ChIP-on-chip

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The first ChIP refers to chromatin immunoprecipitation and the second to microarray technology, thus ChIP-chip is a technique combining the use of the two technologies. Like regular ChIP, ChIP-chip is used for deducing interactions between proteins and DNA in vivo.

A whole genome ChIP-chip analysis can be performed to determine the locations of binding sites for proteins of interest; this allows the identification of the cistrome, which are the total number of binding sites for DNA binding proteins.

The goal of ChIP-chip is the localisation of protein binding sites in the genome, in the context of chromatin. Examples of proteins operating around chromatin including transcription factors, replication-related proteins, and histones. ChIP-chip may be used to determine transcription factor binding sites (TFBSs) in the genome; these TFBSs may be promoters, enhancers, repressors and silencing elements, insulators, boundary elements, and sequences that control DNA replication. Using ChIP-chip for studying histones may allow the identification of modification sites, which may offer insights into the mechanisms of transcriptional regulation.

One powerful use of ChIP-chip is the cataloguing of all protein DNA interactions under different conditions, which is one of the long term goals. This knowledge will further our understanding of the machinery behind gene regulation, cell proliferation and disease progression. It is also commonly used in epigenetics studies.