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A Reporter Based Cellular Assay for Monitoring Splicing Efficiency
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The SWI/SNF subunit BRG1 affects alternative splicing by changing RNA binding factor interactions with nascent RNA.

Antoni Gañez-Zapater1,2, Sebastian D Mackowiak3,4, Yuan Guo1

  • 1Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden.

Molecular Genetics and Genomics : MGG
|February 21, 2022
PubMed
Summary

The SWI/SNF ATPases BRG1 and BRM regulate alternative splicing by influencing RNA binding factors. Some splicing changes occur independently of ATPase activity, affecting exon inclusion and skipping.

Keywords:
BRGG1Chromatin remodellingExon GC contentSAM68SWI/SNFhnRNPLhnRNPUmRNA alternative splicing

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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.