SNF5/SMARCB1 Perturbation Results in Alternative Splicing for Specific Genes Rather Than Global Genomic Splicing Changes

Abstract

Alternative splicing is a major source of protein diversity in cells of higher eukaryotes by having several different mRNAs potentially produced from the same pre-mRNA. Chromatin structure has been reported to be a regulator of alternative splicing, but much of the evidence is correlative in nature. To investigate this connection more directly, we analyzed alternative splicing events in RNA sequencing data from human cells expressing a regulated, degradable SWI/SNF chromatin remodeling complex subunit (SNF5). A total of 65 genes with significant isoform switching were identified, with 53 showing alternative splicing events. Exon skipping was the most prevalent alternative splicing event. In addition, examination of splice site strength indicated a majority of alternative 5’ and 3’ splice sites switched from a stronger site to a weaker site. This small proportion of alternative splicing effects support chromatin as a gene-specific rather than genome-wide regulator of alternative splicing. With this in mind, genes with alternative isoforms in response to SNF5 degradation were combined with a traditional differential expression gene set to explore function and protein interaction networks for a comprehensive gene expression set. This analysis revealed a majority of genes had functions related to zinc finger transcriptional pathways, glycoproteins, cancer pathways, cadherins and cell adhesion, axon guidance, differentiation, metallopeptidase, transcription/RNA pol II binding, and chromatin and nucleosome structure.