Transcriptome-Wide Analysis of Gene Expression and Alternative Splicing in a Splicing Regulator Mutant: Role of SR45 in Thermotolerance

Serine/arginine-rich (SR) and SR-like RNA binding proteins are key regulators of pre-mRNA splicing.  SR45, one of the SR-like proteins, regulates alternative splicing (AS) of pre-mRNAs of SR genes and multiple developmental processes. However, the role of SR45 in global regulation of AS and gene expression is not known.  To address this and to gain insights into the mode of action of SR45 in controlling diverse processes we compared the transcriptomes of the sr45 mutant and wild type (WT) using high throughput sequencing.  This analysis has allowed us to identify differentially expressed (DE) and differentially spliced (DS) genes in the mutant.  The top over-represented Gene Ontology (GO) terms in DE and DS genes in the biological processes category are hormonal signaling and response to abiotic stresses including heat and in the molecular functions space is sequence-specific DNA binding transcription factors (TF) activity, suggesting that AS of TFs likely mediates some functions of SR45.  Based on GO enrichment, we analyzed heat stress responses in the mutant. The sr45 mutant was highly sensitive to high temperature (38^oC and 45^oC) at different developmental stages.  Expression and splicing of several TFs and heat shock proteins implicated in heat tolerance are misregulated in the mutant. In addition, SR45 binds to an intron of a heat shock TF.  These results suggest that SR45 is a positive regulator of heat stress response and that the expression and splicing of genes involved in heat signaling might mediate SR45 function in heat tolerance. 

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