Nucleotide Excision Repair: a Versatile and Smart Toolkit

Overview

Journal Acta Biochim Biophys Sin (Shanghai)

Specialties Biochemistry
Biophysics

Date 2022 Aug 17

PMID 35975604

Authors

Xiping Zhang

Mengdie Yin

Jinchuan Hu

Affiliations

Soon will be listed here.

Abstract

Nucleotide excision repair (NER) is a major pathway to deal with bulky adducts induced by various environmental toxins in all cellular organisms. The two sub-pathways of NER, global genome repair (GGR) and transcription-coupled repair (TCR), differ in the damage recognition modes. In this review, we describe the molecular mechanism of NER in mammalian cells, especially the details of damage recognition steps in both sub-pathways. We also introduce new sequencing methods for genome-wide mapping of NER, as well as recent advances about NER in chromatin by these methods. Finally, the roles of NER factors in repairing oxidative damages and resolving R-loops are discussed.

Citing Articles

Proteins Associated with Neurodegenerative Diseases: Link to DNA Repair.

Khodyreva S, Dyrkheeva N, Lavrik O Biomedicines. 2025; 12(12.

PMID: 39767715 PMC: 11673744. DOI: 10.3390/biomedicines12122808.

Whole Genome Sequencing Analysis of Model Organisms Elucidates the Association Between Environmental Factors and Human Cancer Development.

Hasegawa S, Shoji Y, Kato M, Elzawahry A, Nagai M, Gi M Int J Mol Sci. 2024; 25(20).

PMID: 39456974 PMC: 11508241. DOI: 10.3390/ijms252011191.

STK19 is a transcription-coupled repair factor that participates in UVSSA ubiquitination and TFIIH loading.

Tan Y, Gao M, Huang Y, Zhan D, Wu S, An J Nucleic Acids Res. 2024; 52(21):12767-12783.

PMID: 39353615 PMC: 11602130. DOI: 10.1093/nar/gkae787.

Nucleotide excision repair of aflatoxin-induced DNA damage within the 3D human genome organization.

Wu Y, Adeel M, Xia D, Sancar A, Li W Nucleic Acids Res. 2024; 52(19):11704-11719.

PMID: 39258558 PMC: 11514448. DOI: 10.1093/nar/gkae755.

Gene architecture is a determinant of the transcriptional response to bulky DNA damages.

Merav M, Bitensky E, Heilbrun E, Hacohen T, Kirshenbaum A, Golan-Berman H Life Sci Alliance. 2024; 7(3).

PMID: 38167611 PMC: 10761554. DOI: 10.26508/lsa.202302328.

References

HANAWALT P . DNA repair. The bases for Cockayne syndrome. Nature. 2000; 405(6785):415-6. DOI: 10.1038/35013197. View

Kemp M . Damage removal and gap filling in nucleotide excision repair. Enzymes. 2019; 45:59-97. DOI: 10.1016/bs.enz.2019.06.001. View

Edenberg H, Hanawalt P . Size of repair patches in the DNA of ultraviolet-irradiated HeLa cells. Biochim Biophys Acta. 1972; 272(3):361-72. DOI: 10.1016/0005-2787(72)90389-9. View

Nakazawa Y, Sasaki K, Mitsutake N, Matsuse M, Shimada M, Nardo T . Mutations in UVSSA cause UV-sensitive syndrome and impair RNA polymerase IIo processing in transcription-coupled nucleotide-excision repair. Nat Genet. 2012; 44(5):586-92. DOI: 10.1038/ng.2229. View

Selby C, Sancar A . Human transcription-repair coupling factor CSB/ERCC6 is a DNA-stimulated ATPase but is not a helicase and does not disrupt the ternary transcription complex of stalled RNA polymerase II. J Biol Chem. 1997; 272(3):1885-90. DOI: 10.1074/jbc.272.3.1885. View

Geijer M, Marteijn J . What happens at the lesion does not stay at the lesion: Transcription-coupled nucleotide excision repair and the effects of DNA damage on transcription in cis and trans. DNA Repair (Amst). 2018; 71:56-68. DOI: 10.1016/j.dnarep.2018.08.007. View

