Identification of VvMADS28 DNA Targets

DAP-seq was performed as an outservice by Bluescape Scientific, Hebei, China. Genomic DNA (gDNA) was extracted from leaves, and a DAP library was constructed after fragmentation of the gDNA. Recombinant VvMADS28 protein was obtained by engineering the VvMADS28 cDNA into the pGEX 4 T expression vector, followed by expression and purification following the manufacturer’s specifications (Pierce™ Glutathione Magnetic Agarose Beads, Thermo Fisher). VvMADS28 protein and the gDNA library were incubated in vitro and DNA bound to VvMADS28 was isolated as described elsewhere [53 (link), 54 (link)]. DNA obtained after affinity purification and elution was subjected to paired-end sequencing on an Illumina HiSeq platform. Quality-filtered reads were aligned to a Grapevine genome sequence (https://urgi.versailles.inra.fr/Species/Vitis/Annotations) by Bowtie2 [55 (link)]. Conserved motifs within peak regions were identified using MEME [56 (link)].