The SWI/SNF subunit BRG1 affects alternative splicing by changing RNA binding factor interactions with nascent RNA

Area of Science:

• Molecular Biology
• Genetics
• Epigenetics

Background:

• BRG1 and BRM are core subunits of human SWI/SNF chromatin remodeling complexes.
• SWI/SNF complexes are primarily linked to transcriptional initiation but also influence alternative splicing.
• Previous studies showed BRM-containing SWI/SNF complexes affect splicing at specific genes.

Purpose of the Study:

• To identify genes with alternative exons regulated by SWI/SNF ATPases BRG1 and BRM.
• To investigate the mechanism of SWI/SNF-mediated alternative splicing regulation.

Main Methods:

• Expressing BRG1 and BRM in a deficient cell line (C33A).
• Analyzing splicing changes using RNA sequencing.
• Investigating ATPase-dependent and independent mechanisms.
• Assessing RNA polymerase II CTD phosphorylation and protein-RNA interactions.

Main Results:

• Identified subsets of genes with alternative exons affected by BRG1 and BRM, influencing both exon inclusion and skipping.
• Discovered that some splicing alterations are independent of ATPase activity, linked to high GC content exons.
• Observed accumulation of phosphorylated RNA pol II CTD in ATPase-deficient conditions.
• Showed SWI/SNF recruitment to alternative exons and promotion of RNA binding factor association with chromatin and RNA.

Conclusions:

• SWI/SNF ATPases BRG1 and BRM play a significant role in alternative splicing regulation.
• Regulation can occur through both ATPase-dependent and -independent mechanisms.
• SWI/SNF influences alternative splicing by modulating the binding of splicing-related RNA binding factors to nascent pre-mRNA.