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RAI1  ( retinoic acid induced-1 ) is a dosage-sensitive gene that causes Smith-Magenis syndrome (SMS) when mutated or deleted and Potocki-Lupski Syndrome (PTLS) when duplicated, with psychiatric features commonly observed in both syndromes. How common genetic variants regulate this gene, however, is unknown. In this study, we found that  RAI1  mRNA expression in Chinese prefrontal and temporal cortex correlate with genotypes of common single nucleotide polymorphisms (SNPs) located in the  RAI1  5′-upstream region. Using genotype imputation, “R 2 -Δ 2 ” analysis, and data from the RegulomeDB database, we identified SNPs rs4925102 and rs9907986 as possible regulatory variants, accounting for approximately 30–40% of the variance in  RAI1  mRNA expression in both brain regions. Specifically, rs4925102 and rs9907986 are predicted to disrupt the binding of retinoic acid RXR-RAR receptors and the transcription factor DEAF1 (Deformed epidermal autoregulatory factor-1), respectively. Consistent with these predictions, we observed binding of RXRα and RARα to the predicted  RAI1  target in chromatin immunoprecipitation assays. Retinoic acid is crucial for early development of the central neural system, and  DEAF1  is associated with intellectual disability. The observation that a significant portion of  RAI1  mRNA expression is genetically controlled raises the possibility that common  RAI1  5′-region regulatory variants contribute more generally to psychiatric disorders.

Evidence for genetic regulation of mRNA expression of the dosage-sensitive gene retinoic acid induced-1 (RAI1) in human brain