The Arabidopsis ARF3-AIP1/2-SAP18 module specifies the root stem cell niche in response to auxin.

In the root apical meristem, the stem cell niche (SCN) comprises a mitotically inactive quiescent center (QC) and adjacent, mitotically active stem cells that divide to form root tissues. Auxin dynamics are essential for specification and maintenance of the root SCN; however, the underlying mechanisms remain to be explored. Here, we report that Arabidopsis (Arabidopsis thaliana) AUXIN RESPONSE FACTOR3 (ARF3), ARF3-INTERACTING PROTEIN1/2 (AIP1/2), and SIN3-ASSOCIATED POLYPEPTIDE OF 18 KDA (SAP18) form a protein complex that specifies root SCN cell fate in response to auxin level. In cells proximal to the QC, the ARF3-AIP1/2-SAP18 complex bound the WOX5 promoter and restricted WOX5 expression to the QC by decreasing H3 histone acetylation, thereby maintaining the SCN. Disrupting the ARF3-AIP1/2-SAP18 complex via mutation or exposure to excessive amounts of auxin resulted in proximal and lateral expansion of WOX5 expression and inhibited root elongation by repressing cell division. During de novo specification of the SCN in lateral root primordia or regenerating root tips, accumulated auxin caused the ARF3-AIP1/2-SAP18 complex to dissociate, allowing the induction of WOX5 expression. In the reestablished meristem, the ARF3-AIP1/2-SAP18 complex confines WOX5 expression to the newly formed QC. Our findings provide insights into the roles of auxin dynamics in determining root SCN.