Chromatin Immunoprecipitation Assays of Histone Modifications in Daphnia magna

Daphnia magna is a widely distributed freshwater planktonic crustacean that has been extensively used as a model organism in ecotoxicological studies, due to its sensitivity to environmental pollutants. It has recently received enough attention as a model organism to study transgenerational epigenetic mechanisms, owing to its ability to reproduce via parthenogenesis. This unique ability of D. magna to generate clonal offspring makes it an ideal model organism to study how environmental cues-including environmental pollutants-can affect the epigenome of future generations. This is important since several of these cues can have a profound impact on behavior and other phenotypes such as disease mechanisms in mammals. Chromatin immunoprecipitation (ChIP) assays have proved to be essential tools in the field of epigenetics, namely, for their ability to study in a quantitative fashion the genomic localization of numerous chromatin epigenetic marks such as histone posttranslational modifications and histone variants. However, there are few studies that document the use of ChIP assays in D. magna. Here, we describe in detail an optimized protocol for ChIP assays in whole Daphnia organisms that is suitable to study histone posttranslational modifications as well as several potential epigenetic regulators.Running title: ChIP in Daphnia magna.