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We have determined how most of the 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(More)
Genome-wide expression analysis was used to identify genes whose expression depends on the functions of key components of the transcription initiation machinery in yeast. Components of the RNA polymerase II holoenzyme, the general transcription factor TFIID, and the SAGA chromatin modification complex were found to have roles in expression of distinct sets(More)
Genome-wide location analysis was used to determine how the yeast cell cycle gene expression program is regulated by each of the nine known cell cycle transcriptional activators. We found that cell cycle transcriptional activators that function during one stage of the cell cycle regulate transcriptional activators that function during the next stage. This(More)
SUMMARY To better understand the regulatory networks that control plant gene expression, tools are needed to systematically analyze and visualize promoter regulatory sequences in Arabidopsis thaliana. We have developed the Athena database, which contains 30,067 predicted Arabidopsis promoter sequences and consensus sequences for 105 previously characterized(More)
In the past year, great strides have been made in our understanding of the regulatory networks that control gene expression in the model eukaryote Saccharomyces cerevisiae. The development and use of a number of genomic tools, including genome-wide location and expression analysis, has fueled this progress. In addition, a variety of computational algorithms(More)
UNLABELLED Covalent modifications to histone proteins play a critical role in regulating gene transcription. Previous studies have used chromatin immunoprecipitation (ChIP) based microarray assays to profile genomic regions that are enriched or depleted for a particular histone modification. Such studies have been conducted extensively in the yeast(More)
Methylation of specific histone lysine residues regulates gene expression and heterochromatin function, but little is known about its role in DNA repair. To examine how changes in conserved methylated residues of histone H3 affect nucleotide excision repair (NER), viable H3K4R and H3K79R mutants were generated in Saccharomyces cerevisiae. These mutants show(More)
SUMMARY Rice (Oryza sativa L.) is an important model monocot and cereal crop. While the rice genome sequence has been published and annotated, relatively little is known about the transcriptional networks that regulate rice gene expression. For this reason, we have developed Osiris, a database containing promoter sequences, predicted transcription factor(More)
MOTIVATION There is accumulating evidence that the chromatin environment of transcription factor (TF) binding sites in promoter regions has a critical influence on their regulatory potential. Recent studies have mapped TF binding sites and nucleosome positions throughout the yeast genome; however, there is a lack of computation tools to integrate these data(More)