Lessons from a Model Organism

We have determined how the 200 transcriptional regulators encoded in the eukaryote Saccharomyces cerevisiae associate with genes across the genome in living cells. Just as maps of metabolic networks describe the potential pathways that may be used by a cell to accomplish metabolic processes, this network of regulator-gene interactions describes potential pathways yeast cells can use to regulate global gene expression programs. We used this information to identify regulatory motifs, the simplest units of network architecture, and demonstrated that an automated process can use motifs to assemble a transcriptional regulatory network structure. Our results revealed that eukaryotic cellular functions are highly connected through networks of transcriptional regulators that regulate other transcriptional regulators.

Chromatin plays a fundamental role in the regulation of nuclear processes such as gene expression and chromosome maintenance. We have mapped nucleosome modifications that occur during transcription genome-wide, thus revealing how gene transcription and histone modification is linked at all genes. OResults provide new insights into the temporal association of chromatin regulators with protein coding genes and reveal how numerous chromatin regulators are recruited to specific regions of the genome.