Molecular basis for damage recognition and verification by XPC-RAD23B and TFIIH in nucleotide excision repair

Mu, Hong; Geacintov, Nicholas E.; Broyde, Suse; Yeo, Jung-Eun; Schärer, Orlando D.

doi:10.1016/j.dnarep.2018.08.005

Molecular basis for damage recognition and verification by XPC-RAD23B and TFIIH in nucleotide excision repair

Journal Article · Thu Aug 23 04:00:00 EDT 2018 · DNA Repair

DOI:https://doi.org/10.1016/j.dnarep.2018.08.005· OSTI ID:1543540

Mu, Hong ^[1]; Geacintov, Nicholas E. ^[1]; Broyde, Suse ^[1]; Yeo, Jung-Eun ^[2]; Schärer, Orlando D. ^[3]

New York Univ. (NYU), NY (United States)
Inst. for Basic Science, Ulsan (Korea, Republic of)
Inst. for Basic Science, Ulsan (Korea, Republic of); Ulsan National Institute of Science and Technology, Ulsan (Korea, Republic of)

Global genome nucleotide excision repair (GG-NER) is the main pathway for the removal of bulky lesions from DNA and is characterized by an extraordinarily wide substrate specificity. Remarkably, the efficiency of lesion removal varies dramatically and certain lesions escape repair altogether and are therefore associated with high levels of mutagenicity. Central to the multistep mechanism of damage recognition in NER is the sensing of lesion-induced thermodynamic and structural alterations of DNA by the XPC-RAD23B protein and the verification of the damage by the transcription/repair factor TFIIH. Additional factors contribute to the process: UV-DDB, for the recognition of certain UV-induced lesions in particular in the context of chromatin, while the XPA protein is believed to have a role in damage verification and NER complex assembly. In this paper, we consider the molecular mechanisms that determine repair efficiency in GG-NER based on recent structural, computational, biochemical, cellular and single molecule studies of XPC-RAD23B and its yeast ortholog Rad4. We discuss how the actions of XPC-RAD23B are integrated with those of other NER proteins and, based on recent high-resolution structures of TFIIH, present a structural model of how XPC-RAD23B and TFIIH cooperate in damage recognition and verification.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

Sponsoring Organization:: USDOE; National Cancer Institute (NCI); National Institutes of Health (NIH); National Science Foundation (NSF); Institute for Basic Science, Daejeon (South Korea)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1543540

Journal Information:: DNA Repair, Journal Name: DNA Repair Journal Issue: C Vol. 71; ISSN 1568-7864

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (114)

Thermodynamic and structural factors in the removal of bulky DNA adducts by the nucleotide excision repair machinery Geacintov, Nicholas E.; Broyde, Suse; Buterin, Tonko Biopolymers, Vol. 65, Issue 3 https://doi.org/10.1002/bip.10239	journal	September 2002
The Amber biomolecular simulation programs Case, David A.; Cheatham, Thomas E.; Darden, Tom Journal of Computational Chemistry, Vol. 26, Issue 16 https://doi.org/10.1002/jcc.20290	journal	January 2005
Stable binding of human XPC complex to irradiated DNA confers strong discrimination for damaged sites 1 1Edited by M. Yaniv Batty, Dawn; Rapic’-Otrin, Vesna; Levine, Arthur S. Journal of Molecular Biology, Vol. 300, Issue 2 https://doi.org/10.1006/jmbi.2000.3857	journal	July 2000
Orchestral maneuvers at the damaged sites in nucleotide excision repair Alekseev, Sergey; Coin, Frédéric Cellular and Molecular Life Sciences, Vol. 72, Issue 11 https://doi.org/10.1007/s00018-015-1859-5	journal	February 2015
Xeroderma pigmentosum group C sensor: unprecedented recognition strategy and tight spatiotemporal regulation Puumalainen, Marjo-Riitta; Rüthemann, Peter; Min, Jun-Hyun Cellular and Molecular Life Sciences, Vol. 73, Issue 3 https://doi.org/10.1007/s00018-015-2075-z	journal	October 2015
Mammalian DNA nucleotide excision repair reconstituted with purified protein components Aboussekhra, Abdelilah; Biggerstaff, Maureen; Shivji, Mahmud K. K. Cell, Vol. 80, Issue 6 https://doi.org/10.1016/0092-8674(95)90289-9	journal	March 1995
