Chromosome-wide analysis of protein binding and modifications

In order to fully understand the functions of a DNA-binding protein it is necessary to identify all of its binding sites in chromosomes, so that the role of each site in the overall biological function of the factor can be assessed. An approach called ChIP-on-Chip, which combines the chromatin immunoprecipitation technique with chromosomal DNA microarray analysis, has proven to be a powerful means for the chromosome-wide identification of protein binding sites. This approach can also be used to characterize chromosome-wide variations in patterns of post-translational protein modifications, for example histone modifications. This chapter presents methodologies for the ChIP-on-Chip analysis, using as an example the identification of chromosome-wide binding sites for the TATA-binding protein in mitotic cells.