Chromatin immunoprecipitation of activated yeast signal transduction protein kinases
ABSTRACT: Cellular signal transduction pathways modify gene expression programs in response to changes in the environment, but the mechanisms by which they regulate populations of genes under their control are not entirely understood. We present evidence that most mitogen-activated protein kinases and protein kinase A subunits become physically associated with the genes they regulate in the yeast genome. The ability to detect this interaction of signaling kinases with target genes can be used to map more precisely and comprehensively the regulatory circuitry that eukaryotic cells use to respond to their environment.
Eukaryotic genomes are packaged into nucleosomes whose position and chemical modification state can profoundly influence regulation of gene expression. We profiled nucleosome modifications across the yeast genome using chromatin immunoprecipitation coupled with DNA microarrays to produce high-resolution genome-wide maps of histone acetylation and methylation. These maps take into account changes in nucleosome occupancy at actively transcribed genes and, in doing so, revise previous assessments o ...[more]
Project description:We explore the genome-wide occupancy of 4 different chromatin regulating complexes encoded in S. cerevisiae. We provide the data for histone acetyltransferases Gcn5 and Esa1 and histone deacetylases Hst1 and Rpd3/Sin3 under rich growth condition (YPD medium). We also include the occupancy data for RNA polymerase II under the same growth condition.
Project description:Genomic binding of 203 transcriptional regulatory proteins under various conditions. Hybridizations of fluorescently-labelled immunoprecipitated vs. whole-cell extract samples on S. cerevisiae intergenic arrays.
Project description:Genomes are packaged into nucleosomes whose position and modification state can profoundly influence regulation of gene expression. We have established new ChIP-based high-resolution genome-wide maps of histone acetylation and methylation that take into account changes in nucleosome occupancy at actively transcribed genes. These maps provide a more accurate picture of nucleosome occupancy and the nature of modifications associated with transcriptional activity in this eukaryotic genome. We describe the combination of modifications that occur at the average transcribed gene.
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