Molecular basis of RNA-binding and autoregulation by the cancer-associated splicing factor RBM39

Area of Science:

• Molecular Biology
• Structural Biology
• Cancer Therapeutics

Background:

• Pharmacologic depletion of RNA-binding motif 39 (RBM39) is a promising anti-cancer strategy.
• Current therapies rely on high levels of the DCAF15 adaptor protein, limiting their application.
• There is a need for DCAF15-independent methods to deplete RBM39.

Purpose of the Study:

• To investigate DCAF15-independent mechanisms for RBM39 depletion.
• To elucidate the autoregulatory mechanism of RBM39.
• To determine the structural basis of RBM39-RNA interactions.

Main Methods:

• Identification of cis-acting elements involved in RBM39 autoregulation.
• Nuclear Magnetic Resonance (NMR) spectroscopy to determine the solution structures of RBM39's RNA recognition motifs (RRMs).
• Analysis of RBM39's interaction with its pre-mRNA targets.

Main Results:

• RBM39 autoregulates its expression through the inclusion of a poison exon in its pre-mRNA.
• The tandem RRMs of RBM39 (RRM1 and RRM2) exhibit distinct RNA binding specificities: RRM1 recognizes RNA stem loops, while RRM2 binds single-stranded N(G/U)NUUUG sequences.
• A model is proposed where RBM2 selects the poison exon's 3'-splice site, with RRM3 and RS domains stabilizing the U2 snRNP at the branchpoint.

Conclusions:

• This study reveals a novel autoregulatory mechanism for RBM39, offering a DCAF15-independent target.
• Molecular insights into RBM39-dependent 3'-splice site selection are provided.
• The findings lay the groundwork for developing alternative anti-cancer therapies targeting RBM39.