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

Dellong, A.; Fallet, M.; Stenger, P.-L.; Chaparro, C.; Vidal-Dupiol, J.; Clement, J. A. J.; Cosseau, C.; Grunau, C.

doi:10.1101/2024.12.28.630603

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bioRxiv · 10.1101/2024.12.28.630603

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

Dellong, A.·Fallet, M.·Stenger, P.-L.·Chaparro, C.·Vidal-Dupiol, J.·Clement, J. A. J.·Cosseau, C.·Grunau, C.

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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.

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Dellong, A., Fallet, M., Stenger, P.-L., Chaparro, C., Vidal-Dupiol, J., Clement, J. A. J., Cosseau, C., Grunau, C.. 2024-12-28. Benchmarking of Chromatin Immunoprecipitation (ChIP-Seq) methods in the Pacific oyster Magallana gigas. https://doi.org/10.1101/2024.12.28.630603

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