Chromatin Remodeller BRD9 Orchestrates Odontoblastic Differentiation via Coordinating RUNX2-KLF4

Dentinogenesis, a process essential for tooth function, relies on the precise differentiation of dental papilla cells into odontoblasts. This lineage commitment is governed by complex transcription factor networks. RUNX2 and KLF4, known key TFs co-expressed in this process, were proven to operate synergistically, but the specific cofactors coordinating their activity at the chromatin level remain unknown. Here, we identify the chromatin remodeller BRD9 as a novel interactor of both RUNX2 and KLF4 during odontoblastic differentiation. To probe their shared function, we generated neural crest-specific conditional knockout mice. Wnt1-Cre; Brd9^fl/fl mice exhibited a disordered odontoblast layer with reduced secretion of extracellular matrix proteins (DMP1 and DSPP), strikingly phenocopying the compound Wnt1-Cre; Runx2^fl/wt; Klf4^fl/fl mutants. In vitro, chemical BRD9 degradation suppressed odontoblastic differentiation and mineral deposition. Integrative analyses of RNA-seq and ATAC-seq revealed that BRD9 maintained chromatin accessibility at odontogenesis-associated regions enriched with RUNX2 and KLF4 motifs, specifically at the Fam20c enhancer, thereby facilitating RUNX2 and KLF4 binding for transcriptional activation. Crucially, exogenous supplementation of FAM20C protein partially rescued the odontoblastic differentiation defects upon BRD9 loss. These findings establish BRD9 as a critical epigenetic orchestrator that coordinates RUNX2-KLF4 synergy to activate key odontogenic genes like Fam20c, thus affecting odontoblastic differentiation and dentinogenesis.