Investigation of transcription initiation from cryptic promoter sites in Saccharomyces cerevisiae

Previous studies in Saccharomyces cerevisiae have shown that mutations in SPT6, SPT16, SET2, and other genes encoding particular chromatin and transcription factors cause the activation of cryptic promoters within coding regions, resulting in the expression of short RNA transcripts. In this work, we examine cryptic initiation in S. cerevisiae on a genome-wide scale to identify all factors required for repressing cryptic promoters and to determine the extent and possible role of cryptic initiation. Using large-scale mutant selections and synthetic genetic array analysis, we have identified mutants affecting histone gene regulators, chromatin remodeling factors, and histories as allowing cryptic initiation. Through microarray analysis, we show that approximately 1,000 genes, or almost one-sixth of the S. cerevisiae genome, express short transcripts in spt6 or spt16 mutants. A significant number of these genes are shown to be conserved with respect to synonymous substitution rates in the transcribed regions corresponding to the short transcripts. Furthermore, we show that short transcripts are capable of being translated into corresponding short proteins. Finally, we show that cryptic initiation can occur in wild-type cells following a nutritional shift from rich to minimal media. Our results demonstrate that maintenance of chromatin structure and modifications is important for repressing a large number of cryptic promoters distributed throughout the genome and suggest that cryptic initiation has the potential to play a physiological role in expressing alternate genetic information in response to environmental changes.