated by RNA-binding proteins (RBPs), enables the generation of diverse transcript isoforms critical for cellular function. However, how RNA secondary structure impacts RBP binding and function remains poorly understood. Here, we unravel how RNA G-quadruplexes (rG4s) facilitate cooperativity in splicing regulation by the RBP heterogeneous nuclear ribonucleoprotein H (HNRNPH). Through high-throughput in vivo and in vitro studies combined with theoretical modeling, we dissect how rG4s mediate cooperative HNRNPH binding to RNA, ultimately modulating the splicing of hundreds of exons. rG4 unfolding by HNRNPH exposes multiple G-rich binding sites, thereby establishing indirect cooperativity, which is further amplified to achieve switch-like splicing regulation. HNRNPH-mediated regulation is evident in breast cancer patients, with tumors showing rG4-disrupting variants and global HNRNPH alterations, driving distinct splicing patterns that distinguish tumor subtypes. Overall, our findings offer valuable insights into the mechanistic role of RNA secondary structures in cooperative RBP binding and splicing regulation and highlight the clinical relevance of HNRNPH-dependent splicing in cancer.
Funding Information
  • Deutsche Forschungsgemeinschaft (DFG) (S.L. (LE 3473/2-3))
  • Deutsche Forschungsgemeinschaft (DFG) (K.Z. (ZA 881/2-3))
  • Deutsche Forschungsgemeinschaft (DFG) (J.K. (KO 4566/4-3))
  • SFB 1551 (464588647)
  • SFB902 (B13)
  • CureBRCA and the Basser Center for BRCA pilot grants
  • NIH Grant (R01 LM013437)
  • NIH Grant (R01 GM-147739)
  • NSF Cooperative Agreement (DBI-2400327)
  • Deutsche Forschungsgemeinschaft (533767322 – EXC 3113/1)

This publication has 79 references indexed in Scilit: