Comparative Analysis of Alternative Splicing Profiles in Th Cell Subsets Reveals Extensive Cell Type–Specific Effects Modulated by a Network of Transcription Factors and RNA-Binding Proteins

Abstract

Alternative splicing (AS) plays an important role in the development of many cell types; however, its contribution to Th subsets has been clearly defined. In this study, we compare mice naive CD4+ Th cells with Th1, Th2, Th17, and T regulatory cells and observed that the majority of AS events were retained intron, followed by skipped-exon events, with at least 1200 genes across cell types affected by AS events. A significant fraction of the AS events, especially retained intron events from the 72-h time point, were no longer observed 2 wk postdifferentiation, suggesting a role for AS in early activation and differentiation via preferential expression of specific isoforms required during T cell activation, but not for differentiation or effector function. Examining the protein consequence of the exon-skipping events revealed an abundance of structural proteins encoding for intrinsically unstructured peptide regions, followed by transmembrane helices, β strands, and polypeptide turn motifs. Analyses of expression profiles of RNA-binding proteins (RBPs) and their cognate binding sites flanking the discovered AS events revealed an enrichment for specific RBP recognition sites in each of the Th subsets. Integration with publicly available chromatin immunoprecipitation sequencing datasets for transcription factors support a model wherein lineage-determining transcription factors impact the RBP profile within the differentiating cells, and this differential expression contributes to AS of the transcriptome via a cascade of cell type-specific posttranscriptional rewiring events.