GO:0006284 base-excision repair: Mechanism, Genes, Functions and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0006284 base-excision repair (BER) is the biological process that removes altered or damaged bases from DNA via DNA glycosylases, followed by excision of the resulting sugar phosphate and gap-filling by DNA polymerase and DNA ligase.
• BER is the primary pathway for repairing small, non-helix-distorting base lesions such as oxidized, alkylated, deaminated, and oxidized bases, and it is essential for genome stability.
• The core BER machinery includes DNA glycosylases (e.g., OGG1, UNG, MUTYH, NTHL1, NEIL1/2), AP endonuclease APEX1, DNA polymerase beta (POLB), and DNA ligase III/XRCC1.
• Defects in BER are linked to cancer predisposition, neurodegeneration, and accelerated aging; BER is also a major determinant of resistance to alkylating and oxidizing chemotherapies.
• BER operates in the context of chromatin and is regulated by protein-protein interactions, post-translational modifications, and accessory factors that influence its efficiency and fidelity.
• CRISPR-based knockout, point-mutation, knock-in, and overexpression models are powerful tools to dissect BER gene function and to validate therapeutic targets in cancer and other diseases.
Description
Base-excision repair (BER) is a highly conserved DNA repair pathway that protects cells from the mutagenic and cytotoxic effects of endogenous and exogenous DNA base damage. The term GO:0006284 base-excision repair is defined as the process in which an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate, and the small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. BER is essential for maintaining genome integrity because it repairs small, non-helix-distorting lesions that arise from oxidation, alkylation, deamination, and hydrolysis, which would otherwise lead to mutations or cell death. Researchers study BER because it is central to cancer biology, aging, and the response to genotoxic therapies. Deficiencies in BER genes such as MUTYH, NTHL1, and OGG1 are associated with hereditary cancer syndromes and increased mutation burden. Moreover, BER activity modulates the efficacy of alkylating agents, radiation, and certain targeted therapies, making it an attractive target for precision oncology. Understanding the molecular steps, regulatory mechanisms, and disease connections of BER is therefore critical for developing new diagnostic and therapeutic strategies.
base-excision repair At A Glance
| GO ID | GO:0006284 |
|---|---|
| GO term | base-excision repair |
| Ontology | biological_process |
| Synonym | BER |
| Definition | In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. |
| Major function | Removal of damaged or altered DNA bases and restoration of the correct DNA sequence |
| Key enzymes | DNA glycosylases, AP endonuclease (APEX1), DNA polymerase beta (POLB), DNA ligase III/XRCC1 |
| Subpathways | Short-patch (single-nucleotide) and long-patch (2-10 nucleotide) BER |
| Disease relevance | Cancer predisposition, neurodegeneration, aging, and chemotherapy resistance |
What Is GO:0006284?
Base-excision repair (BER) is a biological process that removes a damaged or altered DNA base through the action of a DNA glycosylase, which cleaves the N-glycosidic bond between the base and the deoxyribose phosphate backbone. The resulting apurinic/apyrimidinic (AP) site is then processed by an AP endonuclease, leaving a single-strand break with a 5'-deoxyribose phosphate (dRP) residue. The dRP group is removed by a lyase activity, and the one-nucleotide gap is filled by DNA polymerase and sealed by DNA ligase. This coordinated sequence restores the original DNA sequence and maintains genomic integrity.
Why Is base-excision repair Important in Cell Biology?
Base-excision repair is essential for maintaining genome stability because it repairs the most common types of endogenous DNA damage, including oxidized, alkylated, and deaminated bases, which would otherwise cause mutations or cell death. Defects in BER lead to accumulation of mutations and are associated with cancer predisposition, neurodegeneration, and premature aging. Furthermore, BER activity influences the response to chemotherapy and radiotherapy, making it a critical determinant of treatment outcome and a promising target for therapeutic intervention.
• BER repairs small, non-helix-distorting base lesions that are not recognized by nucleotide excision repair or mismatch repair.
• Deficiency in BER genes such as MUTYH and NTHL1 causes hereditary cancer syndromes with increased mutation burden.
• BER is a major mechanism of resistance to alkylating agents (e.g., temozolomide) and oxidizing agents used in cancer therapy.
