Epigenetic priming is a potential molecular mechanism that creates a state of readiness prior to gene expression without altering gene expression. It creates a state of readiness for future gene expression by unwinding nucleosomes and opening chromatin. Epigenetic priming has been observed in stem cell differentiation and precancerous stages of cell transformation, but there have been no reports of its involvement in plant organ regeneration. We identified the histone demethylase LYSINE-SPECIFIC DEMETHYLASE 1-LIKE 3 (LDL3) as a plant epigenetic priming factor by screening mutants in Arabidopsis thaliana. In roots, LDL3 was mainly expressed in pericycle cells around vascular bundles. In callus derived from roots on callus induction medium, the expression pattern of LDL3 gradually expanded and its expression was observed throughout the callus. In shoot-induced callus, LDL3 expression was more frequently detected in the shoot apical meristem primordium. Next, chromatin immunoprecipitation was used to compare the histone H3K4me status in roots, callus, and shoot-induced callus. H3K4me2 accumulated specifically in ldl3 mutant callus. Surprisingly, the pattern of H3K4me2 accumulation was almost the same in callus and shoot-induced callus. In other words, H3K4me2 did not change when transferred from the callus induction medium to the shoot induction medium. This means that during callus formation, LDL3 removes H3K4me2 and puts the shoot regeneration gene cluster in a standby state for gene expression in preparation for future shoot induction. Our studies suggest that epigenetic priming is involved in the molecular mechanisms underlying the organ-regenerative capacity of plants.