Genome-wide binding of tomato AP1/FUL-like proteins determined by DNA-affinity purification sequencing (DAP-seq)

By function dissection in planta, we identified that tomato AP1/FUL-like genes have overlapping and specific functions in flowering and inflorescece development. In this experiment, we aim to identify the binding sites of AP1/FUL-like complexes (FUL2-J, FUL2-J2, FUL2-TM3, MC-J, MC-J2, MC-TM3) and determine if they exhibit binding to different targets or with differing affinities, which could be a mechanism to acquire target gene specificity. Specifically, we investigated this phenomenon for all the tetramers, as they are enriched in shoot reproductive meristems to fulfil the functions. Using the DAP-seq protocol, we established their genome-wide binding profiles and included input as control. We use DAP-seq to determine the genome-wide binding patterns of AP1/FUL-like protein FUL2 and MC with their interactors J, J2, and TM3 (FUL2-J, FUL2-J2, FUL2-TM3, MC-J, MC-J2, MC-TM3).