Genome-wide mapping of protein-DNA interaction by chromatin immunoprecipitation and DNA microarray hybridization (ChIP-chip). Part A: ChIP-chip molecular methods.

Chromatin immunoprecipitation in combination with DNA-microarray hybridization (ChIP-chip) allows the identification of chromatin regions that are associated with modified forms of histones on a genomic scale. The ChIP-chip workflow consists of the following steps: generation of biological material, in vivo formaldehyde-fixation of protein-DNA and protein-protein interactions, chromatin preparation and shearing, immunoprecipitation of chromatin with specific antibodies, fixation reversal and DNA purification, DNA amplification, microarray hybridization, and data analysis. In Part A of this chapter, we describe molecular methods of the experimental procedure employed to identify chromosomal regions of Arabidopsis thaliana associated with H3K27me3. In addition, some general information on the microarray platform from Roche-NimbleGen will be provided. Part B of this chapter focuses on ChIP-chip data analysis of H3K27me3 on the Roche-NimbleGen platform.