Combining chromatin immunoprecipitation and oligonucleotide tiling arrays (ChIP-Chip) for functional genomic studies

Central to systems biology are genome-wide technologies and high-throughput experimental approaches. Completion of the sequencing of the human genome as well as those of a number of other higher eukaryotes now allows for the first time the mapping of all of the cis-regulatory regions of genes as well as the details of nucleosome position and modification. One approach to achieving this goal involves chromatin immunoprecipitation combined with DNA oligonucleotide tiling arrays (ChIP-chip). This allows for the identification of genomic regions bound by a given factor, its cistrome, or harboring a given epigenomic modification through hybridization on tiling arrays covering the entire genome or specific regions of interest. This technology offers an unbiased assessment of the potential biological function of any DNA associated factor or epigenomic mark. Through integration of ChIP-chip data with complementary genome-wide approaches including expression profiling, CGH and SNP arrays, novel paradigms of transcriptional regulation and chromatin structure are emerging.