• BER protects neurons from oxidative DNA damage, and its dysfunction is implicated in neurodegeneration.
• BER operates in chromatin and its efficiency is influenced by histone modifications and chromatin remodelers.
• Protein-protein interactions within BER complexes regulate pathway choice and coordination.
• BER accessory factors modulate senescence avoidance and resistance to treatments.
• BER is essential for transcription-replication conflict resolution in pancreatic ductal adenocarcinoma.
• Targeting BER is a promising strategy in precision oncology, especially in tumors with specific DNA repair defects.
• CRISPR screens have identified BER genes as vulnerabilities in certain cancer contexts.
What Happens During base-excision repair?
Base recognition and removal by DNA glycosylases
In simple terms: A damaged base is recognized and cut out of the DNA by a specific enzyme.
The first step of BER is the recognition and removal of a damaged or altered base by a DNA glycosylase. Different glycosylases are specific for different lesions: OGG1 removes 8-oxoguanine, UNG removes uracil, MUTYH removes adenine mispaired with 8-oxoguanine, NTHL1 removes oxidized pyrimidines, and NEIL1/2 remove oxidized purines and pyrimidines. The glycosylase cleaves the N-glycosidic bond, releasing the damaged base and creating an apurinic/apyrimidinic (AP) site.
AP site processing and strand incision
In simple terms: The abasic site left behind is cut to create a single-strand break.
The AP site is recognized by AP endonuclease 1 (APEX1), which incises the DNA backbone 5' to the AP site, generating a single-strand break with a 5'-deoxyribose phosphate (dRP) terminus and a 3'-hydroxyl group. In some cases, bifunctional glycosylases with lyase activity can also incise the backbone, producing different termini that require further processing.
Gap filling and ligation
In simple terms: The missing DNA base is replaced and the break is sealed.
The 5'-dRP group is removed by the lyase activity of DNA polymerase beta (POLB) in short-patch BER, and POLB then fills the single-nucleotide gap. In long-patch BER, 2-10 nucleotides are incorporated by POLB or POL delta/epsilon, and the displaced flap is removed by FEN1. Finally, DNA ligase III/XRCC1 or DNA ligase I seals the nick to restore the intact DNA strand.
Coordination and subpathways
In simple terms: The repair can happen in two ways: a short patch or a longer patch.
BER proceeds via two subpathways: short-patch BER, which replaces a single nucleotide, and long-patch BER, which replaces 2-10 nucleotides. The choice between these subpathways depends on the type of lesion, the cell cycle phase, and the availability of specific proteins. Protein-protein interactions among BER factors, such as between APEX1, POLB, and XRCC1, ensure efficient handoff of intermediates and prevent the accumulation of toxic repair intermediates.
BER in chromatin context
In simple terms: Repair must happen on DNA that is wrapped around proteins, so it needs extra help.
In eukaryotic cells, DNA is packaged into chromatin, and BER must access lesions within nucleosomes. Chromatin remodeling complexes and histone chaperones facilitate BER by exposing damaged bases and promoting the assembly of repair factors. Post-translational modifications of histones and BER proteins also regulate the efficiency of the pathway.
Key Genes Involved in GO:0006284 base-excision repair
The following genes encode core and accessory proteins that carry out and regulate base-excision repair.
