Engineering structural variation to understand human genome function.

When do we truly understand a mammalian genome? Such understanding requires more than describing the function, or lack thereof, of each base pair. It also requires the ability to predict the consequences of sequence and structural variants and to design new genomes that function as intended. We still lack methods to systematically engineer genome architecture at larger scales through structural variation (SV).

Recent advances have begun to change this. A convergence of new genome engineering technologies has brought programmable SV engineering within reach, making this an especially exciting moment for the field. By combining genome engineering strategies such as prime editing, recombinases, and CRISPR-Cas3, we have generated highly engineered human cell systems that enable SV formation in mammalian genomes at an unprecedented scale. We pair these perturbation strategies with long-read sequencing, phage polymerase-based genotyping, and emerging single-cell approaches to directly resolve engineered variants and connect them to changes in fitness and gene expression.

Building on this foundation, our lab will develop and apply technologies to design, generate, and phenotype thousands of defined SVs, advancing a functional understanding of mammalian genome architecture, illuminating the mechanisms by which SVs cause disease, and laying the foundation for designing streamlined mammalian genomes.