The DOI matches its Crossref record; 61 of the 62 references it cites were found in a registry or an index.
Subpathways of nucleotide excision repair and their regulation
Abstract
Nucleotide excision repair provides an important cellular defense against a large variety of structurally unrelated DNA alterations. Most of these alterations, if unrepaired, may contribute to mutagenesis, oncogenesis, and developmental abnormalities, as well as cellular lethality. There are two subpathways of nucleotide excision repair; global genomic repair (GGR) and transcription coupled repair (TCR), that is selective for the transcribed DNA strand in expressed genes. Some of the proteins involved in the recognition of DNA damage (including RNA polymerase) are also responsive to natural variations in the secondary structural features of DNA. Gratuitous repair events in undamaged DNA might then contribute to genomic instability. However, damage recognition enzymes for GGR are normally maintained at very low levels unless the cells are genomically stressed. GGR is controlled through the SOS stress response in E. coli and through the activated p53 tumor suppressor in human cells. These inducible responses in human cells are important, as they have been shown to operate upon chemical carcinogen DNA damage at levels to which humans are environmentally exposed. Interestingly, most rodent tissues are deficient in the p53-dependent GGR pathway. Since rodents are used as surrogates for environmental cancer risk assessment, it is essential that we understand how they differ from humans with respect to DNA repair and oncogenic responses to environmental genotoxins. In the case of terminally differentiated mammalian cells, a new paradigm has appeared in which GGR is attenuated but both strands of expressed genes are repaired efficiently.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“One sub-pathway of NER, global genome NER (GG-NER), removes damage from the entire genome, whereas DNA damage in the transcribed strand of active genes is preferentially eliminated by transcription-coupled NER (TC-NER) [3].”
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 [3]
In the citing paper
“The NER pathway is subdivided into global genome repair (GG-NER) and transcription-coupled repair (TC-NER) [4].”
From Gap-filling and bypass at the replication fork are both active mechanisms for tolerance of low-dose ultraviolet-induced DNA damage in the human genome (2014) · cites this paper as [4]
Citations
Cites
Lindahl, T. L., & Wood, R. D. (1999) · Science · doi:10.1126/science.286.5446.1897 · Cited by 1,521
Bohr, V (1985) · Cell · doi:10.1016/0092-8674(85)90150-3 · Cited by 1,237 · cited 2×
“The analysis of the repair of UV-induced cyclobutane pyrimidine dimers (CPDs) in transcriptionally active versus inactive regions of the genome, and within transcribed and non-transcribed strands of expressed genes revealed the two distinct subpathways of nucleotide excision repair: TCR and GGR (Bohr et al., 1985; Mel…”
BackgroundMELLON, I. (1987) · Cell · doi:10.1016/0092-8674(87)90151-6 · Cited by 1,228
Sancar, A. (1996) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.65.070196.000355 · Cited by 1,131
Sugasawa, K., Ng, J. M. Y., Masutani, C., Iwai, S., van der Spek, P. J., Eker, A. P. M., Hanaoka, F., Bootsma, D., & Hoeijmakers, J. H. J. (1998) · Molecular Cell · doi:10.1016/s1097-2765(00)80132-x · Cited by 899
Courcelle, J., Khodursky, A., Peter, B., Brown, P. O., & Hanawalt, P. C. (2001) · Genetics · doi:10.1093/genetics/158.1.41 · Cited by 853
Self-citationMolecular Mechanisms for Repair of DNA
Hanawalt, P. C., & Setlow, R. B. (1975) · Springer eBooks · doi:10.1007/978-1-4684-2895-7 · Cited by 671
Self-citationMolecular Mechanism of Transcription-Repair Coupling
Selby, C. P., & Sancar, A. (1993) · Science · doi:10.1126/science.8465200 · Cited by 656
Hwang, B. J., Ford, J. M., Hanawalt, P. C., & Chu, G. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.2.424 · Cited by 581
Self-citationMellon, I., & Hanawalt, P. C. (1989) · Nature · doi:10.1038/342095a0 · Cited by 573
Self-citationEvidence for repair-replication of ultraviolet damaged DNA in bacteria
Pettijohn, D., & Hanawalt, P. (1964) · Journal of Molecular Biology · doi:10.1016/s0022-2836(64)80216-3 · Cited by 515