| Gene | Major Role | Research Relevance |
|---|---|---|
| OGG1 | DNA glycosylase that removes 8-oxoguanine | Oxidative DNA damage repair; cancer and neurodegeneration models |
| UNG | Uracil-DNA glycosylase | Removes uracil from DNA; studies on mutagenesis and immunity |
| MUTYH | Adenine glycosylase that removes mispaired adenine | Hereditary colorectal cancer (MAP); mutation burden studies |
| NTHL1 | DNA glycosylase for oxidized pyrimidines | Hereditary cancer predisposition; base damage repair |
| NEIL1 | DNA glycosylase for oxidized bases | Oxidative stress response; cancer and metabolic studies |
| NEIL2 | DNA glycosylase for oxidized bases | Transcription-coupled BER; genome stability |
| APEX1 | AP endonuclease | Central BER enzyme; redox regulation; cancer therapy resistance |
| POLB | DNA polymerase beta | Gap filling and dRP lyase; chemotherapy response |
| XRCC1 | Scaffold protein | Coordinates BER; polymorphisms linked to cancer risk |
| LIG3 | DNA ligase III | Seals nicks in short-patch BER; mitochondrial DNA repair |
| LIG1 | DNA ligase I | Seals nicks in long-patch BER; replication-associated repair |
| FEN1 | Flap endonuclease | Long-patch BER; removes displaced flaps |
| PCNA | Proliferating cell nuclear antigen | Stimulates long-patch BER; coordination with replication |
| PARP1 | Poly(ADP-ribose) polymerase 1 | Detects strand breaks; recruits BER factors; target for cancer therapy |
| PARG | Poly(ADP-ribose) glycohydrolase | Regulates PARP1 activity; BER coordination |
| SMUG1 | Single-strand selective monofunctional uracil DNA glycosylase | Backup uracil removal; cancer and immune studies |
| TDG | Thymine DNA glycosylase | Removes mismatched bases; epigenetic regulation |
| MBD4 | Methyl-CpG binding domain protein 4 | Removes mismatched bases at CpG sites; cancer risk |
How Is base-excision repair Regulated?
Base-excision repair is regulated at multiple levels, including protein-protein interactions, post-translational modifications, and chromatin context. For example, PARP1 detects DNA strand breaks and recruits BER factors through poly(ADP-ribosyl)ation, while PARG reverses this modification to allow repair progression. Phosphorylation, acetylation, and ubiquitination of BER proteins such as APEX1 and POLB modulate their activity and stability. Accessory factors, including chromatin remodelers and histone chaperones, facilitate BER within nucleosomes. Additionally, BER is coordinated with transcription and replication to avoid conflicts, as shown in pancreatic ductal adenocarcinoma models. The pathway is also influenced by the cellular redox state and by the availability of cofactors such as NAD+ for PARP1 activity.
base-excision repair and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| MUTYH | MUTYH-associated polyposis (colorectal cancer) | Knockout or point-mutation knock-in in colorectal cell lines |
| NTHL1 | Hereditary cancer predisposition | Knockout in cancer cell lines; organoids |
| OGG1 | Oxidative stress-related neurodegeneration and cancer | Knockout in neuronal and cancer cell lines |
| APEX1 | Chemotherapy resistance in cancer | Overexpression and knockout in cancer cell lines |
| POLB | Alkylating agent resistance | Point-mutation knock-in in cancer cell lines |
Base-excision repair and cancer
Defects in BER genes are associated with increased cancer risk and mutational signatures. Biallelic mutations in MUTYH cause MUTYH-associated polyposis, a hereditary colorectal cancer syndrome. Germline mutations in NTHL1 predispose to colorectal and other cancers. OGG1 deficiency leads to accumulation of 8-oxoguanine and increased mutations, contributing to carcinogenesis. Furthermore, BER activity modulates the response to alkylating agents such as temozolomide, and targeting BER is a promising strategy in precision oncology. In pancreatic ductal adenocarcinoma, BER regulates transcription-replication conflicts, and its inhibition may selectively kill cancer cells.
Base-excision repair in neurodegeneration and aging
Neurons are highly susceptible to oxidative DNA damage due to high metabolic activity and limited replication. BER is the primary pathway for repairing oxidative lesions in the brain, and its dysfunction is implicated in neurodegeneration. For example, OGG1 deficiency leads to accumulation of 8-oxoguanine in neuronal DNA, which is associated with cognitive decline and neurodegenerative diseases. Defects in BER also contribute to premature aging phenotypes, as seen in mouse models with mutations in XRCC1 or other BER genes. Accessory factors that regulate BER influence senescence avoidance and resistance to treatments.
Base-excision repair and chemotherapy resistance
BER is a major determinant of resistance to alkylating and oxidizing chemotherapies. Upregulation of BER enzymes such as APEX1 and POLB increases repair capacity and reduces drug efficacy. Conversely, inhibition of BER sensitizes cancer cells to these agents. Targeting BER in combination with DNA-damaging therapies is an active area of clinical investigation, with PARP inhibitors being the most successful example. Understanding the regulation of BER in tumors is critical for predicting treatment response and developing combination strategies.
