Identification of transcription factor target genes by ChIP display

Abstract

Transcription factors play pivotal roles in the control of cell growth and differentiation in health and disease. In the post-genomic era, it has become possible to locate the regions occupied by transcription factors throughout the genome, leading to better understanding of their mechanism of action and the genes that they regulate. All methods for transcription factor location analysis utilize chromatin immunoprecipitation (ChIP). Although ChIP was initially used to test whether a protein binds to a candidate promoter in living cells, newly developed methods allow the unbiased identification of novel targets of transcription factors. This chapter describes ChIP Display, an affordable method for transcription factor location analysis. Despite being relatively low throughput compared with alternative methods such as ChIP-chip and ChIP-SAGE, ChIP Display provides even small molecular biology laboratories with the opportunity to discover novel targets of any transcription factor, for which high-quality antibodies are available. © 2008 Humana Press, a part of Springer Science+Business Media, LLC.