Finding primary targets of transcriptional regulators

Transcriptional regulators directly regulate the transcription of primary target genes by occupying genomic response elements proximal to the target promoters. In turn, regulation of primary target genes triggers subsequent physiological events by acting on distinct biological pathways and modulating the expression of secondary target genes. Thus, distinguishing primary and secondary target genes is critical for our understanding of mechanisms underlying the biological effects of a regulator. In this article, four distinct strategies for identification of primary target genes are compared and discussed: bioinformatic approaches, ChIP on chip, and two novel strategies, ChIP scanning and in vitro genomic selection. Overall, these approaches complement each other, and depending on available information and resources, the appropriate methods can be chosen to identify primary target genes for a particular regulator.