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Binding data for nine transcription factors for S. cerevisiae salt response

ABSTRACT: Complex biological processes are often regulated, at least in part, by the binding of transcription factors to their targets. Recently, considerable effort has been made to analyze the binding of relevant factors to the suite of targets they regulate, thereby generating a regulatory circuit map. However, for most studies the dynamics of binding have not been analyzed and thus the temporal order of events and mechanisms by which this occur are poorly understood. We have globally analyzed in detail the temporal order of binding of several key factors involved in the salt response of yeast to their target genes. Analysis of Yap4 and Sko1 binding to their target genes revealed multiple classes of binding patterns to target genes: 1) constant binding (Yap4 and Sko1 Class 1), 2) rapid induction (Yap4 and Sko1 Class 2) 3) slow induction (Yap4 Class 3) and 4) transient induction (Sko1 Class 3, Yap4 minor binding Class 4). These results demonstrate that individual transcription factors can have multiple binding patterns and help define the different types of temporal binding patterns used in eukaryotic gene regulation. To investigate these binding patterns further, we also analyzed the binding of seven other key transcription factors implicated in osmotic regulation, including Hot1, Msn1, Msn2, Msn4, Skn7 and Yap6, and found significant coassociation among the different factors at their gene targets. Moreover, the binding of several key factors was correlated with distinct classes of Yap4 and Sko1 binding patterns and with distinct types of genes. Correlation of each class with gene expression studies revealed association of Yap4, Sko1 and other transcription factor binding patterns with different gene expression patterns. The integration and analysis of binding and expression information reveals a complex dynamic and hierarchical circuit in which specific combinations of transcription factors target distinct sets of genes at discrete times to coordinate a rapid and important biological response.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE15639 | GEO | 2009/04/16

SECONDARY ACCESSION(S): PRJNA115641

REPOSITORIES: GEO

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Project description:Complex biological processes are often regulated, at least in part, by the binding of transcription factors to their targets. Recently, considerable effort has been made to analyze the binding of relevant factors to the suite of targets they regulate, thereby generating a regulatory circuit map. However, for most studies the dynamics of binding have not been analyzed and thus the temporal order of events and mechanisms by which this occur are poorly understood. We have globally analyzed in detail the temporal order of binding of several key factors involved in the salt response of yeast to their target genes. Analysis of Yap4 and Sko1 binding to their target genes revealed multiple classes of binding patterns to target genes: 1) constant binding (Yap4 and Sko1 Class 1), 2) rapid induction (Yap4 and Sko1 Class 2) 3) slow induction (Yap4 Class 3) and 4) transient induction (Sko1 Class 3, Yap4 minor binding Class 4). These results demonstrate that individual transcription factors can have multiple binding patterns and help define the different types of temporal binding patterns used in eukaryotic gene regulation. To investigate these binding patterns further, we also analyzed the binding of seven other key transcription factors implicated in osmotic regulation, including Hot1, Msn1, Msn2, Msn4, Skn7 and Yap6, and found significant coassociation among the different factors at their gene targets. Moreover, the binding of several key factors was correlated with distinct classes of Yap4 and Sko1 binding patterns and with distinct types of genes. Correlation of each class with gene expression studies revealed association of Yap4, Sko1 and other transcription factor binding patterns with different gene expression patterns. The integration and analysis of binding and expression information reveals a complex dynamic and hierarchical circuit in which specific combinations of transcription factors target distinct sets of genes at discrete times to coordinate a rapid and important biological response. Yeast was grown in minimal medium to mid-log phase, then salt concentration was raised to 0.6M for various time periods before harvesting. Chromatin from a strain containing myc-labeled transcription factor and from a control strain were processed for chromatin immunoprecipitation, and hybridized to a chromosome-tiling microarray. Yap4 and Sko1 time courses data were normalized across time points using calibration curves derived from ChIP-qPCR data for various chromosomal locations. These calibration data can be obtained from http://archive.gersteinlab.org/proj/yeast_salt/. The same Web site also has the processed form of the data as it was used in the analysis reported in Ni, Bruce et al, (2009, Genes & Development).

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Binding data for nine transcription factors for S. cerevisiae salt response

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