Project Grant F31MH145830

LOSS OF CONSERVED REGULATORY ELEMENTS IN HUMAN BRAIN EVOLUTION - PROJECT ABSTRACT CIS-REGULATORY ELEMENTS (CRES) CONTROL THE SPATIAL AND TEMPORAL EXPRESSION OF GENES AND ARE CENTRAL TO BRAIN DEVELOPMENT. DISRUPTION OF THESE ELEMENTS CONTRIBUTES TO NEUROLOGICAL DISEASES, YET THE FUNCTIONAL LANDSCAPE OF NON-CODING VARIATION REMAINS POORLY DEFINED. HUMAN BRAIN EVOLUTION IS MARKED BY REGULATORY DIVERGENCE, BUT PRIOR STUDIES HAVE LARGELY FOCUSED ON ACCELERATED SUBSTITUTIONS OR ENHANCER GAIN. TO ADDRESS THE UNEXPLORED DIMENSION OF ENHANCER LOSS, THIS PROJECT BUILDS UPON OUR RECENT CROSS-SPECIES SINGLE-NUCLEUS MULTIOMIC WORK THAT IDENTIFIED 1,091 HUMAN-LOST CRES, WHICH ARE DEEPLY CONSERVED ENHANCERS ACTIVE ACROSS OTHER MAMMALS BUT INACTIVE IN THE HUMAN BRAIN. THESE ELEMENTS ARE ENRICHED IN NEURONAL CRES, OCCUR NEAR GENES SUCH AS SRGAP2 AND SCN2A, AND HARBOR DERIVED SUBSTITUTIONS PREDICTED TO DISRUPT TRANSCRIPTION FACTOR BINDING, SUGGESTING ADAPTIVE REGULATORY INACTIVATION. THE PROPOSED RESEARCH WILL TEST THE HYPOTHESIS THAT ENHANCER LOSS CONTRIBUTES TO HUMAN-SPECIFIC BRAIN TRAITS AND THAT RARE VARIANTS IN THESE LOCI INFLUENCE RISK FOR NEURODEVELOPMENTAL DISORDERS (NDDS). AIM 1 WILL PERFORM RARE VARIANT BURDEN ANALYSES ACROSS HUMAN-LOST CRES AND OTHER CLASSES OF HUMAN- SPECIFIC REGULATORY CHANGES TO ASSESS WHETHER ENHANCER LOSS AND GAIN DIFFERENTIALLY CONTRIBUTE TO DISEASE RISK. AIM 2 WILL EMPLOY MASSIVELY PARALLEL REPORTER ASSAYS IN HUMAN IPSC-DERIVED NEURONS AND NEURAL PROGENITOR CELLS TO ASSESS REGULATORY ACTIVITY OF HUMAN AND CHIMPANZEE ORTHOLOGOUS SEQUENCES AND TO EVALUATE RARE VARIANTS IDENTIFIED IN NDD COHORTS. LOCI WITH DIFFERENTIAL ACTIVITY WILL UNDERGO CRISPR INHIBITION IN CHIMPANZEE NEURONS TO DETERMINE THE ANCESTRAL ROLE OF THESE CRES. THE FELLOWSHIP PROVIDES COMPREHENSIVE TRAINING IN EXPERIMENTAL AND COMPUTATIONAL GENOMICS AT THE UNIVERSITY OF ALABAMA AT BIRMINGHAM AND THE HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY. UNDER THE MENTORSHIP OF DRS. NICHOLAS COCHRAN AND GREGORY COOPER, THE CANDIDATE WILL GAIN EXPERTISE IN FUNCTIONAL GENOMICS, VARIANT INTERPRETATION, AND STATISTICAL GENETICS, WITHIN A COLLABORATIVE ENVIRONMENT THAT INTEGRATES HUMAN DISEASE GENETICS WITH EVOLUTIONARY BIOLOGY. THIS WORK WILL DETERMINE HOW ENHANCER LOSS HAS SHAPED HUMAN BRAIN EVOLUTION AND HOW ITS DISRUPTION CONTRIBUTES TO NEURODEVELOPMENTAL DISEASE.