The DNA helicase and adenosine triphosphatase activities of yeast Rad3 protein are inhibited by DNA damage. A potential mechanism for damage-specific recognition. Naegeli, H.; Bardwell, L.; Friedberg, E. C. Journal of Biological Chemistry, Vol. 267, Issue 1 https://doi.org/10.1016/S0021-9258(18)48507-9	journal	January 1992
Xeroderma Pigmentosum Group F Caused by a Defect in a Structure-Specific DNA Repair Endonuclease Sijbers, Anneke M.; de Laat, Wouter L.; Ariza, Rafael R. Cell, Vol. 86, Issue 5 https://doi.org/10.1016/S0092-8674(00)80155-5	journal	September 1996
The Ubiquitin Ligase Activity in the DDB2 and CSA Complexes Is Differentially Regulated by the COP9 Signalosome in Response to DNA Damage Groisman, Regina; Polanowska, Jolanta; Kuraoka, Isao Cell, Vol. 113, Issue 3 https://doi.org/10.1016/S0092-8674(03)00316-7	journal	May 2003
Xeroderma Pigmentosum Group C Protein Complex Is the Initiator of Global Genome Nucleotide Excision Repair Sugasawa, Kaoru; Ng, Jessica M. Y.; Masutani, Chikahide Molecular Cell, Vol. 2, Issue 2 https://doi.org/10.1016/S1097-2765(00)80132-X	journal	August 1998
Xeroderma Pigmentosum p48 Gene Enhances Global Genomic Repair and Suppresses UV-Induced Mutagenesis Tang, Jean Y.; Hwang, Byung Joon; Ford, James M. Molecular Cell, Vol. 5, Issue 4 https://doi.org/10.1016/S1097-2765(00)80252-X	journal	April 2000
Sequential Assembly of the Nucleotide Excision Repair Factors In Vivo Volker, Marcel; Moné, Martijn J.; Karmakar, Parimal Molecular Cell, Vol. 8, Issue 1 https://doi.org/10.1016/S1097-2765(01)00281-7	journal	July 2001
The carboxy-terminal domain of the XPC protein plays a crucial role in nucleotide excision repair through interactions with transcription factor IIH Uchida, Akio; Sugasawa, Kaoru; Masutani, Chikahide DNA Repair, Vol. 1, Issue 6 https://doi.org/10.1016/S1568-7864(02)00031-9	journal	June 2002
UV-Induced Ubiquitylation of XPC Protein Mediated by UV-DDB-Ubiquitin Ligase Complex Sugasawa, Kaoru; Okuda, Yuki; Saijo, Masafumi Cell, Vol. 121, Issue 3 https://doi.org/10.1016/j.cell.2005.02.035	journal	May 2005
Structure of the DNA Repair Helicase XPD Liu, Huanting; Rudolf, Jana; Johnson, Kenneth A. Cell, Vol. 133, Issue 5 https://doi.org/10.1016/j.cell.2008.04.029	journal	May 2008
XPD Helicase Structures and Activities: Insights into the Cancer and Aging Phenotypes from XPD Mutations Fan, Li; Fuss, Jill O.; Cheng, Quen J. Cell, Vol. 133, Issue 5 https://doi.org/10.1016/j.cell.2008.04.030	journal	May 2008
Structural Basis of UV DNA-Damage Recognition by the DDB1–DDB2 Complex Scrima, Andrea; Koníčková, Renata; Czyzewski, Bryan K. Cell, Vol. 135, Issue 7 https://doi.org/10.1016/j.cell.2008.10.045	journal	December 2008
The Molecular Basis of CRL4DDB2/CSA Ubiquitin Ligase Architecture, Targeting, and Activation Fischer, Eric S.; Scrima, Andrea; Böhm, Kerstin Cell, Vol. 147, Issue 5 https://doi.org/10.1016/j.cell.2011.10.035	journal	November 2011
DNA Quality Control by Conformational Readout on the Undamaged Strand of the Double Helix Buterin, Tonko; Meyer, Christoph; Giese, Bernd Chemistry & Biology, Vol. 12, Issue 8 https://doi.org/10.1016/j.chembiol.2005.06.011	journal	August 2005
DNA Quality Control by a Lesion Sensor Pocket of the Xeroderma Pigmentosum Group D Helicase Subunit of TFIIH Mathieu, Nadine; Kaczmarek, Nina; Rüthemann, Peter Current Biology, Vol. 23, Issue 3 https://doi.org/10.1016/j.cub.2012.12.032	journal	February 2013
Probing for DNA damage with β-hairpins: Similarities in incision efficiencies of bulky DNA adducts by prokaryotic and human nucleotide excision repair systems in vitro Liu, Yang; Reeves, Dara; Kropachev, Konstantin DNA Repair, Vol. 10, Issue 7 https://doi.org/10.1016/j.dnarep.2011.04.020	journal	July 2011
The relationships between XPC binding to conformationally diverse DNA adducts and their excision by the human NER system: Is there a correlation? Lee, Yuan-Cho; Cai, Yuqin; Mu, Hong DNA Repair, Vol. 19 https://doi.org/10.1016/j.dnarep.2014.03.026	journal	July 2014
XPC: Going where no DNA damage sensor has gone before Nemzow, Leah; Lubin, Abigail; Zhang, Ling DNA Repair, Vol. 36 https://doi.org/10.1016/j.dnarep.2015.09.004	journal	December 2015
