GO:0070914 UV-damage excision repair: Pathway Mechanism, Genes, Functions and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0070914 (UV-damage excision repair) is a DNA repair process initiated by an endonuclease that introduces a single-strand incision immediately 5' of a UV-induced lesion, acting on both cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone 6-4 photoproducts (6-4PPs).
• It is also known as alternative excision repair (AER) or UVDE-dependent excision repair, distinguishing it from canonical nucleotide excision repair (NER).
• In bacteria, UV-damage excision repair is a major pathway for removing UV photoproducts, and its mechanism has been characterized in detail.
• In eukaryotic cells, NER is the dominant UV repair pathway, but alternative endonuclease-dependent repair can act when NER is compromised, as shown in NER-deficient cells.
• Chromatin organization and 3D genome architecture influence the efficiency of UV-damage repair, including excision repair processes.
• Studying GO:0070914 requires combining genetic knockout, point mutation, and reporter assays with methods such as lesion-specific PCR, comet assay, and sequencing-based damage mapping.
Description
UV-damage excision repair (GO:0070914) is a biological process that removes UV-induced DNA lesions through an endonuclease-initiated mechanism. Unlike nucleotide excision repair (NER), which relies on dual incisions flanking the damage, UV-damage excision repair introduces a single-strand incision immediately 5' of the lesion, followed by excision and resynthesis. This process acts on both cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone 6-4 photoproducts (6-4PPs), the two major UV photoproducts. The pathway is also referred to as alternative excision repair (AER) or UVDE-dependent excision repair, reflecting its dependence on a UV-damage endonuclease. Researchers study GO:0070914 to understand how cells cope with UV damage when canonical NER is impaired. In NER-deficient cells, topoisomerase I can drive repair of UV-induced damage, revealing backup mechanisms that may involve alternative excision repair. In bacteria, UV-damage excision repair is a primary defense against UV lethality and mutagenesis, and its components have been genetically and biochemically defined. In eukaryotic cells, the interplay between chromatin organization, 3D genome architecture, and UV repair efficiency is an active area of investigation. Understanding UV-damage excision repair has implications for cancer biology, aging, and the development of therapeutic strategies that exploit DNA repair defects. For example, aflatoxin-induced DNA damage is repaired by NER within the context of 3D genome organization, highlighting how repair pathways are spatially regulated. Similarly, active DNA damage eviction by HLTF stimulates NER, suggesting that chromatin remodeling is critical for efficient repair. These findings underscore the importance of GO:0070914 and related repair processes in maintaining genomic integrity.
UV-damage excision repair At A Glance
| GO ID | GO:0070914 |
|---|---|
| GO term | UV-damage excision repair |
| Ontology | biological_process |
| Synonym | AER, alternative excision repair, UV-damaged DNA endonuclease-dependent excision repair, UVDE-dependent excision repair, UVER |
| Major function | Removal of UV-induced DNA lesions (CPDs and 6-4PPs) via endonuclease-initiated single-strand incision |
| Organisms | Bacteria (e.g., Escherichia coli), yeast, and eukaryotic cells |
| Key enzyme | UV damage endonuclease (UVDE) in bacteria and some eukaryotes |
| Related pathways | Nucleotide excision repair (NER), base excision repair (BER), topoisomerase I-mediated repair |
What Is GO:0070914?
UV-damage excision repair (GO:0070914) is a DNA repair process that is initiated by an endonuclease which introduces a single-strand incision immediately 5' of a UV-induced damage site. This pathway acts on both cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone 6-4 photoproducts (6-4PPs). It is synonymous with alternative excision repair (AER), UV-damaged DNA endonuclease-dependent excision repair, UVDE-dependent excision repair, and UVER.
Why Is UV-damage excision repair Important in Cell Biology?
UV-damage excision repair is critical for maintaining genomic integrity in organisms exposed to ultraviolet radiation. Defects in this pathway can lead to increased mutation rates, cell death, and carcinogenesis. In bacteria, UV-damage excision repair is a primary mechanism for removing UV photoproducts, and its loss results in extreme UV sensitivity. In eukaryotic cells, alternative excision repair can compensate for defective NER, as demonstrated by topoisomerase I-driven repair in NER-deficient cells. Understanding this pathway provides insights into DNA repair plasticity and may inform strategies to overcome chemoresistance in cancer cells with repair defects.
