Abstract
Fission yeast, Schizosaccharomyces pombe, is an attractive model organism for transcriptional and chromatin biology research. Such research is contingent of accurate annotation of transcription start sites (TSSs). However, comprehensive genome-wide maps of TSS and their usage across commonly applied laboratorial conditions and treatments for S. pombe are lacking. To this end, we profiled TSSs activity genome-wide in S. pombe cultures exposed to heat shock, nitrogen starvation, peroxide and two commonly applied media, YES and EMM2, using Cap Analysis of Gene Expression (CAGE). We show that CAGE-based annotation of TSS is substantially more accurate than existing PomBase annotation, and that S. pombe core promoters commonly initiate transcription bidirectionally at the edges of nucleosomes, but do not show sharp and dispersed TSS distributions as higher eukaryotes. Our data recapitulate known S. pombe stress expression response patterns, but also identify stress-responsible alternative TSSs. Importantly, growth media change induces changes of similar magnitude as some stressors. Integration of genetic variation data shows a link between nucleosome occupancy and genetic variation, and that the proximal promoter region is genetically diverse between S. pombe strains compared to the TATA and TSS regions. Our data constitute a central resource for S. pombe gene regulation research.