ChIP-chip is the first, and most simple of the advanced ChIP technologies (it also has the most fun to say name). First described in 2000 (Ren et al., 2000), ChIP-chip couples chromatin IP to microarray analysis allowing genome-wide analysis of protein or modifications of interest distribution (Aparicio et al., 2004).
Chromatin IP is done using an antibody against a protein or protein modification of interest. The resulting purified DNA sample and the input sample (DNA prior to IP) are each fluorescently labeled and co-hybridized to a microarray. Any of the variety of commercially available microarrays can be used giving researchers control of the experimental scale.
Another major advantage is cost: microarray technology is now relatively inexpensive, allowing many samples to be processed. The disadvantages of ChIP-chip are derived from the inherent limitations of microarray technology.
Microarrays are limited in resolution compared to sequencing, which can be very important in pinpointing POI binding sites in the genome. Further, ChIP-chip has a higher signal to noise ratio than sequencing technologies, meaning subtle interactions are lost (Ho et al., 2011). ChIP-chip has been instrumental in understanding the structure and function of the human genome (Kim et al., 2005).
ChIP-chip Additional Reading
This review is one of the seminary documents describing ChIP-chip. The authors give a good intro to the technology, and describe in a step-by-step, FAQ manner how ChIP-chip is performed.
Reference List
- Aparicio, O., Geisberg, J.V., and Struhl, K. (2004). Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo. Curr. Protoc. Cell. Biol. Chapter 17, Unit 17.7.
- Ho, J.W., Bishop, E., Karchenko, P.V., Negre, N., White, K.P., and Park, P.J. (2011). ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis. BMC Genomics 12, 134-2164-12-134.
- Kim, T.H., Barrera, L.O., Zheng, M., Qu, C., Singer, M.A., Richmond, T.A., Wu, Y., Green, R.D., and Ren, B. (2005). A high-resolution map of active promoters in the human genome. Nature 436, 876-880.
- Ren, B., Robert, F., Wyrick, J., Aparicio, O., Jennings, E., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E., et al. (2000). Genome-wide location and function of DNA binding proteins. Science 290, 2306-+.