Chromatin dynamics after DNA damage: The legacy of the access–repair–restore model Polo, Sophie E.; Almouzni, Geneviève DNA Repair, Vol. 36 https://doi.org/10.1016/j.dnarep.2015.09.014	journal	December 2015
Molecular mechanisms of DNA damage recognition for mammalian nucleotide excision repair Sugasawa, Kaoru DNA Repair, Vol. 44 https://doi.org/10.1016/j.dnarep.2016.05.015	journal	August 2016
XPA: A key scaffold for human nucleotide excision repair Sugitani, Norie; Sivley, Robert M.; Perry, Kelly E. DNA Repair, Vol. 44 https://doi.org/10.1016/j.dnarep.2016.05.018	journal	August 2016
Structural basis of DNA lesion recognition for eukaryotic transcription-coupled nucleotide excision repair Wang, Wei; Xu, Jun; Chong, Jenny DNA Repair, Vol. 71 https://doi.org/10.1016/j.dnarep.2018.08.006	journal	November 2018
The Sequence Dependence of Human Nucleotide Excision Repair Efficiencies of Benzo[a]pyrene-derived DNA Lesions: Insights into the Structural Factors that Favor Dual Incisions Kropachev, Konstantin; Kolbanovskii, Marina; Cai, Yuqin Journal of Molecular Biology, Vol. 386, Issue 5 https://doi.org/10.1016/j.jmb.2008.12.082	journal	March 2009
XPG Stabilizes TFIIH, Allowing Transactivation of Nuclear Receptors: Implications for Cockayne Syndrome in XP-G/CS Patients Ito, Shinsuke; Kuraoka, Isao; Chymkowitch, Pierre Molecular Cell, Vol. 26, Issue 2 https://doi.org/10.1016/j.molcel.2007.03.013	journal	April 2007
Sealing of Chromosomal DNA Nicks during Nucleotide Excision Repair Requires XRCC1 and DNA Ligase IIIα in a Cell-Cycle-Specific Manner Moser, Jill; Kool, Hanneke; Giakzidis, Ioannis Molecular Cell, Vol. 27, Issue 2 https://doi.org/10.1016/j.molcel.2007.06.014	journal	July 2007
Nucleotide Excision Repair Driven by the Dissociation of CAK from TFIIH Coin, Frédéric; Oksenych, Valentyn; Mocquet, Vincent Molecular Cell, Vol. 31, Issue 1 https://doi.org/10.1016/j.molcel.2008.04.024	journal	July 2008
Two-Step Recognition of DNA Damage for Mammalian Nucleotide Excision Repair: Directional Binding of the XPC Complex and DNA Strand Scanning Sugasawa, Kaoru; Akagi, Jun-ichi; Nishi, Ryotaro Molecular Cell, Vol. 36, Issue 4 https://doi.org/10.1016/j.molcel.2009.09.035	journal	November 2009
Three DNA Polymerases, Recruited by Different Mechanisms, Carry Out NER Repair Synthesis in Human Cells Ogi, Tomoo; Limsirichaikul, Siripan; Overmeer, René M. Molecular Cell, Vol. 37, Issue 5 https://doi.org/10.1016/j.molcel.2010.02.009	journal	March 2010
Tripartite DNA Lesion Recognition and Verification by XPC, TFIIH, and XPA in Nucleotide Excision Repair Li, Chia-Lung; Golebiowski, Filip M.; Onishi, Yuki Molecular Cell, Vol. 59, Issue 6 https://doi.org/10.1016/j.molcel.2015.08.012	journal	September 2015
Single-Molecule Imaging Reveals that Rad4 Employs a Dynamic DNA Damage Recognition Process Kong, Muwen; Liu, Lili; Chen, Xuejing Molecular Cell, Vol. 64, Issue 2 https://doi.org/10.1016/j.molcel.2016.09.005	journal	October 2016
XPB: An unconventional SF2 DNA helicase Fan, Li; DuPrez, Kevin T. Progress in Biophysics and Molecular Biology, Vol. 117, Issue 2-3 https://doi.org/10.1016/j.pbiomolbio.2014.12.005	journal	March 2015
Structural Insight into the Mechanism of TFIIH Recognition by the Acidic String of the Nucleotide Excision Repair Factor XPC Okuda, Masahiko; Kinoshita, Minoru; Kakumu, Erina Structure, Vol. 23, Issue 10 https://doi.org/10.1016/j.str.2015.07.009	journal	October 2015
Recognition of Damaged DNA for Nucleotide Excision Repair: A Correlated Motion Mechanism with a Mismatched cis-syn Thymine Dimer Lesion Mu, Hong; Geacintov, Nicholas E.; Zhang, Yingkai Biochemistry, Vol. 54, Issue 34 https://doi.org/10.1021/acs.biochem.5b00840	journal	August 2015
Nucleotide Excision Repair Lesion-Recognition Protein Rad4 Captures a Pre-Flipped Partner Base in a Benzo[ a ]pyrene-Derived DNA Lesion: How Structure Impacts the Binding Pathway Mu, Hong; Geacintov, Nicholas E.; Min, Jung-Hyun Chemical Research in Toxicology, Vol. 30, Issue 6 https://doi.org/10.1021/acs.chemrestox.7b00074	journal	May 2017
Repair-Resistant DNA Lesions Geacintov, Nicholas E.; Broyde, Suse Chemical Research in Toxicology, Vol. 30, Issue 8 https://doi.org/10.1021/acs.chemrestox.7b00128	journal	July 2017