Self-citationTranscription-Coupled Repair and Human Disease
Hanawalt, P. C. (1994) · Science · doi:10.1126/science.7801121 · Cited by 494
Self-citationA phylogenomic study of DNA repair genes, proteins, and processes
Eisen, J. A., & Hanawalt, P. C. (1999) · Mutation Research/DNA Repair · doi:10.1016/s0921-8777(99)00050-6 · Cited by 469
Self-citationSmith, M. L., Ford, J. M., Hollander, M. C., Bortnick, R. A., Amundson, S. A., Seo, Y. R., Deng, C., Hanawalt, P. C., & Fornace, A. J. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.10.3705-3714.2000 · Cited by 438
Self-citationFord, J. M., & Hanawalt, P. C. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.44.28073 · Cited by 357
Self-citationFord, J. M., & Hanawalt, P. C. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.19.8876 · Cited by 343
Self-citationXeroderma Pigmentosum p48 Gene Enhances Global Genomic Repair and Suppresses UV-Induced Mutagenesis
Tang, J. Y., Hwang, B. J., Ford, J. M., Hanawalt, P. C., & Chu, G. (2000) · Molecular Cell · doi:10.1016/s1097-2765(00)80252-x · Cited by 341
Self-citationp53 and DNA damage-inducible expression of the xeroderma pigmentosum group C gene
Adimoolam, S., & Ford, J. M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202485699 · Cited by 321
Human biomonitoring and the 32P-postlabeling assay
Beach, A. C., & Gupta, R. C. (1992) · Carcinogenesis · doi:10.1093/carcin/13.7.1053 · Cited by 299
Birrell, G. W., Brown, J. A. L., Wu, H. I., Giaever, G. N., Chu, A. M., Davis, R. W., & Brown, J. M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.132275199 · Cited by 255
Repair Replication, Unscheduled DNA Synthesis, and the Repair of Mammalian DNA
Painter, R. B., & Cleaver, J. E. (1969) · Radiation Research · doi:10.2307/3572686 · Cited by 242
Nucleotide excision repair: From E. coli to man
Petit, C. R., & Sancar, A. (1999) · Biochimie · doi:10.1016/s0300-9084(99)80034-0 · Cited by 237
DNA repair in terminally differentiated cells
Nouspikel, T. (2002) · DNA repair · doi:10.1016/s1568-7864(01)00005-2 · Cited by 228
Wakasugi, M., Kawashima, A., Morioka, H., Linn, S., Sancar, A., Mori, T., Nikaido, O., & Matsunaga, T. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.c100610200 · Cited by 227
Leadon, S. A., & Cooper, P. K. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.22.10499 · Cited by 215
Batty, D. P., Rapić-Otrin, V., Levine, A. S., & Wood, R. D. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3857 · Cited by 211
Xeroderma pigmentosum complementation group E and UV-damaged DNA-binding protein
Tang, J. Y., & Chu, G. (2002) · DNA repair · doi:10.1016/s1568-7864(02)00052-6 · Cited by 208
Nouspikel, T., & Hanawalt, P. C. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.5.1562-1570.2000 · Cited by 194
Self-citationThe Induction of Thymine Dimers in Ultraviolet-Irradiated Mammalian Cells
Trosko, J. E., Chu, E. H. Y., & Carrier, W. L. (1965) · Radiation Research · doi:10.2307/3571885 · Cited by 168
Hwang, B. J., Peters, S. T., Francke, U., & Chu, G. (1998) · Molecular and Cellular Biology · doi:10.1128/mcb.18.7.4391 · Cited by 157
van Zeeland, A. A., Smith, C. A., & Hanawalt, P. C. (1981) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/0027-5107(81)90148-2 · Cited by 124
Self-citationFord, J. M., Baron, E. L., & Hanawalt, P. C. (1998) · PubMed · Cited by 122
Self-citationDNA Repair Excision Nuclease Attacks Undamaged DNA
Branum, M. E., Reardon, J. T., & Sancar, A. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m101032200 · Cited by 103
Strand opening by the UvrA2B complex allows dynamic recognition of DNA damage
Zou, Y., & Houten, B. V. (1999) · The EMBO Journal · doi:10.1093/emboj/18.17.4889 · Cited by 98
Crowley, D. J., & Hanawalt, P. C. (1998) · Journal of Bacteriology · doi:10.1128/jb.180.13.3345-3352.1998 · Cited by 96
Self-citationChanging capacity for DNA excision repair in mouse embryonic cells in vitro
Peleg, L., Raz, E., & Ben-Ishai, R. (1977) · Experimental Cell Research · doi:10.1016/0014-4827(77)90095-7 · Cited by 96
Therrien, J., Drouin, R., Baril, C., & Drobetsky, E. A. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.26.15038 · Cited by 92
Dunkern, T. R., & Kaina, B. (2002) · Molecular Biology of the Cell · doi:10.1091/mbc.01-05-0225 · Cited by 90
Nonconservative DNA replication in bacteria after thymine starvation.
