A multistep damage recognition mechanism for global genomic nucleotide excision repair
Open accessAbstract
A mammalian nucleotide excision repair (NER) factor, the XPC–HR23B complex, can specifically bind to certain DNA lesions and initiate the cell-free repair reaction. Here we describe a detailed analysis of its binding specificity using various DNA substrates, each containing a single defined lesion. A highly sensitive gel mobility shift assay revealed that XPC–HR23B specifically binds a small bubble structure with or without damaged bases, whereas dual incision takes place only when damage is present in the bubble. This is evidence that damage recognition for NER is accomplished through at least two steps; XPC–HR23B first binds to a site that has a DNA helix distortion, and then the presence of injured bases is verified prior to dual incision. Cyclobutane pyrimidine dimers (CPDs) were hardly recognized by XPC–HR23B, suggesting that additional factors may be required for CPD recognition. Although the presence of mismatched bases opposite a CPD potentiated XPC–HR23B binding, probably due to enhancement of the helix distortion, cell-free excision of such compound lesions was much more efficient than expected from the observed affinity for XPC–HR23B. This also suggests that additional factors and steps are required for the recognition of some types of lesions. A multistep mechanism of this sort may provide a molecular basis for ensuring the high level of damage discrimination that is required for global genomic NER.
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The hHR23B-XPC complex, or XPC alone, binds UV-induced single-stranded and double-stranded DNA with similar high affinity, prefers DNA containing various lesions, and can bind small bubble structures with or without a lesion.
“hHR23B-XPC complex or only XPC exhibits a similar high affinity for both UV-induced single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) [230, 259], preferentially binds to DNA with various lesions [259] and even to small bubble structures with or without a lesion [260].”
From Molecular Mechanisms of Ultraviolet Radiation‐Induced DNA Damage and Repair (2010) · cites this paper as [260]
6-4PP lesions are directly recognized by XPC independent of DDB.
“whereas 6-4PP lesions are directly recognized by XPC independent of DDB [5–8].”
From ATR- and ATM-Mediated DNA Damage Response Is Dependent on Excision Repair Assembly during G1 but Not in S Phase of Cell Cycle (2016) · cites this paper as [7]
The DDB complex initially recognizes CPD lesions and helps recruit XPC.
“The DDB complex initially recognizes the CPD lesions and helps in recruiting XPC”
From ATR- and ATM-Mediated DNA Damage Response Is Dependent on Excision Repair Assembly during G1 but Not in S Phase of Cell Cycle (2016) · cites this paper as [7]
XPC helps recruit XPA, XPG, and TFIIH components that open the DNA helix around the damage to form a bubble.
“In turn, XPC helps in recruiting XPA, XPG, and TFIIH components that enable opening of the DNA helix around the damage site to form a bubble [8].”
From NER initiation factors, DDB2 and XPC, regulate UV radiation response by recruiting ATR and ATM kinases to DNA damage sites (2013) · cites this paper as [8]
The DDB complex first recognizes CPD lesions and recruits XPC, whereas XPC can recognize 6-4PP lesions on its own.
“The DDB complex initially recognizes the CPD lesions and recruits XPC [4, 5, 8, 9], whereas XPC can independently recognize 6-4PP lesions [5].”
From NER initiation factors, DDB2 and XPC, regulate UV radiation response by recruiting ATR and ATM kinases to DNA damage sites (2013) · cites this paper as [8]
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Nucleotide Excision Repair Eliminates Unique DNA-Protein Cross-links from Mammalian Cells
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“In turn, XPC helps in recruiting XPA, XPG, and TFIIH components that enable opening of the DNA helix around the damage site to form a bubble [8].”
BackgroundBlockage of RNA Polymerase II at a Cyclobutane Pyrimidine Dimer and 6-4 Photoproduct
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Kropachev, K. Y., Ding, S., Terzidis, M. A., Masi, A., Liu, Z., Cai, Y., Kolbanovskiy, M., Chatgilialoglu, C., Broyde, S. B., Geacintov, N. E., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku162 · Cited by 76 · see citing works
- Authors
- Sugasawa, K., Okamoto, T., Shimizu, Y., Masutani, C., Iwai, S., & Hanaoka, F.
- Affiliations
- Japan Science and Technology Agency (JP)
- ORCID
- Venue
- Genes & Development
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2001-03-01
- Volume
- 15
- Issue
- 5
- Pages
- 507-521
- ISSN
- 0890-9369 (ISSN-L)
- 1549-5477
- PMC
- PMC312644
- OpenAlex
- W2106443150
- Cited by
- 435
- References
- 61
- Citations by year
- 2026: 10 · 2025: 10 · 2024: 4 · 2023: 14 · 2022: 8 · 2021: 12 · 2020: 12 · 2019: 14 · 2018: 12 · 2017: 18 · 2016: 30 · 2015: 26 · 2014: 16 · 2013: 17 · 2012: 20
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genes & Development (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Japan Science and Technology Corporation (CREST)
- RIKEN
- Core Research for Evolutional Science and Technology
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Carcinogens and Genotoxicity Assessment
- Keywords
- nucleotide excision repair, DNA damage recognition, helix distortion, cyclobutane pyrimidine dimers
- MeSH terms
- Deoxyribonuclease I, DNA Damage, DNA Repair, DNA-Binding Proteins, Humans, Models, Biological, Nucleic Acid Conformation, Plasmids, Protein Binding, Pyrimidine Dimers, Tumor Cells, Cultured, Genome, Human, DNA Footprinting, Base Pair Mismatch
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