AlphaSpace: Fragment-Centric Topographical Mapping To Target Protein–Protein Interaction Interfaces Rooklin, David; Wang, Cheng; Katigbak, Joseph Journal of Chemical Information and Modeling, Vol. 55, Issue 8 https://doi.org/10.1021/acs.jcim.5b00103	journal	July 2015
Solution conformation of the (+)-cis-anti-[BP]dG adduct in a DNA duplex: Intercalation of the covalently attached benzo[a]pyrenyl ring into the helix and displacement of the modified deoxyguanosine Cosman, Monique; de los Santos, Carlos; Fiala, Radovan Biochemistry, Vol. 32, Issue 16 https://doi.org/10.1021/bi00067a001	journal	April 1993
Molecular Mechanisms of Mammalian Global Genome Nucleotide Excision Repair Gillet, Ludovic C. J.; Schärer, Orlando D. Chemical Reviews, Vol. 106, Issue 2 https://doi.org/10.1021/cr040483f	journal	February 2006
The Efficiencies of Damage Recognition and Excision Correlate with Duplex Destabilization Induced by Acetylaminofluorene Adducts in Human Nucleotide Excision Repair Yeo, Jung-Eun; Khoo, Andy; Fagbemi, Adebanke F. Chemical Research in Toxicology, Vol. 25, Issue 11 https://doi.org/10.1021/tx3003033	journal	August 2012
Adenine–DNA Adducts Derived from the Highly Tumorigenic Dibenzo[ a , l ]pyrene Are Resistant to Nucleotide Excision Repair while Guanine Adducts Are Not Kropachev, Konstantin; Kolbanovskiy, Marina; Liu, Zhi Chemical Research in Toxicology, Vol. 26, Issue 5 https://doi.org/10.1021/tx400080k	journal	April 2013
NMR Solution Structures of Stereoisomeric Covalent Polycyclic Aromatic Carcinogen−DNA Adducts: Principles, Patterns, and Diversity Geacintov, Nicholas E.; Cosman, Monique; Hingerty, Brian E. Chemical Research in Toxicology, Vol. 10, Issue 2 https://doi.org/10.1021/tx9601418	journal	February 1997
Two-stage dynamic DNA quality check by xeroderma pigmentosum group C protein Camenisch, Ulrike; Träutlein, Daniel; Clement, Flurina C. The EMBO Journal, Vol. 28, Issue 16 https://doi.org/10.1038/emboj.2009.187	journal	July 2009
Molecular insights into the recruitment of TFIIH to sites of DNA damage Oksenych, Valentyn; de Jesus, Bruno Bernardes; Zhovmer, Alexander The EMBO Journal, Vol. 28, Issue 19 https://doi.org/10.1038/emboj.2009.230	journal	August 2009
Coordination of dual incision and repair synthesis in human nucleotide excision repair Staresincic, Lidija; Fagbemi, Adebanke F.; Enzlin, Jacqueline H. The EMBO Journal, Vol. 28, Issue 8 https://doi.org/10.1038/emboj.2009.49	journal	March 2009
Functional and structural studies of the nucleotide excision repair helicase XPD suggest a polarity for DNA translocation: Crystal structure of an XPD-DNA complex Kuper, Jochen; Wolski, Stefanie C.; Michels, Gudrun The EMBO Journal, Vol. 31, Issue 2 https://doi.org/10.1038/emboj.2011.374	journal	November 2011
Regulation of translocation polarity by helicase domain 1 in SF2B helicases: HD1 regulates polarity in SF2B helicases Pugh, Robert A.; Wu, Colin G.; Spies, Maria The EMBO Journal, Vol. 31, Issue 2 https://doi.org/10.1038/emboj.2011.412	journal	November 2011
Recognition of DNA damage by the Rad4 nucleotide excision repair protein Min, Jung-Hyun; Pavletich, Nikola P. Nature, Vol. 449, Issue 7162 https://doi.org/10.1038/nature06155	journal	September 2007
The cryo-electron microscopy structure of human transcription factor IIH Greber, Basil J.; Nguyen, Thi Hoang Duong; Fang, Jie Nature, Vol. 549, Issue 7672 https://doi.org/10.1038/nature23903	journal	September 2017
Structures of transcription pre-initiation complex with TFIIH and Mediator Schilbach, S.; Hantsche, M.; Tegunov, D. Nature, Vol. 551, Issue 7679 https://doi.org/10.1038/nature24282	journal	November 2017
Chromatin retention of DNA damage sensors DDB2 and XPC through loss of p97 segregase causes genotoxicity Puumalainen, Marjo-Riitta; Lessel, Davor; Rüthemann, Peter Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms4695	journal	April 2014
Kinetic gating mechanism of DNA damage recognition by Rad4/XPC Chen, Xuejing; Velmurugu, Yogambigai; Zheng, Guanqun Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms6849	journal	January 2015
SUMO and ubiquitin-dependent XPC exchange drives nucleotide excision repair van Cuijk, Loes; van Belle, Gijsbert J.; Turkyilmaz, Yasemin Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms8499	journal	July 2015
