GO:0010569 regulation of double-strand break repair via homologous recombination: DNA Repair Pathway, Genes, Functions and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0010569 describes any process that modulates the frequency, rate or extent of error-free repair of a DNA double-strand break using homologous sequences.
• Homologous recombination (HR) is a high-fidelity repair pathway that is tightly regulated to occur primarily in S/G2 phases of the cell cycle.
• Key regulators include BRCA1-BARD1, 53BP1, MRE11, RAD51, and cohesin, which control end resection, strand invasion, and homology search.
• Dysregulation of HR regulation leads to genomic instability and is implicated in cancers, particularly those with BRCA1/2 mutations.
• Emerging evidence shows that metabolic modifications such as lactylation of MRE11 and BLM directly regulate HR activity.
• Experimental models for studying GO:0010569 include CRISPR knockout, point mutation, knock-in, and overexpression cell lines, as well as library screening.
Description
Double-strand breaks (DSBs) are among the most cytotoxic DNA lesions, and their repair by homologous recombination (HR) is essential for maintaining genomic integrity. GO:0010569, regulation of double-strand break repair via homologous recombination, encompasses all processes that modulate the frequency, rate, or extent of this error-free repair pathway. This regulation ensures that HR is activated at the right time and place, primarily during the S and G2 phases of the cell cycle when a sister chromatid is available as a template. Researchers study this term to understand how cells balance repair fidelity with cell cycle progression and how its disruption contributes to diseases such as cancer. The regulation of HR involves a complex network of proteins, including BRCA1-BARD1, which promotes DNA end resection, and 53BP1, which antagonizes resection to favor non-homologous end joining. Post-translational modifications, such as lactylation of MRE11 and BLM, have emerged as critical metabolic inputs that fine-tune HR activity. Additionally, structural components like cohesin facilitate the homology search during RAD51-mediated strand invasion. Understanding these regulatory layers is vital for developing targeted therapies, especially for HR-deficient tumors that rely on alternative repair pathways. This article provides a comprehensive overview of GO:0010569, covering its definition, biological significance, key genes, regulatory mechanisms, disease associations, and experimental approaches. By integrating authoritative QuickGO data with real PubMed literature, we aim to equip researchers with a publication-ready resource for studying this critical DNA repair regulatory process.
regulation of double-strand break repair via homologous recombination At A Glance
| GO ID | GO:0010569 |
|---|---|
| GO term | regulation of double-strand break repair via homologous recombination |
| Ontology | biological_process |
| Synonym | none |
| Major function | Modulates the frequency, rate or extent of error-free repair of double-strand breaks using homologous sequences |
| Cell cycle context | Primarily active in S/G2 phases when a sister chromatid is available |
| Key regulators | BRCA1-BARD1, 53BP1, MRE11, RAD51, cohesin |
| Disease relevance | Cancer predisposition, chemoresistance, genomic instability |
What Is GO:0010569?
GO:0010569, regulation of double-strand break repair via homologous recombination, is defined as any process that modulates the frequency, rate or extent of the error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. In simpler terms, it covers all the cellular mechanisms that control how often and how efficiently homologous recombination fixes broken DNA, ensuring repair occurs accurately and at the appropriate cell cycle stage.
Why Is regulation of double-strand break repair via homologous recombination Important in Cell Biology?
Regulation of homologous recombination is critical for maintaining genomic stability and preventing tumorigenesis. Disruption of this regulation leads to improper repair, genomic rearrangements, and increased sensitivity to DNA-damaging agents. Understanding GO:0010569 is essential for cancer research, as HR-deficient tumors often depend on alternative repair pathways like Polθ-mediated repair, offering therapeutic targets. Moreover, metabolic and post-translational modifications of HR proteins, such as lactylation, link cellular metabolism to DNA repair, opening new avenues for intervention.
• Maintains genomic integrity by ensuring error-free DSB repair.
• Prevents chromosomal rearrangements and mutations that drive cancer.
• Determines sensitivity to PARP inhibitors and platinum-based chemotherapies.
• Links metabolic states to DNA repair through modifications like lactylation.
• Regulates cell cycle progression by restricting HR to S/G2 phases.
• Influences immune responses through cGAS-STING activation by cytosolic DNA.
• Provides targets for synthetic lethality in HR-deficient cancers.
• Guides development of CRISPR-based models to study repair mechanisms.
What Happens During regulation of double-strand break repair via homologous recombination?
DNA End Resection and Commitment to HR
In simple terms: The broken DNA ends are chewed back to create single-stranded tails, a key step that commits the cell to homologous recombination.
