Genome-Wide Mapping of DNase I Hypersensitive Sites in Tomato

DNase I hypersensitive sites (DHSs) are genomic regions that exhibit hypersensitivity to DNase I cleavage. DHSs appear to be an essential feature of "open chromatin" structure in eukaryotes. Most of regulatory elements and the majority of transcription factor-binding sites are associated with open chromatin marked by DHSs. DNase I digestion followed by high-throughput DNA sequencing (DNase-seq) has become a powerful tool to reveal chromatin status and identify regulatory elements at genome-wide level. Here, we developed a DNase-seq procedure in tomato revised from previous methods in other plants, involving plant nuclei isolation, digestion of purified nuclei with DNase I, collection of DNase-trimmed DNA fragments, validation of DHS sample quality by qPCR, and DNase-seq library preparation. We introduced an AMPure XP beads system for the selection of the desirable DNA fragment. DHS datasets will provide the dynamic profiles of regulatory elements during plant development.