A fundamental challenge in modern biology is to identify the noncoding regulatory elements (REs) that control gene expression, which could inform the interpretation of the thousands of noncoding genetic variants associated with human diseases through genome-wide association studies (GWAS). Interpreting the functions of REs and noncoding genetic variants has been challenging because we have lacked the ability to systematically perturb REs in their native locations in the genome. To address this challenge, I recently developed a high-throughput method to map the functions of thousands of REs in their native genomic contexts and measure their quantitative effects on gene expression (CRISPRi tiling). I also developed a novel analytical approach to model and predict gene-RE connections based on maps of chromatin state and 3D folding. Together, these advances motivate a strategy to allow systematic mapping of all of the REs that control any given gene in any given cell type. In the K99 phase, I propose to: (i) apply CRISPRi tiling to map ~6,000 additional gene-RE connections, and (ii) use these data to extend and optimize a model to predict gene-RE connections from chromatin state. I will use human immune cells as a model system to compare predictions across cell types. In the R00 phase, I will (iii) use these tools to identify and dissect molecular mechanisms that specify gene-RE connections, and (iv) apply these insights to study gene regulatory mechanisms in loci associated with immune diseases. Together, these aims will provide insights into the mechanisms and architecture of gene-RE connectivity, generate tools for mapping gene-RE connectivity in any cell type, and reveal mechanisms underlying common immune diseases. To succeed in these aims, I will pursue additional training in immunology and common disease genetics, supported by my co-mentors Dr. Nir Hacohen (systems immunology and genetics) and Dr. Eric Lander (genetics and genomics) as well as by a Mentorship Committee including Drs. Aviv Regev (systems immunology), Sekar Kathiresan (common disease genetics), and Bradley Bernstein (epigenomics). My career development plan integrates practical training in immunology, a working group comprising leaders in common disease genetics, close mentorship in writing faculty applications and grants, and seminars in grant-writing and academic job searches. The Broad Institute is an ideal environment, providing all of the facilities needed for the proposed research and a rich interdisciplinary environment for collaborative studies. Together, these aims will launch my independent scientific career at the interface of regulatory genomics and immune disease genetics.
The human genome encodes a hidden wiring diagram that plays a role in determining an individual's risk for disease. To map this wiring diagram, we will develop a new strategy that involves breaking many wires to determine their functions and using computational models to predict the functions of all of the other wires. This will help to discover the molecular basis for many diseases and may eventually lead to the development of precise medicines.