DNA end resection is the initial and rate-limiting step in HR, generating 3' single-stranded DNA (ssDNA) tails that invade a homologous template. This process is promoted by BRCA1-BARD1, which counteracts 53BP1-mediated protection of broken ends. The regulation of resection determines pathway choice between HR and non-homologous end joining. Recent studies show that BRCA1-BARD1 directly stimulates resection through its interaction with CtIP and MRN complex.
RAD51 Filament Formation and Homology Search
In simple terms: RAD51 proteins coat the single-stranded DNA tails and search for matching sequences on a sister chromatid to use as a repair template.
After resection, RAD51 replaces RPA on ssDNA to form a nucleoprotein filament that performs homology search and strand invasion. Cohesin complexes drive chromatin scanning during this RAD51-mediated homology search, facilitating the identification of homologous sequences. This step is tightly regulated by accessory factors like BRCA2 and RAD51 paralogs.
Post-translational Modifications and Metabolic Regulation
In simple terms: Chemical tags added to repair proteins can turn their activity up or down in response to the cell's metabolic state.
Lactylation of MRE11 enhances its exonuclease activity and promotes HR repair, linking glycolysis to DNA repair. Similarly, lactylation of BLM inhibits its helicase activity, affecting HR and chemoresistance. These modifications provide a direct connection between cellular metabolism and the regulation of homologous recombination.
Chromatin Context and 53BP1 Antagonism
In simple terms: The packaging of DNA and specific proteins like 53BP1 can block or allow homologous recombination to proceed.
53BP1 binds to H4K20me2 marks and protects DNA ends from resection, thereby antagonizing HR. During replication, H4K20me2 is diluted, reducing 53BP1 binding and permitting HR to occur. This chromatin-based regulation ensures that HR is favored in S/G2 phases when sister chromatids are available.
Key Genes Involved in GO:0010569 regulation of double-strand break repair via homologous recombination
The following genes and proteins are central to the regulation of double-strand break repair via homologous recombination, as supported by published literature.
| Gene | Major Role | Research Relevance |
|---|---|---|
| BRCA1 | Promotes DNA end resection and antagonizes 53BP1 | Mutations cause hereditary breast and ovarian cancer; target for PARP inhibitors |
| BARD1 | Partners with BRCA1 to stimulate resection | Essential for BRCA1 stability and function; mutations linked to cancer |
| 53BP1 | Binds H4K20me2 to protect DNA ends and inhibit HR | Determines pathway choice; loss restores HR in BRCA1-deficient cells |
| MRE11 | Component of MRN complex; involved in resection and lactylation-regulated HR | Lactylation enhances exonuclease activity; metabolic link to HR |
| RAD51 | Forms nucleoprotein filament for homology search and strand invasion | Central recombinase; target for inhibitor development |
| BLM | Helicase that regulates HR; lactylation inhibits its activity | Lactylation affects chemoresistance; potential biomarker |
| Cohesin | Drives chromatin scanning during RAD51-mediated homology search | Structural role in homology search; mutations in cohesinopathies |
| CtIP | Promotes end resection with BRCA1 | Regulated by phosphorylation; critical for HR initiation |
| RPA | Binds ssDNA and is replaced by RAD51 | Protects ssDNA and facilitates filament formation |
| BRCA2 | Mediates RAD51 loading onto ssDNA | Mutations cause Fanconi anemia and cancer |
| PALB2 | Links BRCA1 and BRCA2 to promote HR | Mutations increase cancer risk |
| RAD51C | RAD51 paralog; involved in filament stability | Mutations cause Fanconi anemia-like disorders |
| RAD51D | RAD51 paralog; required for HR | Associated with ovarian cancer |
| Polθ | Mediates alternative end joining in HR-deficient cells | Synthetic lethal target in BRCA-mutated cancers |
| H4K20me2 | Chromatin mark bound by 53BP1 | Diluted during replication to allow HR |
| AARS1 | Lactylates BLM to inhibit HR | Metabolic enzyme linking translation to HR |
How Is regulation of double-strand break repair via homologous recombination Regulated?
