CAREER: Engineering genome topology to attenuate pathologic short tandem repeat instability

DNA sequences store information, and access to this information is controlled at many levels. Scattered across DNA are random, repeated sequences referred to as short tandem repeats (STRs). STRs help regulate gene expression and can also expand and contract in length. Overexpansion of STR's can lead to a number of diseases, including ALS (Lou Gehrig's disease), Alzheimer's, and Huntington's. This project will focus on what causes STR expansion that leads to disease. The proper application of statistics and computational tools are key to making progress in this effort. A training program will provide students with the opportunity to learn those techniques.

Much is already known regarding how transcription factors and epigenetic marks work in the context of the linear genome to regulate neural synapses in the brain. Yet, severe limitations still exist in our ability to understand the mechanisms by which synapses are severely disrupted in neurological disorders such as fragile X syndrome (FXS), Huntington's disease, and Alzheimer's disease. Recently, the Cremins lab discovered that nearly all disease-associated STRs (daSTRs) are located at boundaries demarcating a genome folding pattern termed the topologically associating domain (TAD). The lab went on to discover that TAD boundaries are severely disrupted in FXS, thus revealing higher-order folding of the genetic sequence as a new dimension in understanding neurological disorders with synaptic defects. A fundamental unresolved question is why some STRs are susceptible to pathologic expansion, whereas hundreds of thousands of repeat tracts across the human genome are relatively stable. The overall objective of this project is to understand the mechanistic link between occupancy of the architectural protein CTCF and STR instability at TAD boundaries. Our central hypothesis is that TAD boundaries with ultra-high CTCF density represent hotspots in the human genome susceptible to instability. To test this hypothesis, we propose experimental and computational studies to (1) quantitatively measure the role for CTCF density and double strand breaks on STR instability and (2) engineer CTCF occupancy to induce a functional change in STR expansion.

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.