Understanding nucleotide excision repair and its roles in cancer and ageing Marteijn, Jurgen A.; Lans, Hannes; Vermeulen, Wim Nature Reviews Molecular Cell Biology, Vol. 15, Issue 7 https://doi.org/10.1038/nrm3822	journal	June 2014
Recognition of helical kinks by xeroderma pigmentosum group A protein triggers DNA excision repair Camenisch, Ulrike; Dip, Ramiro; Schumacher, Sylvie Briand Nature Structural & Molecular Biology, Vol. 13, Issue 3 https://doi.org/10.1038/nsmb1061	journal	February 2006
ASH1L histone methyltransferase regulates the handoff between damage recognition factors in global-genome nucleotide excision repair Balbo Pogliano, Chiara; Gatti, Marco; Rüthemann, Peter Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-01080-8	journal	November 2017
The human DNA repair factor XPC-HR23B distinguishes stereoisomeric benzo[a]pyrenyl-DNA lesions Mocquet, Vincent; Kropachev, Konstantin; Kolbanovskiy, Marina The EMBO Journal, Vol. 26, Issue 12 https://doi.org/10.1038/sj.emboj.7601730	journal	May 2007
Structural basis for the recruitment of ERCC1-XPF to nucleotide excision repair complexes by XPA Tsodikov, Oleg V.; Ivanov, Dmitri; Orelli, Barbara The EMBO Journal, Vol. 26, Issue 22 https://doi.org/10.1038/sj.emboj.7601894	journal	October 2007
SUMOylation of xeroderma pigmentosum group C protein regulates DNA damage recognition during nucleotide excision repair Akita, Masaki; Tak, Yon-Soo; Shimura, Tsutomu Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep10984	journal	June 2015
Aristolochic acid and the etiology of endemic (Balkan) nephropathy Grollman, A. P.; Shibutani, S.; Moriya, M. Proceedings of the National Academy of Sciences, Vol. 104, Issue 29 https://doi.org/10.1073/pnas.0701248104	journal	July 2007
Strand- and site-specific DNA lesion demarcation by the xeroderma pigmentosum group D helicase Mathieu, Nadine; Kaczmarek, Nina; Naegeli, Hanspeter Proceedings of the National Academy of Sciences, Vol. 107, Issue 41 https://doi.org/10.1073/pnas.1004339107	journal	September 2010
Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair Yeh, J. I.; Levine, A. S.; Du, S. Proceedings of the National Academy of Sciences, Vol. 109, Issue 41 https://doi.org/10.1073/pnas.1110067109	journal	July 2012
Role of poly(ADP-ribose) polymerase-1 in the removal of UV-induced DNA lesions by nucleotide excision repair Robu, M.; Shah, R. G.; Petitclerc, N. Proceedings of the National Academy of Sciences, Vol. 110, Issue 5 https://doi.org/10.1073/pnas.1209507110	journal	January 2013
Twist-open mechanism of DNA damage recognition by the Rad4/XPC nucleotide excision repair complex Velmurugu, Yogambigai; Chen, Xuejing; Slogoff Sevilla, Phillip Proceedings of the National Academy of Sciences, Vol. 113, Issue 16 https://doi.org/10.1073/pnas.1514666113	journal	March 2016
Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis Adar, Sheera; Hu, Jinchuan; Lieb, Jason D. Proceedings of the National Academy of Sciences, Vol. 113, Issue 15 https://doi.org/10.1073/pnas.1603388113	journal	March 2016
Chromosomal landscape of UV damage formation and repair at single-nucleotide resolution Mao, Peng; Smerdon, Michael J.; Roberts, Steven A. Proceedings of the National Academy of Sciences, Vol. 113, Issue 32 https://doi.org/10.1073/pnas.1606667113	journal	July 2016
Dynamic maps of UV damage formation and repair for the human genome Hu, Jinchuan; Adebali, Ogun; Adar, Sheera Proceedings of the National Academy of Sciences, Vol. 114, Issue 26 https://doi.org/10.1073/pnas.1706522114	journal	June 2017
Poly(ADP-ribose) polymerase 1 escorts XPC to UV-induced DNA lesions during nucleotide excision repair Robu, Mihaela; Shah, Rashmi G.; Purohit, Nupur K. Proceedings of the National Academy of Sciences, Vol. 114, Issue 33 https://doi.org/10.1073/pnas.1706981114	journal	July 2017
Nucleosome rearrangement in human chromatin during UV-induced DNA- reapir synthesis. Smerdon, M. J.; Lieberman, M. W. Proceedings of the National Academy of Sciences, Vol. 75, Issue 9 https://doi.org/10.1073/pnas.75.9.4238	journal	September 1978
