# Mechanistic Insights into Single-Strand Break Repair Within Chromatin

> **NIH NIH R35** · CASE WESTERN RESERVE UNIVERSITY · 2024 · $402,500

## Abstract

Project Summary
 With cells constantly encountering DNA damaging agents, mechanisms for prompt DNA repair are
crucial for maintaining genomic stability. Aberrations and mutations in the proteins involved these processes are
closely associated with a plethora of diseases, including cancer and neurological disorders. Among various
types of DNA damage, single-strand breaks (SSBs) are the most prevalent, occurring at a rate of 55,000 per
cell daily. Understanding the repair of SSBs within chromatin through the base excision repair (BER) mechanism
is the primary focus of the proposed research project. The proposed research project primarily aims to unravel
the complexities of SSB repair within chromatin through the BER mechanism. This multifaceted pathway
involves poly-ADP-ribosylation (PARylation) and histone acetylation, both closely associated with DNA repair.
PARP1, the most abundant member of the PARP family, is the enzyme that confers poly-ADP-ribosyl groups to
histones upon detection of SSBs. This PARylation then recruits and activates various repair proteins like DNA
Ligase III (LIG3) and Polynucleotide Kinase 3'-Phosphatase (PNKP). PNKP has dual functions in the process,
particularly for SSBs induced by radioactivity, by adding a phosphate group to the 5'-end of DNA breaks and
removing one from the 3'-end. This prepares the DNA ends for the action of DNA ligases, such as LIG3, thereby
playing a vital role in DNA repair mechanisms. This proposal aims to understand how three DNA repair
proteins—PARP1, LIG3, and PNKP—recognize and repair SSBs within the context of nucleosomes and to
explore the interplay between PARylation and acetylation of histones in these processes. We will investigate
how PARP1 identifies and recognizes SSBs within nucleosomal contexts, a critical phase in the DNA damage
repair process. Additionally, we will explore the roles of enzymes LIG3 and PNKP in repairing SSBs within
nucleosomal structures. To achieve these goals, we will map the accessibility of SSB sites within nucleosomes
using DNA libraries and next-generation sequencing, aiming to optimize the positioning of an SSB for facilitating
the formation of nucleosome complexes with the DNA repair proteins. Subsequently, we will employ biophysical
tools and functional assays to characterize these interactions and functions, both in the presence and absence
of histone modifications. Finally, we will leverage state-of-the-art NMR techniques and cryo-EM to obtain detailed
structural and dynamic information about the nucleosome when complexed with PARP1 (or its zinc finger
domains), LIG3, and PNKP. The long-term goal of this research is to provide an enhanced fundamental
understanding of BER mechanisms within nucleosomal contexts, laying a molecular foundation for the design
of drugs and therapeutics that can beneficially modulate these mechanisms in various disease states.

## Key facts

- **NIH application ID:** 10937145
- **Project number:** 1R35GM154859-01
- **Recipient organization:** CASE WESTERN RESERVE UNIVERSITY
- **Principal Investigator:** Tae Hun Kim
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $402,500
- **Award type:** 1
- **Project period:** 2024-07-15 → 2029-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10937145

## Citation

> US National Institutes of Health, RePORTER application 10937145, Mechanistic Insights into Single-Strand Break Repair Within Chromatin (1R35GM154859-01). Retrieved via AI Analytics 2026-05-27 from https://api.ai-analytics.org/grant/nih/10937145. Licensed CC0.

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