|Title||Genomewide identification of protein binding locations using chromatin immunoprecipitation coupled with microarray.|
|Publication Type||Journal Article|
|Year of Publication||2008|
|Authors||Cho B-K, Knight EM, Palsson BØ|
|Journal||Methods in molecular biology (Clifton, N.J.)|
|Keywords||Base Sequence, Chromatin Immunoprecipitation, DNA Primers, Genome, Oligonucleotide Array Sequence Analysis, Protein Binding|
Interactions between cis-acting elements and proteins play a key role in transcriptional regulation of all known organisms. To better understand these interactions, researchers developed a method that couples chromatin immunoprecipitation with microarrays (also known as ChIP-chip), which is capable of providing a whole-genome map of protein-DNA interactions. This versatile and high-throughput strategy is initiated by formaldehyde-mediated cross-linking of DNA and proteins, followed by cell lysis, DNA fragmentation, and immunopurification. The immunoprecipitated DNA fragments are then purified from the proteins by reverse-cross-linking followed by amplification, labeling, and hybridization to a whole-genome tiling microarray against a reference sample. The enriched signals obtained from the microarray then are normalized by the reference sample and used to generate the whole-genome map of protein-DNA interactions. The protocol described here has been used for discovering the genomewide distribution of RNA polymerase and several transcription factors of Escherichia coli.
|Alternate Journal||Methods Mol. Biol.|