Eukaryotic organisms have evolved complex gene regulatory networks to launch coordinated responses to external conditions and stimuli. Under environmental stress, such as nutrient depletion, these responses involve reallocation of cellular resources away from growth and cell cycle stimulating genes and towards stress-responsive genes. This occurs through several mechanisms including changes at the transcriptional level, repression of ribosome biogenesis factors, altered translation initiation, and RNA features which modulate translation efficiency and transcript stability. Upon nutrient starvation in Saccharomyces cerevisiae, diploid cells undergo meiosis (sporulation in yeast). We have previously shown that the catalytic component of the Swi/Snf chromatin remodeling complex, Snf2, is responsible for shifting gene expression away from intron-rich ribosomal protein genes (RPGs) to enhance splicing of meiotic intron-containing genes (ICGs) during sporulation. A similar process occurs during the transition from growth to quiescence known as the diauxic shift in yeast. During both of these complex cell-state transitions, Snf2 levels change dramatically while SNF2 mRNA levels remain relatively stable. Although critical to its activity, the mechanism by which Snf2 protein levels change remains unknown. Here we describe temporally-regulated alternate transcription start sites (TSS) under batch growth conditions, which produce SNF2 transcripts with different 5’ leaders affecting downstream translation propensity. Specifically, a long isoform of SNF2 contains three upstream open reading frames (uORFs), which we hypothesize inhibits the translation of the downstream protein-coding ORF. I used 5’ RACE to identify the previously unannotated TSS of the long isoform, and RNA analysis suggests that the relative levels of each transcript are dynamic and affected by the binding of the highly-conserved transcriptional regulators Ume6 and Cbf1 at the SNF2 locus. Protein analysis via Western blotting shows that this regulation indeed affects Snf2 expression. In light of the conservation of Snf2, investigating its regulation in response to environmental changes in S. cerevisiae may carry important implications for Snf2 chromatin remodeling activity in higher eukaryotes.
Support or Funding Information
This work is supported by funding from the National Institutes of Health (NIH), National Science Foundation (NSF) and Howard Hughes Medical Institute (HHMI).
