Abstract
Chromatin immunoprecipitation (ChIP) is a well-characterized procedure used to reveal specific patterns of protein-DNA interactions and identify the binding sites of proteins on DNA. ChIP has been used to study many aspects of Drosophila biology, including neurobiology. This protocol describes in detail how to prepare cross-linked chromatin from Drosophila antennae and brains followed by immunoprecipitation (X-ChIP). We first describe tissue dissection, chromatin cross-linking with formaldehyde, quenching of the cross-linking, homogenization of tissues, and sonication for shearing the chromatin. Additionally, we describe how to optimize the sonication efficiency and fixation time and concentration using Drosophila brain samples as an example. These parameters are crucial for successful ChIP.
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