Bipartite substrate discrimination by human nucleotide excision repair Hess, M. T.; Schwitter, U.; Petretta, M. Proceedings of the National Academy of Sciences, Vol. 94, Issue 13 https://doi.org/10.1073/pnas.94.13.6664	journal	June 1997
Reconstitution of Human DNA Repair Excision Nuclease in a Highly Defined System Mu, David; Park, Chi-Hyun; Matsunaga, Tsukasa Journal of Biological Chemistry, Vol. 270, Issue 6 https://doi.org/10.1074/jbc.270.6.2415	journal	February 1995
Characterization of DNA Recognition by the Human UV-damaged DNA-binding Protein Fujiwara, Yoshie; Masutani, Chikahide; Mizukoshi, Toshimi Journal of Biological Chemistry, Vol. 274, Issue 28 https://doi.org/10.1074/jbc.274.28.20027	journal	July 1999
The Xeroderma Pigmentosum Group C Protein Complex XPC-HR23B Plays an Important Role in the Recruitment of Transcription Factor IIH to Damaged DNA Yokoi, Masayuki; Masutani, Chikahide; Maekawa, Takafumi Journal of Biological Chemistry, Vol. 275, Issue 13 https://doi.org/10.1074/jbc.275.13.9870	journal	March 2000
TFIIH with Inactive XPD Helicase Functions in Transcription Initiation but Is Defective in DNA Repair Winkler, G. Sebastiaan; Araújo, Sofia J.; Fiedler, Ulrike Journal of Biological Chemistry, Vol. 275, Issue 6 https://doi.org/10.1074/jbc.275.6.4258	journal	February 2000
Mechanism of Release and Fate of Excised Oligonucleotides during Nucleotide Excision Repair Kemp, Michael G.; Reardon, Joyce T.; Lindsey-Boltz, Laura A. Journal of Biological Chemistry, Vol. 287, Issue 27 https://doi.org/10.1074/jbc.M112.374447	journal	June 2012
Nucleotide Excision Repair in Human Cells Hu, Jinchuan; Choi, Jun-Hyuk; Gaddameedhi, Shobhan Journal of Biological Chemistry, Vol. 288, Issue 29 https://doi.org/10.1074/jbc.M113.482257	journal	July 2013
Poly(ADP-ribose) Polymerase 1 Modulates Interaction of the Nucleotide Excision Repair Factor XPC-RAD23B with DNA via Poly(ADP-ribosyl)ation Maltseva, Ekaterina A.; Rechkunova, Nadejda I.; Sukhanova, Maria V. Journal of Biological Chemistry, Vol. 290, Issue 36 https://doi.org/10.1074/jbc.M115.646638	journal	September 2015
Nucleotide Excision Repair and Transcription-coupled DNA Repair Abrogate the Impact of DNA Damage on Transcription Nadkarni, Aditi; Burns, John A.; Gandolfi, Alberto Journal of Biological Chemistry, Vol. 291, Issue 2 https://doi.org/10.1074/jbc.M115.685271	journal	January 2016
Conservation and Divergence in Nucleotide Excision Repair Lesion Recognition Wirth, Nicolas; Gross, Jonas; Roth, Heide M. Journal of Biological Chemistry, Vol. 291, Issue 36 https://doi.org/10.1074/jbc.M116.739425	journal	July 2016
In Vivo Recruitment of XPC to UV-induced Cyclobutane Pyrimidine Dimers by the DDB2 Gene Product Fitch, Maureen E.; Nakajima, Satoshi; Yasui, Akira Journal of Biological Chemistry, Vol. 278, Issue 47 https://doi.org/10.1074/jbc.M307254200	journal	August 2003
Ordered Conformational Changes in Damaged DNA Induced by Nucleotide Excision Repair Factors Tapias, Angels; Auriol, Jerome; Forget, Diane Journal of Biological Chemistry, Vol. 279, Issue 18 https://doi.org/10.1074/jbc.M312611200	journal	April 2004
DDB1-DDB2 (Xeroderma Pigmentosum Group E) Protein Complex Recognizes a Cyclobutane Pyrimidine Dimer, Mismatches, Apurinic/Apyrimidinic Sites, and Compound Lesions in DNA Wittschieben, Birgitte Ø.; Iwai, Shigenori; Wood, Richard D. Journal of Biological Chemistry, Vol. 280, Issue 48 https://doi.org/10.1074/jbc.M507854200	journal	December 2005
Stochastic and reversible assembly of a multiprotein DNA repair complex ensures accurate target site recognition and efficient repair Luijsterburg, Martijn S.; von Bornstaedt, Gesa; Gourdin, Audrey M. Journal of Cell Biology, Vol. 189, Issue 3 https://doi.org/10.1083/jcb.200909175	journal	May 2010
DDB2 promotes chromatin decondensation at UV-induced DNA damage Luijsterburg, Martijn S.; Lindh, Michael; Acs, Klara The Journal of Cell Biology, Vol. 197, Issue 2 https://doi.org/10.1083/jcb.201106074	journal	April 2012
PARP1 promotes nucleotide excision repair through DDB2 stabilization and recruitment of ALC1 Pines, Alex; Vrouwe, Mischa G.; Marteijn, Jurgen A. Journal of Cell Biology, Vol. 199, Issue 2 https://doi.org/10.1083/jcb.201112132	journal	October 2012