From base-excision repair-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of a BER gene increase mutation burden? | CRISPR knockout cell lines followed by whole-genome sequencing |
| Does a specific BER mutation affect enzyme activity? | Point-mutation knock-in cell lines and biochemical assays |
| Does overexpression of a BER gene confer drug resistance? | CRISPR overexpression cell lines and drug sensitivity assays |
| How does a BER protein localize to damage sites? | Tagged knock-in with fluorescent tags and live-cell imaging |
| What are the synthetic lethal partners of BER genes? | CRISPR library screening in isogenic knockout backgrounds |
| How does BER regulate transcription-replication conflicts? | Knockout cell lines and RNA-seq/proteomics in cancer models |
How to Study the base-excision repair Process
| Method | What It Measures | Typical Application |
|---|---|---|
| RNA-seq | Gene expression changes | Identifying BER gene expression signatures in cancer |
| Whole-genome sequencing | Mutation burden and signatures | Quantifying mutational impact of BER deficiency |
| AP-MS | Protein-protein interactions | Mapping BER complex dynamics |
| Live-cell imaging | Recruitment kinetics of repair proteins | Studying BER in chromatin context |
| Comet assay | DNA strand breaks | Measuring repair capacity after damage |
| CRISPR knockout screen | Gene essentiality and synthetic lethality | Identifying BER vulnerabilities in cancer |
| CRISPR activation screen | Gene overexpression effects | Discovering resistance mechanisms to DNA damage |
Genomic and transcriptomic profiling
RNA sequencing (RNA-seq) can reveal changes in BER gene expression and identify pathways affected by BER loss or overexpression. Whole-genome sequencing and mutational signature analysis can quantify the mutational consequences of BER deficiency, such as the signature associated with MUTYH or NTHL1 loss. These methods are essential for linking BER to disease and for identifying biomarkers.
Proteomics and interactomics
Mass spectrometry-based proteomics can identify protein-protein interactions within BER complexes and post-translational modifications that regulate BER. Affinity purification coupled with mass spectrometry (AP-MS) has been used to map the BER interactome, revealing dynamic interactions between glycosylases, APEX1, POLB, and XRCC1. These approaches help understand how BER is coordinated and how mutations affect complex assembly.
Imaging and cellular assays
Live-cell imaging with fluorescently tagged BER proteins (e.g., through knock-in of GFP or Halo tags) allows real-time visualization of repair factor recruitment to DNA damage sites. Comet assays and alkaline unwinding assays measure DNA strand breaks and repair kinetics. These methods are useful for studying BER in chromatin and in response to genotoxic agents.
CRISPR screening and functional genomics
Genome-wide CRISPR knockout or activation screens can identify genes that modulate sensitivity to DNA-damaging agents or that are synthetic lethal with BER defects. Such screens have revealed BER components as vulnerabilities in specific cancer contexts, including pancreatic ductal adenocarcinoma. These functional genomics approaches accelerate target discovery and drug development.
How CRISPR Can Be Used to Study GO:0006284 base-excision repair
Knockout
CRISPR knockout (KO) of BER genes such as OGG1, MUTYH, or APEX1 allows researchers to study loss-of-function phenotypes, including increased mutation burden, sensitivity to DNA-damaging agents, and altered cellular responses. KO cell lines are valuable for validating drug targets and for understanding the role of BER in cancer and neurodegeneration.
Point Mutation
CRISPR point-mutation knock-in can introduce specific disease-associated mutations (e.g., in MUTYH or POLB) to study their functional consequences on enzyme activity, protein stability, and cellular repair capacity. These models are essential for dissecting the molecular mechanisms of BER defects and for testing targeted therapies.
Knock-in
Knock-in of tagged versions of BER proteins (e.g., GFP, Halo, or epitope tags) enables real-time imaging, affinity purification, and proteomic studies. Tagged knock-in cell lines are powerful tools for studying BER protein localization, interactions, and dynamics in a physiological context.
