Transcriptional Genomics

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A major goal in efforts to understand the mechanisms by which signal transduction pathways regulate programs ofgene expression is to identify their direct target genes and to determine the specificcomponents of the transcriptional machinery that are recruited to these genes in response to regulatory signals. To support these goals, the Transcriptional GenomicsCorewill provide three complementary services toPPG investigators; conventional gene expression (Chip)microarray analysis, recently developed genomic(ChlP- Chip) microarrayanalysis, and associated Bioinformaticssupport for experimental design oversight and data analysis. Conventional expression analysis will utilize commercially available microarrays (e.g., Affymetrix, Agilent and Illumina microarrays). Recent progress in combining the use of chromatin immunoprecipitation (ChIP) assays with DNAmicroarrays has allowed genome-wideanalysis oftranscription factor localization to specific promoter sequences in living cells. The PPGTranscriptional GenomicsCorewill fabricate murine intergenic/promoter microarrays for conventional ChlP-Chipand ChlP-DSL approaches to allowgenome- wide location analysis of PPARs,NCoR, SMRT, and other transcription factors of relevanceto this application. Effective utilization of genome-wide approaches requires an understanding ofthe strengths and limitations ofthese technologies, particularly with respect to sources of error and the number of experimental replicates that are required to develop gene lists at defined and acceptable false positive and false negative rates. Personnel within the PPGTranscriptional Genomics Corewill interact with scientists within each ofthe Projects to provide experimental design oversight focused on these issues. Once microarray experiments are performed and raw data is collected, the Transcriptional Genomics Core will utilize standard tools to develop gene lists at specifiedlevels of confidence and perform secondary analysis (e.g., Gene Ontology analysis, mapping to KEGG pathways, etc.). The Transcriptional Genomics Core will provide a database infrastructure for data storage and retrieval to allow integration of data collected across the PPGand the application of more sophisticated bioinformatics approaches outlined in each of the Projects.