A Comprehensive Yeast Epigenome Probed by ChIP-exo Reveals Fundamental Distinctions in Gene Regulation

Hundreds of diverse proteins bind to the Saccharomyces genome to orchestrate transcription. Here we present the most comprehensive look at the yeast “epigenome” (defined here as the set of measurable genome-interacting proteins) through the use of ultra-high resolution chromatin immunoprecipitation followed by exonuclease (ChIP-exo). We collected datasets on over 800 unique proteins from rapidly growing cells in rich media. Approximately 500 produced biologically interpretable data. We created a website that allows users to quickly assess the quality and binding pattern of each protein by visualizing processed sequencing reads, peaks, and lists of bound genes. These data provide a comprehensive DNA-centric structural view of how proteins are organized into complexes across the genome, including the architectural basis of two fundamental gene classes: constitutive and induced. Constitutive genes are not directly controlled by sequence-specific activators and coactivators, despite many having sequence-specific chromatin regulatory factors bound in their promoters. In contrast, induced genes utilize a wide range of activators and coactivators to modulate transcription. Findings that will be discussed include the molecular basis of inducible versus constitutive transcription, including the role of nucleosome organization, and distinct mechanisms of PIC assembly.
This data was created at the Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA