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

Area of Science:

• Molecular Biology
• RNA Biology
• Cancer Genomics

Background:

• Alternative splicing generates transcript diversity, essential for cellular functions.
• The role of RNA secondary structures, like G-quadruplexes (rG4s), in RNA-binding protein (RBP) regulation is not well understood.
• Heterogeneous nuclear ribonucleoprotein H (HNRNPH) is an RBP involved in splicing regulation.

Purpose of the Study:

• To investigate how RNA G-quadruplexes (rG4s) mediate cooperative binding of HNRNPH.
• To elucidate the mechanism by which rG4s facilitate HNRNPH-driven splicing regulation.
• To explore the clinical relevance of HNRNPH-mediated splicing in breast cancer.

Main Methods:

• High-throughput in vivo and in vitro experiments.
• Theoretical modeling of RNA-protein interactions.
• Analysis of RNA sequencing data from breast cancer patients.

Main Results:

• rG4s facilitate cooperative HNRNPH binding by exposing multiple G-rich sites upon unfolding.
• HNRNPH binding to rG4s leads to switch-like regulation of hundreds of exons.
• rG4-disrupting variants and HNRNPH alterations in breast tumors correlate with distinct splicing patterns and subtypes.

Conclusions:

• RNA secondary structures, specifically rG4s, play a key mechanistic role in cooperative RBP binding and splicing.
• HNRNPH-dependent splicing regulation is a significant factor in breast cancer progression and subtype differentiation.
• Understanding rG4-mediated splicing offers insights into cancer therapeutics.