Saccharomyces cerevisiae ChIP-seq

We have combined biochemical purification of Mediator from chromatin with ChIP-sequencing and transcript microarrays to study global effects in vivo of a glucose-to-glycerol switch, which affects expression of about 50% of all yeast genes. Our results reveal changes in nucleosome patterns and DNA binding of Msn2, RNA polymerase II, and subunits from the Mediator Head, Middle, Tail and Kinase modules after the switch. We find that promoters can be clustered in distinct classes according to their nucleosome array patterns, which show very limited global nucleosome rearrangements following nutrient downshift. Moreover, we show that Mediator is associated with a distinct but very limited set of promoters, both before and after the switch. Biochemical purification and ChIP-sequencing reveal that Mediator exists in chromatin in multiple forms that are dynamically recruited or displaced at promoters after the switch.