Mellon I, Spivak G, HANAWALT P . Selective removal of transcription-blocking DNA damage from the transcribed strand of the mammalian DHFR gene. Cell. 1987; 51(2):241-9. DOI: 10.1016/0092-8674(87)90151-6. View

Elia A, Boardman A, Wang D, Huttlin E, Everley R, Dephoure N . Quantitative Proteomic Atlas of Ubiquitination and Acetylation in the DNA Damage Response. Mol Cell. 2015; 59(5):867-81. PMC: 4560960. DOI: 10.1016/j.molcel.2015.05.006. View

Hu J, Lieb J, Sancar A, Adar S . Cisplatin DNA damage and repair maps of the human genome at single-nucleotide resolution. Proc Natl Acad Sci U S A. 2016; 113(41):11507-11512. PMC: 5068337. DOI: 10.1073/pnas.1614430113. View

10.

Nakazawa Y, Hara Y, Oka Y, Komine O, van den Heuvel D, Guo C . Ubiquitination of DNA Damage-Stalled RNAPII Promotes Transcription-Coupled Repair. Cell. 2020; 180(6):1228-1244.e24. DOI: 10.1016/j.cell.2020.02.010. View

11.

Reardon J, NICHOLS A, Keeney S, Smith C, Taylor J, Linn S . Comparative analysis of binding of human damaged DNA-binding protein (XPE) and Escherichia coli damage recognition protein (UvrA) to the major ultraviolet photoproducts: T[c,s]T, T[t,s]T, T[6-4]T, and T[Dewar]T. J Biol Chem. 1993; 268(28):21301-8. View

12.

Coin F, Bergmann E, Tremeau-Bravard A, Egly J . Mutations in XPB and XPD helicases found in xeroderma pigmentosum patients impair the transcription function of TFIIH. EMBO J. 1999; 18(5):1357-66. PMC: 1171225. DOI: 10.1093/emboj/18.5.1357. View

13.

Volker M, Mone M, Karmakar P, van Hoffen A, Schul W, Vermeulen W . Sequential assembly of the nucleotide excision repair factors in vivo. Mol Cell. 2001; 8(1):213-24. DOI: 10.1016/s1097-2765(01)00281-7. View

14.

McKibbin P, Fleming A, Towheed M, Van Houten B, Burrows C, David S . Repair of hydantoin lesions and their amine adducts in DNA by base and nucleotide excision repair. J Am Chem Soc. 2013; 135(37):13851-61. PMC: 3906845. DOI: 10.1021/ja4059469. View

15.

Gorini F, Scala G, Cooke M, Majello B, Amente S . Towards a comprehensive view of 8-oxo-7,8-dihydro-2'-deoxyguanosine: Highlighting the intertwined roles of DNA damage and epigenetics in genomic instability. DNA Repair (Amst). 2020; 97:103027. PMC: 7926032. DOI: 10.1016/j.dnarep.2020.103027. View

16.

Mao P, Wyrick J, Roberts S, Smerdon M . UV-Induced DNA Damage and Mutagenesis in Chromatin. Photochem Photobiol. 2016; 93(1):216-228. PMC: 5315636. DOI: 10.1111/php.12646. View

17.

Pavri R . R Loops in the Regulation of Antibody Gene Diversification. Genes (Basel). 2017; 8(6). PMC: 5485518. DOI: 10.3390/genes8060154. View

18.

Marteijn J, Lans H, Vermeulen W, Hoeijmakers J . Understanding nucleotide excision repair and its roles in cancer and ageing. Nat Rev Mol Cell Biol. 2014; 15(7):465-81. DOI: 10.1038/nrm3822. View

19.

De Bont R, Van Larebeke N . Endogenous DNA damage in humans: a review of quantitative data. Mutagenesis. 2004; 19(3):169-85. DOI: 10.1093/mutage/geh025. View

20.

RUPERT C . Photoreactivation of transforming DNA by an enzyme from bakers' yeast. J Gen Physiol. 1960; 43:573-95. PMC: 2195007. DOI: 10.1085/jgp.43.3.573. View