Identification of Nuclear Receptor Targets by Chromatin Immunoprecipitation in Fatty Liver

Chromatin immunoprecipitation (ChIP) assays allow for the study of protein-DNA interactions in physiological contexts. Briefly, ChIPs consist of the purification and enrichment of a protein of interest together with its associated chromatin and its later identification. Hence, this technique proves to be particularly useful when assessing novel target genes for nuclear receptors. In the field of metabolic liver diseases, the validation of putative nuclear receptor targets is key for furthering the development of nuclear receptor modulators as therapeutic compounds. In this chapter, the protocol described has been optimized for ChIP on mouse fatty (steatotic) livers. Thanks to the use of a "two-step" (double) cross-linking method, this protocol can also be used for the study of other proteins with weaker interactions or that are present in large complexes, such as cofactors.