Using Chromatin Immunoprecipitation (ChIP) to Study the Chromatin State in Drosophila

The chromatin state plays an important role in regulating gene expression, which affects organismal development and plasticity. Proteins, including transcription factors, chromatin modulatory proteins, and histone proteins, usually with modifications, interact with gene loci involved in cellular differentiation, function, and modulation. One molecular method used to characterize protein-DNA interactions is chromatin immunoprecipitation (ChIP). ChIP uses antibodies to immunoprecipitate specific proteins cross-linked to DNA fragments. This approach, in combination with quantitative PCR (qPCR) or high-throughput DNA sequencing, can determine the enrichment of a certain protein or histone modification around specific gene loci or across the whole genome. ChIP has been used in Drosophila to characterize the binding pattern of transcription factors and to elucidate the roles of regulatory proteins in gene expression during development and in response to environment stimuli. This review outlines ChIP procedures using tissues from the Drosophila nervous system as an example and discusses all steps and the necessary optimization.