Benchmarking of Chromatin Immunoprecipitation (ChIP-Seq) methods in the Pacific oyster Magallana gigas

Abstract

Chromatin Immunoprecipitation sequencing (ChIP-seq) is the method of choice to generate chromatin landscapes across genomes. The scarcity of literature on ChIPseq and absence of a canonical "gold standard" method in mollusks and especially the pacific oyster Magallana gigas, prompted us to compare four ChIP-seq methodologies (Native-ChIP, Crosslink-ChIP, ChIPmentation and Cut & Tag) to find the most suitable method for this species. Our results show that Cut & Tag performs best and ChIPmentation worst. We hypothesize that the reason for this lies in a particularly fragile chromatin structure around genes in the oyster.