• Protects against UV-induced mutagenesis and cell death by removing CPDs and 6-4PPs.
• Provides a backup repair mechanism when canonical NER is impaired, as seen in NER-deficient cells.
• Influences the efficacy of DNA-damaging agents used in cancer therapy, such as platinum-based drugs.
• Contributes to the understanding of how chromatin and 3D genome organization affect DNA repair efficiency.
• Relevant to bacterial pathogenesis and survival in UV-rich environments.
• Helps explain species-specific differences in UV sensitivity and repair capacity.
• May play a role in aging and degenerative diseases linked to accumulated DNA damage.
• Offers targets for sensitizing cancer cells to radiation therapy by inhibiting backup repair pathways.
• Facilitates the study of DNA damage tolerance and mutagenesis mechanisms.
• Supports the development of biotechnological tools for genome editing and DNA repair research.
What Happens During UV-damage excision repair?
Damage recognition and endonuclease incision
In simple terms: The repair enzyme finds the UV-damaged spot and cuts the DNA right next to it.
The first step in UV-damage excision repair is the recognition of UV-induced lesions, primarily CPDs and 6-4PPs, by a dedicated UV damage endonuclease (UVDE). This enzyme introduces a single-strand incision immediately 5' of the damage site, creating a free 3'-OH group and a 5'-phosphate. In bacteria, this endonuclease activity is well characterized and is essential for the alternative excision repair pathway. The incision is a critical commitment step that distinguishes this pathway from NER, which uses dual incisions.
Excision of the damaged oligonucleotide
In simple terms: After the cut, the piece of DNA containing the damage is removed.
Following the endonuclease incision, the damaged oligonucleotide is excised. This step may involve additional enzymatic activities, such as exonucleases or the same endonuclease acting in a concerted manner. In bacteria, the excision step generates a short gap that is subsequently filled by DNA polymerase I. The precise mechanism of excision in eukaryotic cells is less defined, but it is thought to involve similar principles, with the damaged fragment being removed to allow repair synthesis.
DNA synthesis and ligation
In simple terms: The missing DNA is rebuilt using the undamaged strand as a template, and the nick is sealed.
After excision, the resulting gap is filled by DNA polymerase, using the complementary strand as a template. In bacteria, DNA polymerase I is the primary enzyme responsible for gap filling, followed by sealing of the nick by DNA ligase. In eukaryotic cells, the repair synthesis step may involve different polymerases, depending on the context and cell cycle stage. This step restores the original DNA sequence, completing the repair process.
Coordination with other repair pathways
In simple terms: This repair pathway doesn't work alone; it cooperates with other DNA repair systems.
UV-damage excision repair can function as a backup to nucleotide excision repair (NER). In NER-deficient cells, topoisomerase I has been shown to drive repair of UV-induced damage, suggesting crosstalk between topoisomerase I and alternative excision repair. Additionally, base excision repair (BER) enzymes such as SMUG1 can be stimulated by UV-DDB to remove oxidized bases, indicating overlapping substrate specificities and coordinated repair responses. The interplay between these pathways ensures efficient removal of diverse UV-induced lesions.
Chromatin context and repair efficiency
In simple terms: How DNA is packaged affects how easily this repair pathway can access damage.
Chromatin structure and 3D genome organization significantly influence the efficiency of UV-damage repair. Studies have shown that DNA damage and repair are non-randomly distributed across the genome, with heterochromatic regions being repaired more slowly. The interplay of 3D genome organization with UV-induced DNA damage and repair has been reviewed, highlighting the importance of spatial organization in repair kinetics. Active DNA damage eviction by chromatin remodelers such as HLTF stimulates NER, and similar mechanisms may facilitate UV-damage excision repair.
