chapter  14
12 Pages

ChIP-on-chip: searching for novel transcription factor targets

ByEsteban Ballestar, Manel Esteller

Chromatin immunoprecipitation (ChIP) is currently the most powerful technique for investigating in vivo interactions between a nuclear factor and its genomic target sequences (1, 2). The technique consists of immunoprecipitating chromatin with specific antibodies to isolate DNA sequences that are bound by the nuclear proteins against which the antibodies are raised. After that, immunoprecipitated DNA is typically analyzed by PCR with specific primers to investigate the presence of a candidate DNA sequence. In practice, two different aspects can be explored. One is the binding of different nuclear factors to their binding sites (3, 4) (Figure 14.1). The other is that, since histones are associated with DNA throughout the entire genome, it is possible to explore the association of different post-translational modifications of histones with specific genomic sequences by using antibodies that recognize these modifications (5, 6) (Figure 14.1). Consequently, ChIPs provide dynamic information about not only nuclear factor occupancy at their target binding sites but also specific histone modification patterns in selected DNA sequences.