The regulation of homologous recombination is controlled at multiple levels, including cell cycle-dependent phosphorylation, ubiquitination, and metabolic modifications. For example, lactylation of MRE11 by acetyltransferase AARS1 enhances HR, while lactylation of BLM inhibits it. Additionally, 53BP1 binding to H4K20me2 is cell cycle-regulated, with dilution during S phase promoting HR. These layers ensure that HR is active only when a sister chromatid is available and that its activity is tuned to the cell's metabolic state.
regulation of double-strand break repair via homologous recombination and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| BRCA1 | Hereditary breast and ovarian cancer | BRCA1 knockout cell lines (e.g., U2OS, HeLa) for HR assays |
| MRE11 | Cancer chemoresistance via lactylation | MRE11 point mutants (lactylation sites) in cancer cells |
| BLM | Chemoresistance to anthracyclines | BLM knockout or lactylation-deficient knock-in cells |
| 53BP1 | Genomic instability and cancer | 53BP1 knockout cells to study HR restoration |
| RAD51 | Fanconi anemia-like disorders | RAD51 overexpression or point mutants for filament studies |
Cancer Predisposition and HR Deficiency
Mutations in HR regulators such as BRCA1 and BRCA2 lead to defective HR and increased cancer risk, particularly breast and ovarian cancers. Tumors with HR deficiency rely on alternative repair pathways like Polθ-mediated end joining, which can be targeted therapeutically. Understanding the regulation of HR is crucial for developing synthetic lethal strategies.
Chemoresistance and Metabolic Reprogramming
Lactylation of MRE11 and BLM alters HR activity and contributes to chemoresistance in cancer cells. For instance, inhibition of AARS1-mediated BLM lactylation sensitizes tumors to anthracyclines. This highlights the interplay between metabolism and DNA repair regulation in drug response.
Genomic Instability Syndromes
Defects in HR regulation cause genomic instability disorders such as Fanconi anemia and predispose to malignancies. Proper regulation of resection and homology search is essential to prevent chromosomal rearrangements.
From regulation of double-strand break repair via homologous recombination-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does gene X regulate HR efficiency? | CRISPR knockout of gene X in reporter cell lines (e.g., DR-GFP) |
| Does a specific mutation affect HR regulation? | Point mutation knock-in of the gene of interest |
| How does a tag affect protein localization during HR? | Tagged knock-in (e.g., GFP, HA) for imaging |
| Does overexpression of gene Y enhance HR? | Overexpression cell lines via lentiviral transduction |
| Which genes are synthetic lethal with BRCA1 loss? | CRISPR library screening in BRCA1-mutant cells |
| How does metabolic modification regulate HR? | Knock-in of lactylation-deficient mutants (e.g., MRE11, BLM) |
How to Study the regulation of double-strand break repair via homologous recombination Process
| Method | What It Measures | Typical Application |
|---|---|---|
| DR-GFP reporter assay | HR repair efficiency | Screening for HR regulators |
| ChIP-qPCR | Binding of HR proteins to DNA damage sites | Studying recruitment kinetics |
| Live-cell imaging | Real-time dynamics of HR foci | Visualizing homology search |
| Mass spectrometry | Post-translational modifications (e.g., lactylation) | Identifying regulatory modifications |
| CRISPR library screening | Genes affecting HR | Synthetic lethal screens |
| Comet assay | DNA damage and repair kinetics | Assessing overall repair capacity |
| Immunofluorescence | Foci formation of RAD51, 53BP1 | Quantifying HR activation |
HR Reporter Assays
The DR-GFP and EJ5-GFP reporter systems are widely used to measure HR and NHEJ efficiency, respectively. These assays involve introducing a DSB via I-SceI and quantifying GFP-positive cells by flow cytometry.
Chromatin Immunoprecipitation (ChIP)
ChIP can assess the recruitment of HR factors like BRCA1, RAD51, and 53BP1 to damage sites. It is often combined with quantitative PCR or sequencing to map binding sites.
Live-Cell Imaging
Fluorescently tagged proteins (e.g., GFP-RAD51) allow real-time visualization of HR foci formation and homology search. Cohesin dynamics during homology search can be tracked using live-cell imaging.
Proteomics and Post-translational Modification Analysis
Mass spectrometry-based proteomics identifies lactylation and other modifications on HR proteins. This approach can reveal novel regulatory sites and their impact on HR.
How CRISPR Can Be Used to Study GO:0010569 regulation of double-strand break repair via homologous recombination
Knockout
CRISPR knockout of HR regulators such as BRCA1, MRE11, or BLM allows researchers to study their essential roles in HR. Knockout cell lines can be used in reporter assays to measure HR efficiency and sensitivity to DNA-damaging agents.
Point Mutation
Introducing point mutations (e.g., lactylation sites on MRE11 or BLM) via CRISPR knock-in helps dissect the functional impact of specific modifications on HR regulation. These models are crucial for understanding post-translational control.
