CAREER: SynTACS - Testing Rules for Engineering Genome Architecture in Human iPSCs

Understanding how genes are turned "on" or "off" (regulatory control) is central to biology, medicine, and biotechnology. Although the human genome has been extensively mapped, scientists still do not know whether the linear arrangement of DNA elements encodes an underlying design logic governing how groups of genes are activated together. This project tests the idea that the functional behavior and three-dimensional organization of the genome are encoded in its linear structure. By systematically re-engineering the spacing and organization of regulatory elements to control coordinated gene activity in human cells, the research aims to move beyond observing the genome toward the ability to predict and design its behavior. These advances have broad implications for the US national interest, including improving the reliability and potency of engineered cells for therapeutic applications, enabling more precise control of gene expression in regenerative medicine and immune engineering, and supporting the development of robust multi-gene systems for biotechnology and biomanufacturing. In parallel, the project integrates research with education through a tiered training program spanning middle school lab visits, undergraduate and master’s research, and graduate training, contributing to the development of a skilled and committed workforce in biotechnology and related fields. This project, SynTACS (Synthetic Transcriptional Architecture of Condensates and Super-enhancers), will test the hypothesis that the linear organization of super-enhancers encodes transcriptional control by shaping transcription factor condensate dynamics and chromatin topology. Using REWRITE, a platform for programmable locus-scale (>100 kb) DNA restructuring in human induced pluripotent stem cells, the project will systematically reconfigure the density, spacing, and orientation of regulatory elements within a 209 kilobase multi-gene region at its native genomic context. Engineered variants will be evaluated through three integrated approaches: (1) transcriptional profiling to quantify gene expression changes across constructs, (2) live-cell imaging of transcription factor condensates to measure their formation, dynamics, and stability, and (3) high-resolution chromatin topology mapping using region-capture Micro-C alongside epigenetic profiling. By linking genome architecture to molecular dynamics and functional output in a controlled, causal framework, this work will establish design principles governing coordinated gene regulation. The outcomes will provide a foundation for engineering synthetic multi-gene regulatory systems and advancing genome-scale biotechnology. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria. NSF Award ID: 2540152 | Program: 01002627DB NSF RESEARCH & RELATED ACTIVIT,01003031DB NSF RESEARCH & RELATED ACTIVIT | Principal Investigator: David Truong | Institution: New York University, NEW YORK, NY | Award Amount: $1,300,227 View on NSF Award Search: https://www.nsf.gov/awardsearch/show-award/?AWD_ID=2540152 View on Research.gov: https://www.research.gov/awardapi-service/v1/awards/2540152.html