Genomewide identification of protein binding locations using chromatin immunoprecipitation coupled with microarray.

TitleGenomewide identification of protein binding locations using chromatin immunoprecipitation coupled with microarray.
Publication TypeJournal Article
Year of Publication2008
AuthorsCho B-K, Knight EM, Palsson BØ
JournalMethods in molecular biology (Clifton, N.J.)
Volume439
Pagination131-45
PubMed Date2008
ISSN1064-3745
KeywordsBase Sequence, Chromatin Immunoprecipitation, DNA Primers, Genome, Oligonucleotide Array Sequence Analysis, Protein Binding
Abstract

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 JournalMethods Mol. Biol.
PubMed ID18370100

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