Review Identifying transcriptional targets Nicola V Taverner, James C Smith and Fiona C Wardle Addresses: Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Zoology, University of Cambridge, Cambridge CB2 1QR, UK. Correspondence: Fiona C Wardle. E-mail: comment reviews Published: 27 February 2004 Genome Biology 2004, 5:210 The electronic version of this article is the complete one and can be found online at © 2004 BioMed Central Ltd reports Abstract Identifying the targets of transcription factors is important for understanding cellular processes. We review how targets have previously been isolated and outline new technologies that are being developed to identify novel direct targets, including chromatin immunoprecipitation. | Review Identifying transcriptional targets Nicola V Taverner James C Smith and Fiona C Wardle Addresses Wellcome Trust Cancer Research UK Gurdon Institute and Department of Zoology University of Cambridge Cambridge CB2 1QR UK. Correspondence Fiona C Wardle. E-mail Published 27 February 2004 Genome Biology 2004 5 210 The electronic version of this article is the complete one and can be found online at http 2004 5 3 210 2004 BioMed Central Ltd Abstract Identifying the targets of transcription factors is important for understanding cellular processes. We review how targets have previously been isolated and outline new technologies that are being developed to identify novel direct targets including chromatin immunoprecipitation combined with microarray screening and bioinformatic approaches. The control of many cellular processes requires the coordinated activation or repression of genes in the correct spatial and temporal patterns. This regulation is carried out in large part by transcription factors which bind to DNA sequences within chromatin and activate or repress the transcription of nearby genes. This binding is frequently sequence-specific with sequence recognition being carried out by the transcription factor itself or by other proteins complexed to it. Identification of the targets of each transcription factor provides information about individual processes and how transcription factors interact in a transcriptional network. These networks can then be used to describe a particular cellular process or even something as complicated as embryonic development 1 2 . The first step in identifying targets of a transcription factor usually involves overexpression or knockdown of the factor in question and analysis of the resulting changes in gene expression. The development of microarray technology has facilitated this kind of analysis allowing identification of many more downstream genes than was previously feasible. But this
