Dissection of noncoding repeats in psychiatric genetics using synthetic regulatory genomics - Resubmission

Project Abstract Genetic scans for neuropsychiatric disorders like schizophrenia have uncovered hundreds of risk loci, yet we lack both the tools and conceptual approaches to dissect mechanism at this scale. One of the most robust schizophrenia and bipolar association signals lies near a human-specific repeat expansion within intron 3 of CACNA1C gene. CACNA1C encodes the predominant L-type voltage-gated calcium channel expressed in human central nervous system neurons, and a single missense mutation is responsible for the monogenic disorder Timothy Syndrome whose presentation includes neuropsychiatric symptoms. Through careful analysis of long-read sequencing data from a broad set of populations, we have decoded the complex structure of the CACNA1C repeat and developed tools for its assessment in commonly available short-read sequence data. We propose to fine map key features of regulatory activity at the CACNA1C repeat using long-read methyltransferase accessibility profiling (Fiber-seq). We will also apply a complementary synthetic regulatory genomics approach, to systematically dissect features of repetitive DNA in terms of repeat structure, unit content, and length. Finally, we will extend this approach to other repeats at potentially relevant genes genome-wide and apply our existing genome engineering pipeline to functionally screen candidates in cultured cells. This work promises to unlock a previously intractable locus as a model for how transcriptional mis-regulation leads to psychiatric disease.