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. Author manuscript; available in PMC: 2009 Aug 17.
Published in final edited form as: Curr Opin Biotechnol. 2006 Jul 12;17(4):422–430. doi: 10.1016/j.copbio.2006.06.015

Figure 1. ChIP-chip.

Figure 1

(a) Types of DNAs used in ChIP-chip. Oligonucleotide tiling genomic regions (left); PCR amplification of genomic regions (right). (b) ChIP-chip experimental design. A large variety of protein-DNA and protein-protein crosslinks are created nonspecifically, due to the nonspecific nature of formaldehyde crosslinking. An antibody (orange) either specific for the protein of interest (blue) or specific for an epitope tag fused to the protein of interest is used in immunoprecipitation (IP) in the experimental sample. This IP will enrich for the target protein, including protein directly bound to genomic DNA binding sites, and also protein indirectly associated with DNA via protein-protein interactions. A control (“mock”) IP is performed using either no antibody, an irrelevant antibody, or pre-immune IgG antibodies. This mock IP is not expected to enrich for the target protein of interest.