Benchmarking of chromatin profiling methods (ChIP-Seq, CUT&Tag) in the Pacific oyster Magallana gigas

Chromatin Immunoprecipitation sequencing (ChIP-seq) is the method of choice to generate chromatin landscapes across genomes. The scarcity of literature on ChIP-seq and absence of a canonical "gold standard" method in mollusks and especially the Pacific oyster Magallana gigas, prompted us to compare four chromatin profiling approaches (Native-ChIP, Crosslink-ChIP, ChIPmentation and CUT&Tag) to find the most suitable method for this species. In our hands the CUT&Tag immuno-tethering method provided most robust and reproducible signal. Our findings establish CUT&Tag as a low-background and versatile method for epigenomic studies in non-model marine organisms, enabling future comparative analyses of chromatin dynamics.