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An important task in deciphering protein function is the identification of other entities with which it interacts. Although C. elegans has not been exploited as an organism for biochemical analysis it is clearly amenable to such studies. Below are protocols describing immunoprecipitation (IP) and chromatin immunoprecipitation (ChIP) that should serve as general guidelines for in vivo interaction studies in C. elegans. These interactions can often be confirmed by standard in vitro techniques such as two-hybrid, GST pull-down studies, and electrophoresis mobility shift assays (EMSA).