Systematic evaluation of chromatin immunoprecipitation sequencing to study histone occupancy in dormancy transitions of grapevine buds

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Abstract The regulation of DNA accessibility by histone modification has emerged as a paradigm of developmental and environmental programming. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a versatile tool widely used to investigate in vivo protein-DNA interaction. The technique has been successfully demonstrated in several plant species and tissues; however, it has remained challenging in woody tissues. Here we developed a ChIP method specifically for mature dormant grapevine buds ( Vitis vinifera cv. Cabernet Sauvignon). Each step of the protocol was systematically optimised, including crosslinking, chromatin extraction, sonication, and antibody validation. Analysis of histone H3-enriched DNA was performed to evaluate the success of the protocol and identify occupancy of histone H3 along grapevine bud chromatin. To our best knowledge, this is the first ChIP experiment protocol optimised for grapevine bud system.