Mechanisms of Base Excision Repair in Nucleosomes

Genomic DNA in human cells is tightly packaged into chromatin, a higher‑order structure that protects the genome but also makes it difficult for essential repair enzymes to access damaged DNA. Because DNA damage threatens organismal function by promoting mutations, aging‑related decline, and disease, cells rely on the base excision repair (BER) pathway to remove and replace damaged bases. However, how BER functions when DNA is packaged into chromatin remains poorly understood. This project investigates how the physical organization of DNA in chromatin influences the ability of BER enzymes to locate and repair damage. By defining how chromatin architectural proteins and chromatin composition regulate BER, the research will advance fundamental knowledge of genome maintenance, an area central to national interests in health, biotechnology, and scientific innovation. The project will also contribute to developing a competitive STEM workforce by mentoring and training graduate student researchers in protein and DNA chemistry, biophysics, and molecular biology. Sustained outreach activities, including tutoring and annual STEM engagement events for elementary, middle, and high‑school students, will broaden participation in science and strengthen public engagement with science and understanding of how cells preserve genetic information. This research program addresses the fundamental mechanistic question of how the BER pathway operates within nucleosome core particles (NCPs), the primary units of chromatin. Leveraging strategies developed to position defined DNA damage within chemically and structurally characterized NCPs, the project applies chemical, biochemical, biophysical, and molecular biology approaches to dissect how chromatin features regulate BER. These approaches will be used to (i) define how the abundant chromatin architectural proteins influence BER efficiency and enzyme access in nucleosomes, and (ii) determine how DNA sequence modulates the catalytic activity of the NTHL1 DNA glycosylase. Together, the results will reveal how both DNA and protein components of NCPs shape the initiation and progression of BER. The outcomes will provide mechanistic insight into how cells overcome the intrinsic barriers imposed by chromatin to maintain genome stability and will generate broadly applicable experimental frameworks for the DNA repair, chromatin biology, and genome maintenance communities. 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: 2611174 | Program: 01002627DB NSF RESEARCH & RELATED ACTIVIT | Principal Investigator: Sarah Delaney | Institution: Brown University, PROVIDENCE, RI | Award Amount: $1,200,000 View on NSF Award Search: https://www.nsf.gov/awardsearch/show-award/?AWD_ID=2611174 View on Research.gov: https://www.research.gov/awardapi-service/v1/awards/2611174.html