Eukaryotic genes respond to their environment by changing the expression of selected genes. The question we address here is whether distinct transcriptional responses to different environmental signals elicit distinct modes of assembly of the transcription machinery. In particular, we examine transcription complex assembly by the stress-directed SAGA complex versus the housekeeping assembly factor TFIID. We focus on genomic responses to the DNA damaging agent methyl methanesulfonate (MMS) in com ...[more]
Project description:High-resolution genome-wide mapping of the yeast transcription machinery. ChIP-chip was performed to identify the genomic binding locations for each factor. <br><br>Processed data files are also available on the FTP server for this experiment.
Project description:Crosslinked chromatin was digested with Micrococcal nuclease and immunopurified for Rpb3, a subunit of RNA Polyermase II. chIP'd DNA was hybridized to Drosophila tiling arrays and nucleosomes that were bound by Pol II were mapped.
Project description:A comprehensive genome-wide binding profile for Hmt1 was obtained through the method of ChIP-chip using NimbleGen high-resolution tiling microarrays. Of the approximately 1000 Hmt1-binding sites found, the majority fall within or proximal to an ORF. However, Hmt1 occupancy is found at a number of other genomic features such as tRNA and snoRNA genes, thereby implicating a regulatory role in the biogenesis of these non-coding RNAs. RNA hybridization analysis shows that Hmt1 loss-of-function mutants display higher steady-state tRNA abundance relative to the wild-type. Co-immunoprecipitation studies show that Hmt1 interacts with the TFIIIB component Bdp1, suggesting a role for Hmt1 in modulating RNA pol III transcription to regulate tRNA production. ChIP-chip of Hmt1-9myc using Nimblegen high-resoluion tiling arrays
Project description:In this study, we generate genomic maps of Mediator, Pol II, TBP, TFIIH, TFIIA, TFIIB, TFIIE, TFIIF, by ChIP coupled to next generation sequencing technology (ChIP-seq), in wild type strains from Saccharomyces cerevisiae and in a mutant for the Mediator essential subunit Med10
Project description:This aim of this experiment is to assess the genome-wide Rad2 occupancy in yeast Saccharomyces cerevisiae by ChIP-chip, in the absence of exogenous genotoxic stress. A related study involving ChIP-seq analysis of Rad2 occupany is also deposited at ArrayExpress under accession number E-MTAB-1595 ( www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1595 ).
Project description:We used a systems approach to identify target genes and genome wide chromatin binding preferences of the transcription factor WUSCHEL (WUS) in Arabidopsis thaliana. First, we recorded changes in the transcriptome after genetically perturbing the regulatory system of the stem cell niche at various developmental stages by loss-of-function and inducible over-expression alleles of WUS and its antagonist CLV3. Then, identified direct WUS target genes by chromatin immuno-precipitation (ChIP.
Project description: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.