Open complex formation around a lesion during nucleotide excision repair provides a structure for cleavage by human XPG protein Evans, E. The EMBO Journal, Vol. 16, Issue 3 https://doi.org/10.1093/emboj/16.3.625	journal	February 1997
Double-check probing of DNA bending and unwinding by XPA-RPA: an architectural function in DNA repair Missura, M. The EMBO Journal, Vol. 20, Issue 13 https://doi.org/10.1093/emboj/20.13.3554	journal	July 2001
The comings and goings of nucleotide excision repair factors on damaged DNA Riedl, T. The EMBO Journal, Vol. 22, Issue 19 https://doi.org/10.1093/emboj/cdg489	journal	October 2003
Structure and stability of DNA containing an aristolactam II-dA lesion: implications for the NER recognition of bulky adducts Lukin, Mark; Zaliznyak, Tanya; Johnson, Francis Nucleic Acids Research, Vol. 40, Issue 6 https://doi.org/10.1093/nar/gkr1094	journal	November 2011
Lack of recognition by global-genome nucleotide excision repair accounts for the high mutagenicity and persistence of aristolactam-DNA adducts Sidorenko, Victoria S.; Yeo, Jung-Eun; Bonala, Radha R. Nucleic Acids Research, Vol. 40, Issue 6 https://doi.org/10.1093/nar/gkr1095	journal	November 2011
Resistance of bulky DNA lesions to nucleotide excision repair can result from extensive aromatic lesion–base stacking interactions Reeves, Dara A.; Mu, Hong; Kropachev, Konstantin Nucleic Acids Research, Vol. 39, Issue 20 https://doi.org/10.1093/nar/gkr537	journal	July 2011
Structural and functional evidence that Rad4 competes with Rad2 for binding to the Tfb1 subunit of TFIIH in NER Lafrance-Vanasse, Julien; Arseneault, Geneviève; Cappadocia, Laurent Nucleic Acids Research, Vol. 41, Issue 4 https://doi.org/10.1093/nar/gks1321	journal	January 2013
Mechanism of DNA loading by the DNA repair helicase XPD Constantinescu-Aruxandei, Diana; Petrovic-Stojanovska, Biljana; Penedo, J. Carlos Nucleic Acids Research, Vol. 44, Issue 6 https://doi.org/10.1093/nar/gkw102	journal	February 2016
Nucleotide Excision Repair in Eukaryotes Scharer, O. D. Cold Spring Harbor Perspectives in Biology, Vol. 5, Issue 10 https://doi.org/10.1101/cshperspect.a012609	journal	October 2013
Recognition and repair of the cyclobutane thymine dimer, a major cause of skin cancers, by the human excision nuclease Reardon, J. T. Genes & Development, Vol. 17, Issue 20 https://doi.org/10.1101/gad.1131003	journal	October 2003
Nucleotide excision repair of DNA with recombinant human proteins: definition of the minimal set of factors, active forms of TFIIH, and modulation by CAK Araújo, Sofia J.; Tirode, Franck; Coin, Frederic Genes & Development, Vol. 14, Issue 3 https://doi.org/10.1101/gad.14.3.349	journal	February 2000
A multistep damage recognition mechanism for global genomic nucleotide excision repair Sugasawa, K. Genes & Development, Vol. 15, Issue 5 https://doi.org/10.1101/gad.866301	journal	March 2001
Xeroderma pigmentosum group C protein interacts with histones: regulation by acetylated states of histone H3 Kakumu, Erina; Nakanishi, Seiya; Shiratori, Hiromi M. Genes to Cells, Vol. 22, Issue 3 https://doi.org/10.1111/gtc.12479	journal	February 2017
CONTRASTING STRUCTURAL IMPACTS INDUCED BY cis-syn CYCLOBUTANE DIMER AND (6–4) ADDUCT IN DNA DUPLEX DECAMERS: IMPLICATION IN MUTAGENESIS AND REPAIR ACTIVITY Kim, Jong-Ki; Patel, Dinshaw; Choi, Byong-Seok Photochemistry and Photobiology, Vol. 62, Issue 1 https://doi.org/10.1111/j.1751-1097.1995.tb05236.x	journal	July 1995
Xeroderma pigmentosum group E cells lack a nuclear factor that binds to damaged DNA Chu, G.; Chang, E. Science, Vol. 242, Issue 4878 https://doi.org/10.1126/science.3175673	journal	October 1988
Mutational Signature of Aristolochic Acid Exposure as Revealed by Whole-Exome Sequencing Hoang, M. L.; Chen, C. -H.; Sidorenko, V. S. Science Translational Medicine, Vol. 5, Issue 197 https://doi.org/10.1126/scitranslmed.3006200	journal	August 2013
Dissection of the Molecular Defects Caused by Pathogenic Mutations in the DNA Repair Factor XPC Bernardes de Jesus, Bruno M.; Bjørås, Magnar; Coin, Frédéric Molecular and Cellular Biology, Vol. 28, Issue 23 https://doi.org/10.1128/MCB.00781-08	journal	September 2008
