An Optimized Chromatin Immunoprecipitation Protocol for Quantification of Protein-DNA Interactions
Wim J. de Jonge, Mariël Brok, Patrick Kemmeren, Frank C. P. Holstege
Abstract
Transcription factors are important regulators of cell fate and function. Knowledge about where transcription factors are bound in the genome is crucial for understanding their function. A common method to study protein-DNA interactions is chromatin immunoprecipitation (ChIP). Here, we present a revised ChIP protocol to determine protein-DNA interactions for the yeast Saccharomyces cerevisiae. We optimized several aspects of the procedure, including cross-linking and quenching, cell lysis, and immunoprecipitation steps. This protocol facilitates sensitive and reproducible quantitation of protein-DNA interactions. For complete details on the use and execution of this protocol, please refer to (de Jonge et al., 2019).