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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 method gives no information about whether targets are regulated directly by the transcription factor through binding to regulatory sequences within the gene or whether regulation is indirect, through the activation of intermediate genes. Other techniques, such as chromatin immunoprecipitation (ChIP) and Dam methylase identification (DamID), have therefore been developed. These reveal where in the genome the transcription factor is bound; these approaches allow identification of many direct target sequences, particularly when it is combined with microarrays of genomic DNA. This type of information, in combination with genomic sequences, is now being used to develop computational algorithms that scan genomic sequence with the aim of distinguishing functional binding sites and target genes of transcription factors. Identification of downstream genesComparison of two cell populations in which a given transcription factor is differentially expressed, either by overexpression or knockdown, has been used to identify the target genes activated by transcription factors in a wide range of systems. The resulting mRNA populations may be analyzed in a number of ways, such as reverse-transcriptase-coupled (RT-)PCR of candidates, subtractive hybridization, differential display or serial analysis of gene expression (SAGE; see Figure 1). For instance, a large-scale screen to describe transcriptional networks in the development of sea urchins has recently been undertaken: genes involved in endomesoderm development -including those encoding tra...

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