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