Budding yeast sporulation is a developmental process that generates stress-resistant progeny under nutritient limitation. Sporulation is regulated by a cascade of transcriptional signals. The transcription factor NDT80 is induced during sporulation, and drives the meiotic divisions and spore formation by inducing the transcription of hundreds of genes. The NDT80 regulon consists of both sporulation-specific genes and constitutively expressed genes that are upregulated during sporulation. For these constitutively expressed genes, tiling array and RNA-seq studies indicate that alternative transcription start sites (TSS) are sometimes seen in sporulating cells as compared to vegetative growth.
Here we investigate a subset of the sporulation specific TSSs that initiate within ORFs and generate a shorter transcript and protein that could serve specific functions during sporulation. One such TSS initiates within an intron of the MRK1 gene, encoding one of the four homologs of GSK-3 kinases in budding yeast. We find that an NDT80 binding site within the intron is required for the induction of this shorter transcript and that the shorter transcript results in the expression of an N-terminally truncated form of Mrk1 that nonetheless contains the entire kinase domain. A survey of published datasets identified additional genes with internally initiated transcripts induced in mid-sporulation that have nearby NDT80 consensus sites. We show using qPCR that four other genes have NDT80-dependent internal transcription initiation. We are currently investigating the regulation of these genes as well as the possible function of the truncated proteins during sporulation.