Regulome-wide association study identifies enhancer properties associated with risk for schizophrenia

ABSTRACT Genetic risk for complex traits is strongly enriched in non-coding genomic regions involved in gene regulation, especially enhancers. However, we lack adequate tools to connect the characteristics of these disruptions to genetic risk. Here, we propose RWAS (Regulome Wide Association Study), a new framework to identify the characteristics of enhancers that contribute to genetic risk for disease. Applying our technique to interrogate genetic risk for schizophrenia, we found that risk-associated enhancers in this disease are predominantly active in the brain, evolutionarily conserved, and AT-rich. The association between AT percentage and risk corresponds to an overrepresentation in risk-associated enhancers for the binding sites of transcription factors that recognize AT-rich cis-regulatory motifs. Several of the TFs identified in our model as being overrepresented in risk-associated enhancers, including MEF2C, are master regulators of neuronal development. The genes that encode several of these TFs are themselves located at genetic risk loci for schizophrenia. This list also includes brain-expressed TFs that have not previously been linked to schizophrenia. In summary, we developed a generalizable approach that integrates GWAS summary statistics with enhancer characteristics to identify risk factors in tissue-specific regulatory regions. AUTHOR SUMMARY Enhancers are regulatory regions that influence gene expression via the binding of transcription factors. Risk for many heritable diseases is enriched in regulatory regions, including enhancers. In this study, we introduce a novel method of testing for association between enhancer attributes and risk and use this method to determine the enhancer characteristics that are associated with risk for schizophrenia. We found that enhancers associated with schizophrenia risk are both evolutionarily conserved and in physical contact with mutation-intolerant genes, many of which have neurodevelopmental functions. Risk-associated enhancers are also AT-rich and contain binding sites for neurodevelopmental transcription factors.