The classic phytohormones play important roles in regulation of plant stem cells,and exhibit complex functional interactions.Among them,auxin was previously found to be essential in the differentiation of meristematic cells in shoot apical meristem.The biosynthesis of auxin occurred universally in the whole meristem,and then transported into the peripheral zone by PIN1 to promoter later organs initiation.Recently,several lines of new evidences suggested that auxin can be also transferred into the central zone of shoot apical meristem where harbored plant stem cells.However the functions of auxin in stem cells are still largely unknown.Previously we have shown that the AUXIN RESPONSE FACTOR5/ MONOPTEROS (MP) transcription factor,mediated the cross talk between auxin and cytokinin in stem cells.By RNA sequencing,we have identified a new MP target,MTA1,which was specifically expressed in stem cells.MP can directly bond MTA1 promoter and repress its expression,and knocking out MP cause transcriptional up regulation of MAT1.While MTA1 as a transcription factor,was sufficient to active CL V3 expression in stem cells to participate in WUS/CLV3 feedback.Our results provide a novel mechanism of auxin in regulating stem cells homeostasis in Arabidopsis thaliana.