Base pair conformation-dependent excision of benzo[a]pyrene diol epoxide-guanine adducts by human nucleotide excision repair enzymes Hess, M. T.; Gunz, D.; Luneva, N. Molecular and Cellular Biology, Vol. 17, Issue 12 https://doi.org/10.1128/MCB.17.12.7069	journal	December 1997
Strong Functional Interactions of TFIIH with XPC and XPG in Human DNA Nucleotide Excision Repair, without a Preassembled Repairosome Araújo, Sofia J.; Nigg, Erich A.; Wood, Richard D. Molecular and Cellular Biology, Vol. 21, Issue 7 https://doi.org/10.1128/MCB.21.7.2281-2291.2001	journal	April 2001
Nucleotide Excision Repair and Transcriptional Regulation: TFIIH and Beyond Compe, Emmanuel; Egly, Jean-Marc Annual Review of Biochemistry, Vol. 85, Issue 1 https://doi.org/10.1146/annurev-biochem-060815-014857	journal	June 2016
Versatile DNA damage detection by the global genome nucleotide excision repair protein XPC Hoogstraten, D.; Bergink, S.; Ng, J. M. Y. Journal of Cell Science, Vol. 121, Issue 17 https://doi.org/10.1242/jcs.031708	journal	September 2008
Crystal Structure of the FeS Cluster–Containing Nucleotide Excision Repair Helicase XPD Wolski, Stefanie C.; Kuper, Jochen; Hänzelmann, Petra PLoS Biology, Vol. 6, Issue 6 https://doi.org/10.1371/journal.pbio.0060149	journal	June 2008
In TFIIH, XPD Helicase Is Exclusively Devoted to DNA Repair Kuper, Jochen; Braun, Cathy; Elias, Agnes PLoS Biology, Vol. 12, Issue 9 https://doi.org/10.1371/journal.pbio.1001954	journal	September 2014
Chromatin remodeler CHD 1 promotes XPC ‐to‐ TFIIH handover of nucleosomal UV lesions in nucleotide excision repair Rüthemann, Peter; Balbo Pogliano, Chiara; Codilupi, Tamara The EMBO Journal, Vol. 36, Issue 22 https://doi.org/10.15252/embj.201695742	journal	October 2017
Regulation of DNA Repair Mechanisms: How the Chromatin Environment Regulates the DNA Damage Response Stadler, Jens; Richly, Holger International Journal of Molecular Sciences, Vol. 18, Issue 8 https://doi.org/10.3390/ijms18081715	journal	August 2017

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A key interaction with RPA orients XPA in NER complexes Topolska-Woś, Agnieszka M.; Sugitani, Norie; Cordoba, John J. Nucleic Acids Research, Vol. 48, Issue 4 https://doi.org/10.1093/nar/gkz1231	journal	January 2020
Single-molecule visualization reveals the damage search mechanism for the human NER protein XPC-RAD23B Cheon, Na Young; Kim, Hyun-Suk; Yeo, Jung-Eun Nucleic Acids Research, Vol. 47, Issue 16 https://doi.org/10.1093/nar/gkz629	journal	August 2019
DNA damage response and repair in perspective: Aedes aegypti, Drosophila melanogaster and Homo sapiens Mota, Maria Beatriz S.; Carvalho, Marcelo Alex; Monteiro, Alvaro N. A. Parasites & Vectors, Vol. 12, Issue 1 https://doi.org/10.1186/s13071-019-3792-1	journal	November 2019
Nucleotide Excision Repair: From Molecular Defects to Neurological Abnormalities Krasikova, Yuliya; Rechkunova, Nadejda; Lavrik, Olga International Journal of Molecular Sciences, Vol. 22, Issue 12 https://doi.org/10.3390/ijms22126220	journal	June 2021
Therapeutic Targeting of DNA Damage Response in Cancer Choi, Wonyoung; Lee, Eun Sook International Journal of Molecular Sciences, Vol. 23, Issue 3 https://doi.org/10.3390/ijms23031701	journal	February 2022
Demethoxycurcumin-Loaded Chitosan Nanoparticle Downregulates DNA Repair Pathway to Improve Cisplatin-Induced Apoptosis in Non-Small Cell Lung Cancer Chen, Ying-Yi; Lin, Yu-Jung; Huang, Wei-Ting Molecules, Vol. 23, Issue 12 https://doi.org/10.3390/molecules23123217	journal	December 2018
A chromatin scaffold for DNA damage recognition: how histone methyltransferases prime nucleosomes for repair of ultraviolet light-induced lesions Gsell, Corina; Richly, Holger; Coin, Frédéric Nucleic Acids Research, Vol. 48, Issue 4 https://doi.org/10.1093/nar/gkz1229	journal	January 2020
A chromatin scaffold for DNA damage recognition: how histone methyltransferases prime nucleosomes for repair of ultraviolet light-induced lesions Gsell, Corina; Richly, Holger; Coin, Frédéric Oxford University Press https://doi.org/10.5167/uzh-197205	text	January 2020

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