Study Design

• Genetic Reagents
• Technology
• Error Rates
• Location Analysis Protocols
• Growth Environments
• Microarray Analysis

Data

• Search Regulatory Code Map
• Download Location Data
• Motif Discovery Data

Insights

• DNA Binding Site Sequences
• Transcriptional Regulatory Code
• Promoter Architecture
• Environment-specific Binding

Additional Insights

• Proteome Genome Interactions
• Discriminative Motifs
• Challenges for the Future: Finishing the Draft Code

Supplementary Materials

• Supplementary Methods
• Supplementary Figures
• Supplementary Tables

Acknowledgements

DNA-binding transcriptional regulators interpret the genome’s regulatory code by binding to specific sequences to induce or repress gene expression. Comparative genomics has recently been used to identify potential cis-regulatory sequences within the yeast genome on the basis of phylogenetic conservation, but this information alone does not reveal if or when transcriptional regulators occupy these binding sites. We have constructed a draft of yeast’s transcriptional regulatory code by mapping the sequence elements that are bound by regulators under various conditions and that are conserved among Saccharomyces species. The organization of regulatory elements in promoters and the environment-dependent use of these elements by regulators are discussed. We find that environment-specific use of regulatory elements predicts mechanistic models for the function of a large population of yeast’s transcriptional regulators.