Genome-wide Studies of Transcriptional Regulation in Yeast

In this thesis, nutrient signalling in yeast is used as a model to study several features of gene regulation, such as combinatorial gene regulation, the role of motif context and chromatin modifications. The nutrient signalling system in yeast consists of several pathways that transmit signals about the availability of key nutrients, and regulate the transcription of a large part of the genome. Some of the signalling pathways are also conserved in other eukaryotic species where they are implicated in processes such as aging and in human disease. Combinatorial gene regulation is examined in papers I and II. In paper I, the role of Mig1, Mig2 and Mig3 is studied. To elucidate how the three proteins contribute to the control of gene expression, we used microarrays to study the expression of all yeast genes in the wild type and in all seven possible combinations of mig1, mig2 and mig3 deletions. In paper II, a similar strategy is used to investigate Gis1 and Rph1, two related transcription factors. Our results reveal that Rph1 is involved in nutrient signalling together with Gis1, and we find that both the activities and the target specificities of Gis1 and Rph1 depend on the growth phase. Paper III describes ContextFinder, a program for identifying constraints on sequence motif locations and orientations. ContextFinder was used to analyse over 300 cases of motifs that are enriched in experimentally selected groups of yeast promoters. Our results suggest that motif context frequently is important for stable DNA binding and/or regulatory activity of transcription factors. In paper IV, we investigated how gene expression changes resulting from nitrogen starvation are accompanied by chromatin modifications. Activation of gene expression is concentrated to specific genomic regions. It is associated with nucleosome depletion (in both promoters and coding regions) and increased levels of H3K9ac (but not H4K5ac)