Knock-in
Tagged knock-in of HR proteins (e.g., GFP-RAD51) enables live-cell imaging and proteomic studies. Knock-in of reporter cassettes (e.g., DR-GFP) provides a quantitative readout of HR activity.
Overexpression
Overexpression of HR genes like RAD51 or BRCA1 can be achieved via lentiviral transduction to study gain-of-function effects. This is useful for assessing whether increased HR activity contributes to chemoresistance.
How EDITGENE Supports regulation of double-strand break repair via homologous recombination Research
Researchers studying regulation of double-strand break repair via homologous recombination-related genes often need to determine whether a candidate gene is causally involved in HR regulation, and to dissect the precise molecular mechanisms. EDITGENE provides a comprehensive suite of CRISPR-based services to accelerate this research.
Contact EDITGENE today to design your custom CRISPR model for regulation of double-strand break repair via homologous recombination research.
Frequently Asked Questions About regulation of double-strand break repair via homologous recombination
What is GO:0010569?
GO:0010569 is the Gene Ontology term for regulation of double-strand break repair via homologous recombination, describing any process that modulates the frequency, rate or extent of error-free repair of a DNA double-strand break using homologous sequences.
What genes are involved in regulation of double-strand break repair via homologous recombination?
Key genes include BRCA1, BARD1, 53BP1, MRE11, RAD51, BLM, and cohesin, among others.
How is homologous recombination regulated during the cell cycle?
HR is primarily restricted to S/G2 phases when a sister chromatid is available, regulated by cyclin-dependent kinases and chromatin modifications such as H4K20me2 dilution.
What is the role of BRCA1 in homologous recombination?
BRCA1 promotes DNA end resection and antagonizes 53BP1, committing cells to HR.
How does lactylation affect homologous recombination?
Lactylation of MRE11 enhances HR, while lactylation of BLM inhibits it, linking metabolism to DNA repair.
What diseases are associated with defective HR regulation?
Defective HR regulation is linked to hereditary breast and ovarian cancer, Fanconi anemia, and chemoresistance.
What experimental models are used to study HR regulation?
Common models include CRISPR knockout, point mutation knock-in, tagged knock-in, overexpression cell lines, and reporter assays like DR-GFP.
How can I measure HR efficiency in cells?
HR efficiency can be measured using reporter assays such as DR-GFP, which quantify GFP-positive cells after I-SceI-induced DSB.
What is the role of 53BP1 in HR regulation?
53BP1 binds H4K20me2 to protect DNA ends and inhibit resection, thereby antagonizing HR.
How does cohesin contribute to homologous recombination?
Cohesin drives chromatin scanning during RAD51-mediated homology search, facilitating the identification of homologous sequences.
Conclusion
GO:0010569, regulation of double-strand break repair via homologous recombination, is a critical biological process that ensures genomic stability through precise control of HR. Its dysregulation is implicated in cancer and other diseases, making it a prime target for therapeutic intervention. Advances in CRISPR-based models and screening technologies continue to unravel the complex regulatory networks, offering new opportunities for drug discovery. EDITGENE's comprehensive services empower researchers to dissect these mechanisms with high precision.
References
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- 2. Chen Y et al.. 2024. Metabolic regulation of homologous recombination repair by MRE11 lactylation.. Cell 187(2):294-311.e21 PMID: 38128537
- 3. Symington LS et al.. 2011. Double-strand break end resection and repair pathway choice.. Annu Rev Genet 45:247-71 PMID: 21910633
- 4. Li X et al.. 2025. Irinotecan alleviates chemoresistance to anthracyclines through the inhibition of AARS1-mediated BLM lactylation and homologous recombination repair.. Signal Transduct Target Ther 10(1):214 PMID: 40634292
- 5. Tarsounas M et al.. 2020. The antitumorigenic roles of BRCA1-BARD1 in DNA repair and replication.. Nat Rev Mol Cell Biol 21(5):284-299 PMID: 32094664
- 6. Ceccaldi R et al.. 2015. Homologous-recombination-deficient tumours are dependent on Polθ-mediated repair.. Nature 518(7538):258-62 PMID: 25642963
- 7. Salunkhe S et al.. 2024. Promotion of DNA end resection by BRCA1-BARD1 in homologous recombination.. Nature 634(8033):482-491 PMID: 39261729
- 8. Marin-Gonzalez A et al.. 2025. Cohesin drives chromatin scanning during the RAD51-mediated homology search.. Science 390(6777):eadw1928 PMID: 41343630
