Genetic regulation of ARID3B confers cleft lip with/without cleft palate susceptibility through LLPS-mediated transcriptional program

Genome-wide association studies have identified numerous loci associated with nonsyndromic cleft lip with/without cleft palate (nsCL/P). However, the causal genes within these loci remain to be systematically investigated. Through a multiomics screening strategy, we identified 20 candidate genes, with ARID3B emerging as the most significant risk gene for nsCL/P. Focusing on the ARID3B locus, we found a casual variant at rs1821848 that diminished the binding affinity of NR2C2, resulting in the upregulation of ARID3B. Notably, we observed the formation of ARID3B granules through liquid-liquid phase separation (LLPS) both in vivo and in vitro. This ARID3B-mediated LLPS could essentially recruit coactivators SMAD2/3 and establish enhancer activity necessary for initiating the gene profile related to nsCL/P. Ultimately, disrupting the LLPS of arid3b effectively rescued migration, apoptosis, and phenotype deficits in zebrafish models. This study systematically revealed biological functions of both rs1821848 and ARID3B during nsCL/P development.