Overexpression
CRISPR-mediated overexpression of BER genes (e.g., APEX1, POLB) can model the upregulation observed in drug-resistant tumors and help identify mechanisms of resistance to alkylating agents. Overexpression models are also useful for testing the efficacy of BER inhibitors in combination with chemotherapy.
How EDITGENE Supports base-excision repair Research
Researchers studying base-excision repair-related genes often need to determine whether a candidate gene is causally involved in DNA repair, disease progression, or therapy response. EDITGENE provides a comprehensive suite of CRISPR-based services to generate precisely engineered cell models, enabling functional validation and mechanistic studies of BER genes.
Contact EDITGENE today to design your custom CRISPR model for base-excision repair research.
Frequently Asked Questions About base-excision repair
What is base-excision repair (BER)?
Base-excision repair (BER) is a DNA repair pathway that removes damaged or altered DNA bases through the action of DNA glycosylases, followed by excision of the sugar phosphate and gap-filling by DNA polymerase and ligase.
What genes are involved in base-excision repair?
Key genes include OGG1, UNG, MUTYH, NTHL1, NEIL1/2, APEX1, POLB, XRCC1, LIG3, LIG1, FEN1, PCNA, and PARP1.
What is the GO term for base-excision repair?
The Gene Ontology term is GO:0006284, defined as the biological process of base-excision repair.
How does base-excision repair work?
A DNA glycosylase removes the damaged base, AP endonuclease incises the backbone, DNA polymerase fills the gap, and DNA ligase seals the nick.
What diseases are associated with defective base-excision repair?
Defects in BER are linked to cancer predisposition (e.g., MUTYH-associated polyposis), neurodegeneration, and premature aging.
Why is base-excision repair important in cancer therapy?
BER activity determines sensitivity to alkylating agents and radiation; inhibiting BER can sensitize tumors to these therapies.
What are the two subpathways of base-excision repair?
Short-patch BER replaces a single nucleotide, while long-patch BER replaces 2-10 nucleotides.
How can CRISPR be used to study base-excision repair?
CRISPR knockout, point-mutation knock-in, and overexpression models allow functional dissection of BER genes in disease and drug response.
What is the role of APEX1 in base-excision repair?
APEX1 is an AP endonuclease that incises the DNA backbone at apurinic/apyrimidinic sites, a central step in BER.
How is base-excision repair regulated?
BER is regulated by protein-protein interactions, post-translational modifications, chromatin context, and accessory factors.
Conclusion
Base-excision repair (GO:0006284) is a fundamental DNA repair pathway that protects cells from endogenous and exogenous base damage. Its core machinery, including DNA glycosylases, APEX1, POLB, and ligases, is highly conserved and essential for genome stability. Defects in BER contribute to cancer, neurodegeneration, and aging, and the pathway is a key determinant of chemotherapy response. Continued research using CRISPR-based models and functional genomics will further elucidate BER mechanisms and facilitate the development of targeted therapies.
References
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- 2. Zhou W et al.. 2025. Base excision repair in human cancer: Emerging diagnostic and therapeutic target.. DNA Repair (Amst) 152:103879 PMID: 40779892
- 3. Grundy GJ et al.. 2020. Base excision repair and its implications to cancer therapy.. Essays Biochem 64(5):831-843 PMID: 32648895
- 4. Rathnaiah G et al.. 2025. Protein-Protein Interactions in Base Excision Repair.. Biomolecules 15(6) PMID: 40563529
- 5. Meng F et al.. 2024. Base-excision repair pathway regulates transcription-replication conflicts in pancreatic ductal adenocarcinoma.. Cell Rep 43(10):114820 PMID: 39368091
- 6. Biechele-Speziale DJ et al.. 2022. Obstacles and opportunities for base excision repair in chromatin.. DNA Repair (Amst) 116:103345 PMID: 35689883
- 7. Montaldo NP et al.. 2025. Targeting base excision repair in precision oncology.. DNA Repair (Amst) 149:103844 PMID: 40359788
- 8. Vickridge E et al.. 2022. Base excision repair accessory factors in senescence avoidance and resistance to treatments.. Cancer Drug Resist 5(3):703-720 PMID: 36176767
