UCSF

Eukaryotic transcriptional regulation is mediated by the organization of chromatin in promoter regions. This thesis describes three projects which examine the relationships between chromatin and transcriptional regulation in the budding yeast S. cerevisiae. First we describe a novel computational algorithm fREDUCE for the elicitation of regulatory motifs given sequence and expression data as inputs. fREDUCE is used to find TnC motifs, novel repetitive sequences occurring prominently within nucleosome-free regions of promoters. The second chapter describes the relationships between TnC and chromatin structure in fine details. We conclude that TnC motifs constitute directional signature sequences which likely play roles in defining the locations of nucleosome-free regions in a majority of yeast promoters. Finally, we also undertake a quantitative and systematic examination of the relationship between transcription factors, their binding sites, and their corresponding chromatin environments. We find that the yeast transcriptome encompasses a diverse set of signature TF-chromatin relationships. Taken together, these three studies examine multiple facets of the intricate nature of chromatin regulation in a simple eukaryotic organism.