(Lead: Jennifer Doudna; Co-I: Alexander Marson & Judd Hultquist)

To support all HARC Center Projects, the Genetics Core will provide innovative high-throughput methods for the discovery and functional characterization of HIV-host protein complexes in primary cells (i.e. activated primary CD4 T cells, resting primary CD4 T cells, and primary macrophages). Working in tandem with the Proteomics, Structural Biology, and Computational Cores, we will develop the HARC endogenous protein structure (HEPS) platform for the discovery and functional characterization of different HIV-host protein complexes by inserting affinity tags at genomic loci to allow affinity purification of endogenous protein complexes directly from HIV infected primary cells. Using our breakthrough CRISPR knock-out (CRISPRko), activation (CRISPRa), interference (CRISPRi), and knock-in (CRISPRki) technologies in primary human T cells, we will (1) generate a systematic map of proviral and antiviral HIV-interacting host factors, (2) functionally validate novel HIV-host interactions, (3) undertake endogenous deep mutational scanning of specific protein domains to identify critical host-pathogen interaction interfaces, and (4) introduce/replace small stretches of DNA at targeted genomic sites to study the function of specific genetic variants. Collectively, these genetic studies will strengthen the central HARC mission to understand interactions between HIV accessory proteins and host factors and open new experimental and therapeutic avenues for a broader HIV research community. In summary, the Genetics Core will develop a toolbox for genetic perturbations to complement innovative structural biology and proteomic efforts.