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 immunopre-cipitating 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-transla-tional 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.

Microarrays provide an excellent platform for investigating changes on a genomic scale. The first microarrays to be designed and used were cDNA microarrays, which have been routinely used to characterize variations in gene expression (7, 8). More recently, genomic microarrays have become available as the entire genome has been sequenced and the gene regulatory regions have become better known. One potential application is the use of comparative genomic hybridization (CGH) to investigate DNA copy-number imbalances in cancer at high resolution (9). The development of novel types of genomic microarray also provides an exceptional opportunity for a new application: hybridization of ChIP samples on a microarray (ChIP-on-chip). With this elegant combination of techniques it is now possible to uncover novel binding target sequences for nuclear factors or DNA sequences with specific histone-modification patterns (10, 11) on a genomic scale.

Specific primers "ChIP"

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