Genome-wide analysis of alternative splicing associated with the transcription factor StuA in Trichophyton rubrum

Successful dermatophyte infection requires adhesion to host tissue, germination, hyphal growth, and secretion of keratinolytic enzymes. The APSES (Asm1p, Phd1p, Sok2p, Efg1p, and StuAp)-class transcription factor StuA is involved in these processes. Also, differential gene expression and alternative splicing (AS) are fundamental components of infection-related regulation. This study aimed to provide an overview of the role of StuA in modulating AS in Trichophyton rubrum cultivated in a keratin-containing medium, which mimics an important aspect of the host environment. Comprehensive analysis of high-throughput RNA-sequencing data using the ASpli package (Bioconductor) revealed differential AS events in 104 genes in ΔstuA vs. wild-type comparisons at the sampled time points. Most of the genes were exclusively associated with alternative splicing (54 genes) or differential expression (2193 genes); however, 50 genes were simultaneously involved with both processes. The absence of StuA was associated with stage-specific changes in alternative splicing, generating alternative isoforms of mRNA potentially involved in pathogenesis, highlighting its critical role during the early and late stages of keratin metabolism. The main genes associated with AS in ΔstuA vs. wild-type comparisons are those involved in carbohydrate metabolic process, regulatory functions, and transmembrane transport. Together, these findings indicate that the absence of StuA is associated with modulation of alternative splicing events, supporting a role for StuA in transcriptional and post-transcriptional regulation during growth under keratin-containing medium.