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Updated: May 4, 2026

Author Spotlight: Decoding DNA Repair by Extrachromosomal NHEJ Assay and HR Assays
Published on: February 2, 2024
Investigations of homologous recombination pathways and their regulation
James M Daley1, YoungHo Kwon1, Hengyao Niu1
1Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, Connecticut.
Abstract:
The DNA double-strand break (DSB), arising from exposure to ionizing radiation or various chemotherapeutic agents or from replication fork collapse, is among the most dangerous of chromosomal lesions. DSBs are highly cytotoxic and can lead to translocations, deletions, duplications, or mutations if mishandled. DSBs are eliminated by either homologous recombination (HR), which uses a homologous template to guide accurate repair, or by nonhomologous end joining (NHEJ), which simply rejoins the two broken ends after damaged nucleotides have been removed. HR generates error-free repair products and is also required for generating chromosome arm crossovers between homologous chromosomes in meiotic cells. The HR reaction includes several distinct steps: resection of DNA ends, homologous DNA pairing, DNA synthesis, and processing of HR intermediates. Each occurs in a highly regulated fashion utilizing multiple protein factors. These steps are being elucidated using a combination of genetic tools, cell-based assays, and in vitro reconstitution with highly purified HR proteins. In this review, we summarize contributions from our laboratory at Yale University in understanding HR mechanisms in eukaryotic cells.
Insights
DNA double-strand breaks (DSBs) are dangerous DNA lesions repaired by homologous recombination (HR) or nonhomologous end joining (NHEJ). This review details HR mechanisms in eukaryotic cells, focusing on key repair steps and protein factors.
Area of Science:
- Molecular Biology
- Genetics
- Cell Biology
Background:
- DNA double-strand breaks (DSBs) are critical DNA lesions arising from radiation, chemotherapy, or replication stress.
- Mishandled DSBs can cause genomic instability, leading to mutations, deletions, or translocations.
- Two major repair pathways exist: homologous recombination (HR) for accurate repair and nonhomologous end joining (NHEJ) for direct end rejoining.
Purpose of the Study:
- To review the mechanisms of homologous recombination (HR) in eukaryotic cells.
- To highlight the distinct steps involved in HR-mediated DNA repair.
- To summarize contributions from the Yale University laboratory in elucidating HR pathways.
Main Methods:
- Utilizing genetic tools for studying HR pathways.
- Employing cell-based assays to investigate HR mechanisms.
- Performing in vitro reconstitution with purified HR proteins.
Main Results:
- HR ensures error-free repair of DSBs.
- HR is essential for generating meiotic crossovers between homologous chromosomes.
- The review elaborates on the sequential steps of HR: resection, pairing, synthesis, and intermediate processing.
Conclusions:
- Understanding HR mechanisms is crucial for comprehending genome stability.
- Multiple protein factors orchestrate the highly regulated HR process.
- Continued research using diverse methodologies is advancing the elucidation of HR pathways.
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