In vivo transcription factor DNA binding analysis

DESCRIPTION (provided by applicant): Currently, there exist a number of methods for the study of transcription factors and gene-promoter activity. These include reporter gene assays, gel shift assays, and expression-profiling methods such as microarray analysis and SAGE. These methods are well established and have been used to generate a wealth of information. Accordingly, there are many commercially available kits designed to facilitate and speed these analyses. However, none of the above methods enables identification of the DNA targets that are actually bound by a particular transcription factor in a particular population of cells. The current best method to generate this type of transcription "snapshot" is the Chromatin Immunoprecipitation (CHIP) assay. This method is technically demanding and is not well supported by commercially available complete kits. Similarly, a powerful extension of the CHIP assay, specifically, the merging of the CHIP assay with microarray analysis of the immunoprecipitated DNA, is not available commercially. We propose to develop reagents to simplify and extend use of the CHIP assay for the study of transcription factor/DNA interactions in living mammalian cells. The long-term objective of this proposal is the development and commercialization of novel kits and reagents that speed the study of in vivo interactions between transcription factors and DNA.