Pauling, C. W., & Hanawalt, P. C. (1965) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.54.6.1728 · Cited by 83
Self-citationRevisiting the rodent repairadox
Hanawalt, P. C. (2001) · Environmental and Molecular Mutagenesis · doi:10.1002/em.1057 · Cited by 82
Self-citationCho, a second endonuclease involved in Escherichia coli nucleotide excision repair
Moolenaar, G. F., van Rossum-Fikkert, S. E., van Kesteren, M., & Goosen, N. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.032584099 · Cited by 81
Hepatitis B x Protein Inhibits p53-dependent DNA Repair in Primary Mouse Hepatocytes
Prost, S., Ford, J. M., Taylor, C., Doig, J., & Harrison, D. J. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.50.33327 · Cited by 77
Plosky, B. S., Samson, L. D., Engelward, B. P., Gold, B. I., Schlaen, B., Millas, T., Magnotti, M., Schor, J., & Scicchitano, D. A. (2002) · DNA repair · doi:10.1016/s1568-7864(02)00075-7 · Cited by 75
Wani, M. A., Zhu, Q., El-Mahdy, M. A., Venkatachalam, S., & Wani, A. A. (2000) · PubMed · Cited by 63
Spivak, G., Itoh, T., Matsunaga, T., Nikaido, O., Hanawalt, P. C., & Yamaizumi, M. (2002) · DNA repair · doi:10.1016/s1568-7864(02)00056-3 · Cited by 59
Self-citationMcKay, B. C., & Ljungman, M. E. (1999) · Neoplasia · doi:10.1038/sj.neo.7900028 · Cited by 56
Bowman, K. K., Sicard, D., Ford, J. M., & Hanawalt, P. C. (2000) · Molecular Carcinogenesis · doi:10.1002/1098-2744(200009)29:1 · Cited by 56
Self-citationKinetics of ultraviolet induced DNA excision repair in rat and human fibroblasts
Vijg, J., Mullaart, E., van der Schans, G. P., Lohman, P. H. M., & Knook, D. L. (1984) · Mutation Research/DNA Repair Reports · doi:10.1016/0167-8817(84)90007-5 · Cited by 55
Karlsson, N. G., Johansson, M., Asker, N., Karlsson, H., Gendler, S. J., Carlstedt, I., & Hansson, G. C. (1996) · Glycoconjugate Journal · doi:10.1007/bf00702346 · Cited by 52
Hierarchy of DNA Damage Recognition in Escherichia coli Nucleotide Excision Repair
Zou, Y., Luo, C., & Geacintov, N. E. (2001) · Biochemistry · doi:10.1021/bi001504c · Cited by 45
A cut above: Discovery of an alternative excision repair pathway in bacteria
Van Houten, B., Eisen, J. A., & Hanawalt, P. C. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.062062599 · Cited by 44
Self-citationDNA repair replication in temperature-sensitive DNA synthesis deficient bacteria
Couch, J. L., & Hanawalt, P. C. (1967) · Biochemical and Biophysical Research Communications · doi:10.1016/0006-291x(67)90287-2 · Cited by 38
Self-citationRepair Replication of DNA in vivoPreprint
Hanawalt, P. C., Pettijohn, D. E., Pauling, E. C., Brunk, C. F., Smith, D. W., Kanner, L. C., & Couch, J. L. (1968) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.1968.033.01.022 · Cited by 37
Self-citationTurnover in bacterial DNA containing thymine or 5-bromouracil
Grivell, A. R., Grivell, M. B., & Hanawalt, P. C. (1975) · Journal of Molecular Biology · doi:10.1016/s0022-2836(75)80110-0 · Cited by 32
Self-citationBen-Ishai, R., & Peleg, L. (1975) · Springer eBooks · doi:10.1007/978-1-4684-2898-8_29 · Cited by 30
Crowley, D. J., & Hanawalt, P. C. (2001) · Mutation Research/DNA Repair · doi:10.1016/s0921-8777(01)00068-4 · Cited by 29
Self-citationDifferences in Pyrimidine Dimer Removal between Rat Skin Cells In Vitro and In Vivo
Mullaart, E., Lohman, P. H. M., & Vijg, J. (1988) · Journal of Investigative Dermatology · doi:10.1111/1523-1747.ep12456316 · Cited by 28
Regulation of Nucleotide Excision Repair in Bacteria and Mammalian CellsPreprint
Hanawalt, P. C., Crowley, D. J., Ford, J. M., Ganesan, A. K., Lloyd, D. R., Nouspikel, T., Smith, C. A., Spivak, G., & Tornaletti, S. (2000) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2000.65.183 · Cited by 18
Self-citationTURING MACHINE APPROACH TO SOLVE PSYCHROMETRIC ATTRIBUTES
Zhang, H., Gates, R. S., & Colliver, D. G. (1997) · Transactions of the ASAE · doi:10.13031/2013.21292 · Cited by 14
The Ion-exchange Capacity of Ti and Zr Lamellar Hydrogenphosphates. TG measurements
de Farias, R. F., Nunes, L. M., & Airoldi, C. (2000) · Journal of Thermal Analysis and Calorimetry · doi:10.1023/a:1010186719282 · Cited by 9
Obstetric Outcome in Homeless Women
PATERSON, C. M., & Roderick, P. (1991) · Obstetrical & Gynecological Survey · doi:10.1097/00006254-199103000-00004 · Cited by 1
Flagged first, then by citations
1 of the 62 references couldn’t be matched to a known paper.
