Important regulators of gene networks are transcription factors because they determine which genes in the network are activated or inhibited at a certain time or condition. The function of a transcription factor (TF) in a given network is determined by its dynamic interaction with other proteins like transcriptional cofactors and the target genes that it controls. Hence, to map transcriptional regulatory networks and get insight in their regulation, we develop genome wide technologies to identify the transcription factors involved, their protein interactions and target cis-regulatory motives (CRMs) or genes.
Target CRMs or genes of TFs can be determined through chromatin immunoprecipitation (ChIP). The traditional ChIP protocols are based on the use of specific antibodies for immunoprecipitation and isolation of TF-bound DNA fragments. However, for each TF a new polyclonal serum must be developed which is time consuming and not easy when working with TFs that belong to protein families with high sequence analogy. To achieve genome wide isolation of target genes, the isolated DNA fragments are hybridized on a genomic array (ChIP on chip). Here, problems often arise with sensitivity and experimental background. We are on the road to develop new CHIP protocols based on TAP technology.