The Chromatin Immunoprecipitation (ChIP) Protocol for African Turquoise Killifish

Abstract

DNA-binding proteins and epigenetic modifications coordinate to regulate the spatiotemporal pattern of gene expression during development, and thus, profiling their genomic distribution on a genome-wide scale is of crucial significance for decoding the underlying gene regulatory networks. Chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) is a powerful and extensively employed approach for studying in vivo protein–DNA interactions and for profiling genomic regions with residence of chromatin modifications. As an emerging model organism for aging and regeneration studies, a stable ChIP-seq protocol for capturing authentic genomic sites enriched for a given transc\ription factor or epigenetic mark in the African killifish Nothobranchius furzeri is critical. Taking caudal fin tissue as an example, we present a detailed experimental ChIP protocol optimized for identifying the genomic sites targeted by transcription factors and/or epigenetic marks for studying their dynamic changes during regeneration. This optimized protocol should also be suited for other fish tissues with available ChIP-grade antibodies.