Research works printed but not linked: 3
- Ganesan AK, Spivak G, Hanawalt PC . 1983 Manipulation and Expression of Genes in Eukaryotes Nagley P, Linnane AW, Peacock WJ, Pateman JA (eds) Australia: Academic Press pp. 45–54
- Hanawalt PC, Bohr VA, Leadon SA, Mansbridge JN, Reush MKH . 1987 Processes in Cutaneous Epidermal Differentiation Bernstein I and Hirone T (eds) New York: Praeger Scientific pp. 217–231
- Nouspikel T, Hanawalt PC . 2003 Bioessays (in press)
Cited by
Sorted by citations
Cellular processing of platinum anticancer drugs
Wang, D., & Lippard, S. J. (2005) · Nature Reviews Drug Discovery · doi:10.1038/nrd1691 · Cited by 3,801
Molecular Mechanisms of Mammalian DNA Repair and the DNA Damage Checkpoints
Sancar, A., Lindsey-Boltz, L. A., Ünsal-Kaçmaz, K., & Linn, S. (2004) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.73.011303.073723 · Cited by 3,317
Hoeijmakers, J. H. J. (2009) · New England Journal of Medicine · doi:10.1056/nejmra0804615 · Cited by 2,239
Transcription-coupled DNA repair: two decades of progress and surprises
Hanawalt, P. C., & Spivak, G. (2008) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2549 · Cited by 1,081
Self-citationBalancing repair and tolerance of DNA damage caused by alkylating agents
Fu, D., Calvo, J. A., & Samson, L. D. (2012) · Nature reviews. Cancer · doi:10.1038/nrc3185 · Cited by 977
Metadata
- Authors
- Hanawalt, P. C.
- Affiliations
- Stanford University (US)
- Corresponding author
- Hanawalt, Philip C
- ORCID
- Hanawalt, Philip C
- Venue
- Oncogene
- Published
- 2002-12-16
- Volume
- 21
- Issue
- 58
- Pages
- 8949-8956
- ISSN
- 0950-9232 (ISSN-L)
- 1476-5594
- OpenAlex
- W1979123830
- Cited by
- 447
- References
- 62
- Citations by year
- 2026: 2 · 2025: 1 · 2024: 7 · 2023: 4 · 2022: 6 · 2021: 12 · 2020: 11 · 2019: 11 · 2018: 9 · 2017: 11 · 2016: 14 · 2015: 20 · 2014: 20 · 2013: 24 · 2012: 24
- FWCI
- 1.74
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Oncogene (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Cancer Institute (CA91456, R01CA077712, CA90915, R01CA090915, CA-44349, R35CA044349, CA-77712, R01CA091456)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Carcinogens and Genotoxicity Assessment
- Health Sciences › Medicine › Pathology and Forensic Medicine › Genetic factors in colorectal cancer
- Keywords
- nucleotide excision repair, transcription-coupled repair, DNA damage recognition, RNA polymerase, genomic instability, SOS response, p53, cancer risk assessment, terminally differentiated cells, mutagenesis
- MeSH terms
- Animals, Cell Differentiation, DNA Damage, DNA Repair, Escherichia coli, Humans, Neurons, Oncogenic Viruses, Species Specificity, Gene Expression Regulation, Bacterial, Tumor Suppressor Protein p53
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