Key Genes Involved in GO:0070914 UV-damage excision repair
The following genes and proteins are key players in UV-damage excision repair and related pathways, based on experimental evidence from bacterial and eukaryotic systems.
| Gene | Major Role | Research Relevance |
|---|---|---|
| uvrA | Component of bacterial NER; also implicated in UV damage recognition | Model for studying UV repair in bacteria |
| uvrB | Helicase subunit of bacterial NER | Essential for UV resistance in E. coli |
| uvrC | Endonuclease subunit of bacterial NER | Required for incision during NER |
| uvrD | DNA helicase involved in NER and other repair pathways | Mutants show UV sensitivity |
| uvde | UV damage endonuclease; initiates alternative excision repair | Key enzyme for GO:0070914 in bacteria and some eukaryotes |
| TOP1 | Topoisomerase I; can drive repair in NER-deficient cells | Backup repair mechanism for UV damage |
| HLTF | Chromatin remodeler; stimulates NER by evicting damage | Regulates repair efficiency in chromatin |
| SMUG1 | Base excision repair glycosylase; stimulated by UV-DDB | Links BER to UV damage response |
| XPA | NER damage recognition protein | Defective in xeroderma pigmentosum |
| XPC | NER damage recognition protein | Defective in xeroderma pigmentosum |
| DDB1 | UV-DDB complex subunit; involved in damage recognition | Mutations cause xeroderma pigmentosum group E |
| DDB2 | UV-DDB complex subunit; binds UV lesions | Stimulates SMUG1 and NER |
| ERCC1 | NER endonuclease complex subunit | Defects cause UV sensitivity and cancer predisposition |
| XPF | NER endonuclease complex subunit | Defects cause xeroderma pigmentosum |
| PCNA | DNA sliding clamp; involved in repair synthesis | Required for gap filling during repair |
| RAD18 | E3 ubiquitin ligase; involved in post-replication repair | Regulates UV damage tolerance |
| REV1 | Translesion synthesis polymerase | Mutagenic bypass of UV lesions |
How Is UV-damage excision repair Regulated?
UV-damage excision repair is regulated at multiple levels. In quiescent yeast cells, the regulation of UV damage repair differs from that in proliferating cells, with distinct roles for checkpoint kinases and chromatin modifiers. In bacteria, the SOS response induces the expression of many DNA repair genes, including components of UV-damage excision repair, upon UV exposure. In eukaryotic cells, post-translational modifications such as ubiquitination and phosphorylation regulate the assembly and activity of repair complexes. For example, HLTF-mediated chromatin remodeling is stimulated by damage-induced ubiquitination. Additionally, the 3D genome organization and chromatin compaction dynamically influence repair efficiency, with repair being more rapid in open chromatin regions.
UV-damage excision repair and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| XPA | Xeroderma pigmentosum | XPA knockout human fibroblasts or iPSCs |
| XPC | Xeroderma pigmentosum | XPC knockout keratinocytes |
| DDB2 | Xeroderma pigmentosum group E | DDB2 point mutation knock-in cells |
| TOP1 | Cancer chemoresistance | TOP1 overexpression in NER-deficient cells |
| uvde | Bacterial UV sensitivity | uvde deletion in E. coli |
Xeroderma pigmentosum and UV hypersensitivity
Defects in nucleotide excision repair (NER) cause xeroderma pigmentosum (XP), a rare autosomal recessive disorder characterized by extreme sensitivity to UV light and a high risk of skin cancer. While GO:0070914 specifically describes alternative excision repair, it can serve as a backup pathway when NER is defective. In NER-deficient cells, topoisomerase I-driven repair of UV-induced damage has been observed, suggesting that alternative mechanisms can partially compensate for NER loss. Understanding these backup pathways may provide therapeutic targets for XP patients.
Cancer and DNA repair deficiency
Many cancers exhibit defects in DNA repair pathways, including NER and alternative excision repair. For example, aflatoxin-induced DNA damage is repaired by NER, and defects in this pathway are associated with hepatocellular carcinoma. The interplay between 3D genome organization and UV damage repair may influence cancer susceptibility, as alterations in chromatin architecture can affect repair efficiency. Targeting backup repair pathways like GO:0070914 could sensitize cancer cells to DNA-damaging therapies.
Bacterial survival and pathogenesis
In bacteria, UV-damage excision repair is critical for survival under UV radiation. Pathogenic bacteria that encounter UV stress during host infection rely on this pathway to maintain genomic integrity. Inhibiting UV-damage excision repair could therefore attenuate bacterial virulence and enhance the efficacy of UV-based sterilization methods.
