WUSCHEL-dependent cis-regulation in maize inflorescence development at single-cell resolution

WUSCHEL (WUS) is a key transcription factor essential for the homeostasis of stem cells in the inflorescence meristem. In maize, ZmWUS1 is expressed in the central zone harboring stem cells, and its overexpression induces significant phenotypic alterations during the early stages of ear development. Here, single-cell ATAC-seq analyses revealed that ZmWUS1 overexpression alters chromatin accessibility exclusively in the central zone. This alteration includes both open and closed chromatin regions, with a notable predominance of the CAATAATGC motif observed in the open chromatin regions. Conversely, the TGAATGAA motif, identified through ZmWUS1-DNA interactions genome-wide, is not prevalent in these open chromatin regions and exhibits lower activity in the central zone compared to other cells. Furthermore, we observed the closed chromatin regions in the central zone involved in regulating auxin response factors genes, illustrating its negative impact on auxin signaling. These findings suggest that ZmWUS1 employs central zone-specific motif utilization and cis-regulation. Overall design: Comparing the chromatin accessibility between wild type and Bif3 of maize immature ear.