CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1

Area of Science:

• Molecular Biology
• Gene Expression Regulation
• RNA Processing

Background:

• RNA splicing removes introns from pre-mRNA, regulated by the spliceosome.
• Spliceosome activation involves complex rearrangements and is a critical control point.
• The kinase responsible for phosphorylating Splicing factor 3B subunit 1 (SF3B1) during activation was unknown.

Purpose of the Study:

• Identify the kinase responsible for SF3B1 phosphorylation.
• Investigate the role of this phosphorylation in spliceosome activation.
• Evaluate the inhibitory effects of OTS964 on CDK11 and spliceosome function.

Main Methods:

• Co-immunoprecipitation to show CDK11-SF3B1 association.
• Mass spectrometry to identify phosphorylated threonine residues on SF3B1.
• In vitro splicing assays to assess the impact of CDK11 inhibition.
• Analysis of spliceosome complex formation (B to Bact transition).

Main Results:

• CDK11 directly associates with and phosphorylates SF3B1 at its N terminus.
• This phosphorylation is crucial for SF3B1's association with U5 and U6 snRNAs in the activated spliceosome (Bact).
• OTS964, a selective CDK11 inhibitor, blocks SF3B1 phosphorylation, prevents the B to Bact transition, and causes intron retention.

Conclusions:

• CDK11 plays a central role in spliceosome assembly and activation through SF3B1 phosphorylation.
• OTS964 effectively inhibits CDK11, suppressing spliceosome activation and leading to widespread splicing defects.
• This study identifies a novel regulatory mechanism in RNA splicing and a potential therapeutic target.