From UV-damage excision repair-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does gene X initiate UV-damage excision repair? | Knockout cell line (e.g., CRISPR-Cas9) followed by UV survival assay |
| Does a specific point mutation in gene X affect repair activity? | Point mutation knock-in via CRISPR |
| Does gene X interact with UVDE? | Tagged knock-in (e.g., GFP) for co-immunoprecipitation |
| Does overexpression of gene X enhance UV resistance? | Overexpression cell line via lentiviral transduction |
| Which genes are essential for UV-damage excision repair? | CRISPR library screening with UV selection |
| How does 3D genome organization affect repair? | Hi-C and damage mapping in knockout cells |
How to Study the UV-damage excision repair Process
| Method | What It Measures | Typical Application |
|---|---|---|
| UV survival assay | Cell viability after UV irradiation | Assessing repair capacity of knockout strains |
| Lesion-specific PCR | Removal of UV photoproducts at specific loci | Kinetics of CPD and 6-4PP repair |
| Comet assay | DNA strand breaks and repair intermediates | Single-cell repair analysis |
| ChIP | Protein binding at damage sites | Recruitment of repair factors |
| RNA-seq | Transcriptional response to UV | Identifying UV-inducible genes |
| Proteomics | Protein interactions and modifications | Discovering new repair components |
| CRISPR library screening | Genes required for UV resistance | High-throughput functional genomics |
UV survival assays
UV survival assays measure the ability of cells to survive after exposure to ultraviolet radiation. Cells are plated, irradiated with increasing doses of UV, and colony-forming ability is quantified. This method is widely used to assess the contribution of specific genes to UV-damage excision repair, as demonstrated in bacterial and yeast studies.
Lesion-specific PCR and sequencing
Lesion-specific PCR uses DNA polymerases that stall at UV photoproducts to detect damage at specific genomic loci. Quantitative PCR of UV-irradiated DNA can measure the removal of CPDs and 6-4PPs over time. Next-generation sequencing-based methods, such as Damage-seq and XR-seq, allow genome-wide mapping of UV lesions and repair at nucleotide resolution.
Comet assay
The comet assay (single-cell gel electrophoresis) detects DNA strand breaks and alkali-labile sites at the single-cell level. It can be adapted to measure UV-induced damage and repair by incorporating lesion-specific enzymes. This method is useful for assessing repair kinetics in different cell types and genetic backgrounds.
Chromatin immunoprecipitation (ChIP)
ChIP is used to study the recruitment of repair proteins to UV-damaged chromatin. By crosslinking proteins to DNA and immunoprecipitating with specific antibodies, researchers can determine the binding dynamics of factors such as UVDE, XPA, or HLTF at damage sites. This approach has been instrumental in understanding the role of chromatin remodelers in repair.
How CRISPR Can Be Used to Study GO:0070914 UV-damage excision repair
Knockout
CRISPR-Cas9 knockout is used to delete candidate genes involved in UV-damage excision repair. For example, knocking out uvde in bacteria or its homologs in eukaryotes allows researchers to test their requirement for UV resistance. Knockout cell lines can be subjected to UV survival assays and lesion-specific PCR to quantify repair defects.
Point Mutation
Point mutation knock-in via CRISPR is used to introduce specific amino acid substitutions that abrogate catalytic activity or protein interactions. For instance, mutating the catalytic residues of a UV endonuclease can distinguish its endonuclease activity from other functions. This approach provides precise mechanistic insights into GO:0070914.
Knock-in
Tagged knock-in (e.g., GFP, FLAG) allows endogenous labeling of repair proteins for imaging and biochemical studies. Knocking in a tag at the UVDE locus enables real-time tracking of its recruitment to damage sites and co-immunoprecipitation of interacting partners. This is valuable for understanding the spatiotemporal dynamics of UV-damage excision repair.
Overexpression
Overexpression of repair genes can enhance UV resistance or perturb pathway balance. For example, overexpressing topoisomerase I in NER-deficient cells can drive alternative repair of UV damage. Overexpression models are useful for testing whether a gene is sufficient to improve repair capacity and for identifying dominant-negative effects.
How EDITGENE Supports UV-damage excision repair Research
Researchers studying UV-damage excision repair-related genes often need to determine whether a candidate gene is causally involved in the pathway, how specific mutations affect its function, and whether its overexpression can modulate UV sensitivity. EDITGENE provides a comprehensive suite of CRISPR-based services to address these questions with precision and reproducibility.
Contact EDITGENE today to design your custom CRISPR model for UV-damage excision repair research.
Frequently Asked Questions About UV-damage excision repair
What is UV-damage excision repair (GO:0070914)?
UV-damage excision repair is a DNA repair process initiated by an endonuclease that cuts immediately 5' of UV-induced lesions such as cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4PPs). It is also known as alternative excision repair (AER).
What genes are involved in UV-damage excision repair?
Key genes include uvde (UV damage endonuclease) in bacteria, as well as TOP1, HLTF, and SMUG1 in eukaryotic cells, which can contribute to backup repair mechanisms.
How does UV-damage excision repair differ from nucleotide excision repair (NER)?
Unlike NER, which uses dual incisions flanking the damage, UV-damage excision repair introduces a single-strand incision immediately 5' of the lesion. This pathway is independent of the classic NER machinery and is often considered a backup mechanism.
What diseases are associated with defective UV-damage repair?
Defects in UV repair pathways are linked to xeroderma pigmentosum, an inherited disorder causing extreme UV sensitivity and skin cancer predisposition. Alternative repair defects may also contribute to cancer and aging.
How can I study UV-damage excision repair in the lab?
Common methods include UV survival assays, lesion-specific PCR, comet assay, and ChIP. CRISPR knockout and point mutation models are powerful tools for dissecting gene function.
What is the role of topoisomerase I in UV-damage repair?
Topoisomerase I can drive repair of UV-induced damage in NER-deficient cells, suggesting it participates in alternative excision repair pathways.
Does chromatin structure affect UV-damage excision repair?
Yes, chromatin organization and 3D genome architecture influence the efficiency of UV damage repair. Heterochromatic regions are repaired more slowly, and chromatin remodelers like HLTF stimulate repair.
Can CRISPR be used to create models for UV-damage excision repair?
Absolutely. CRISPR-Cas9 enables knockout, point mutation knock-in, tagged knock-in, and overexpression of genes involved in UV-damage excision repair, allowing precise functional studies.
What is the role of UVDE in bacteria?
UVDE (UV damage endonuclease) initiates alternative excision repair by incising 5' of UV photoproducts. It is critical for UV resistance in bacteria such as Escherichia coli.
How does 3D genome organization impact UV repair?
3D genome organization affects the spatial accessibility of damage sites to repair machinery. Studies show that repair efficiency varies across different chromatin compartments and topologically associating domains.
Conclusion
UV-damage excision repair (GO:0070914) is a specialized DNA repair pathway that removes UV-induced lesions through an endonuclease-initiated mechanism. While it serves as a backup to NER in many organisms, its importance is underscored by its role in bacterial UV resistance and its potential to compensate for NER defects in eukaryotic cells. Understanding the molecular players and regulatory mechanisms of this pathway can inform cancer therapy, microbial pathogenesis, and basic DNA repair biology. EDITGENE provides comprehensive CRISPR services to facilitate research on UV-damage excision repair, from knockout and point mutation models to library screening and bioinformatics. By leveraging these tools, researchers can accelerate discoveries in DNA repair and genomic stability.
References
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- 2. Wu Y et al.. 2024. Nucleotide excision repair of aflatoxin-induced DNA damage within the 3D human genome organization.. Nucleic Acids Res 52(19):11704-11719 PMID: 39258558
- 3. van Toorn M et al.. 2022. Active DNA damage eviction by HLTF stimulates nucleotide excision repair.. Mol Cell 82(7):1343-1358.e8 PMID: 35271816
- 4. Long LJ et al.. 2020. Regulation of UV damage repair in quiescent yeast cells.. DNA Repair (Amst) 90:102861 PMID: 32403026
- 5. Mao P et al.. 2019. Organization of DNA damage, excision repair, and mutagenesis in chromatin: A genomic perspective.. DNA Repair (Amst) 81:102645 PMID: 31307926
- 6. Goosen N et al.. 2008. Repair of UV damage in bacteria.. DNA Repair (Amst) 7(3):353-79 PMID: 17951115
- 7. Akköse Ü et al.. 2023. The interplay of 3D genome organization with UV-induced DNA damage and repair.. J Biol Chem 299(5):104679 PMID: 37028766
- 8. Jang S et al.. 2023. UV-DDB stimulates the activity of SMUG1 during base excision repair of 5-hydroxymethyl-2'-deoxyuridine moieties.. Nucleic Acids Res 51(10):4881-4898 PMID: 36971122
