1
|
Liu Y, Chen X, Zhao Y, Wang XY, Luo YW, Chen L, Wang W, Zhong S, Hu M, Dai Z, Jiang J, Wang X, Ji H, Cheng XX, Zheng A, Zuo J, Liu H, Ma D, Luo Z, Cao F, Hu S, Huang AL, Tang KF. Small cytosolic double-stranded DNA represses cyclic GMP-AMP synthase activation and induces autophagy. Cell Rep 2023; 42:112852. [PMID: 37481718 DOI: 10.1016/j.celrep.2023.112852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 04/28/2023] [Accepted: 07/07/2023] [Indexed: 07/25/2023] Open
Abstract
The cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway is a major mediator of inflammation following stimulation with >45 bp double-stranded DNA (dsDNA). Herein, we identify a class of ∼20-40 bp small cytosolic dsDNA (scDNA) molecules that compete with long dsDNA (200-1,500 bp herring testis [HT]-DNA) for binding to cGAS, thus repressing HT-DNA-induced cGAS activation. The scDNA promotes cGAS and Beclin-1 interaction, releasing Rubicon, a negative regulator of phosphatidylinositol 3-kinase class III (PI3KC3), from the Beclin-1-PI3KC3 complex. This leads to PI3KC3 activation and induces autophagy, causing degradation of STING and long cytosolic dsDNA. Moreover, DNA damage decreases, and autophagy inducers increase scDNA levels. scDNA transfection and treatment with autophagy inducers attenuate DNA damage-induced cGAS activation. Thus, scDNA molecules serve as effective brakes for cGAS activation, preventing excessive inflammatory cytokine production following DNA damage. Our findings may have therapeutic implications for cytosolic DNA-associated inflammatory diseases.
Collapse
Affiliation(s)
- Yao Liu
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Xiao Chen
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China; Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Yuemei Zhao
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Xing-Yue Wang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Yu-Wei Luo
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Lina Chen
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Weiyun Wang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Shouhui Zhong
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Meizhen Hu
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Zhizheng Dai
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Jiayu Jiang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Xin Wang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Hongyu Ji
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Xiao-Xiao Cheng
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Anqi Zheng
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Jiwei Zuo
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Hui Liu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Di Ma
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Zhicheng Luo
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Fang Cao
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Shanshan Hu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Ai-Long Huang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400016, P.R. China.
| | - Kai-Fu Tang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400016, P.R. China.
| |
Collapse
|
2
|
Bellani MA, Huang J, Zhang J, Gali H, Thazhathveetil AK, Pokharel D, Majumdar I, Shaik A, Seidman MM. Imaging the cellular response to an antigen tagged interstrand crosslinking agent. DNA Repair (Amst) 2023; 128:103525. [PMID: 37320956 PMCID: PMC10413329 DOI: 10.1016/j.dnarep.2023.103525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/02/2023] [Accepted: 06/08/2023] [Indexed: 06/17/2023]
Abstract
Immunofluorescence imaging is a standard experimental tool for monitoring the response of cellular factors to DNA damage. Visualizing the recruitment of DNA Damage Response (DDR) components requires high affinity antibodies, which are generally available. In contrast, reagents for the display of the lesions that induce the response are far more limited. Consequently, DDR factor accumulation often serves as a surrogate for damage, without reporting the actual inducing structure. This limitation has practical implications given the importance of the response to DNA reactive drugs such as those used in cancer therapy. These include interstrand crosslink (ICL) forming compounds which are frequently employed clinically. Among them are the psoralens, natural products that form ICLs upon photoactivation and applied therapeutically since antiquity. However, despite multiple attempts, antibodies against psoralen ICLs have not been developed. To overcome this limitation, we developed a psoralen tagged with an antigen for which there are commercial antibodies. In this report we describe our application of the tagged psoralen in imaging experiments, and the unexpected discoveries they revealed.
Collapse
Affiliation(s)
- Marina A Bellani
- Laboratory of Molecular Biology and Immunology, NIA, NIH, Baltimore MD 21224, USA
| | - Jing Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Jing Zhang
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Himabindu Gali
- Frederick National Laboratory for Cancer Research, Frederick, MD 21703, USA
| | | | | | - Ishani Majumdar
- Laboratory of Molecular Biology and Immunology, NIA, NIH, Baltimore MD 21224, USA
| | - Althaf Shaik
- Laboratory of Molecular Biology and Immunology, NIA, NIH, Baltimore MD 21224, USA
| | - Michael M Seidman
- Laboratory of Molecular Biology and Immunology, NIA, NIH, Baltimore MD 21224, USA.
| |
Collapse
|
3
|
Kufner CL, Krebs S, Fischaleck M, Philippou-Massier J, Blum H, Bucher DB, Braun D, Zinth W, Mast CB. Sequence dependent UV damage of complete pools of oligonucleotides. Sci Rep 2023; 13:2638. [PMID: 36788271 PMCID: PMC9929323 DOI: 10.1038/s41598-023-29833-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
Understanding the sequence-dependent DNA damage formation requires probing a complete pool of sequences over a wide dose range of the damage-causing exposure. We used high throughput sequencing to simultaneously obtain the dose dependence and quantum yields for oligonucleotide damages for all possible 4096 DNA sequences with hexamer length. We exposed the DNA to ultraviolet radiation at 266 nm and doses of up to 500 absorbed photons per base. At the dimer level, our results confirm existing literature values of photodamage, whereas we now quantified the susceptibility of sequence motifs to UV irradiation up to previously inaccessible polymer lengths. This revealed the protective effect of the sequence context in preventing the formation of UV-lesions. For example, the rate to form dipyrimidine lesions is strongly reduced by nearby guanine bases. Our results provide a complete picture of the sensitivity of oligonucleotides to UV irradiation and allow us to predict their abundance in high-UV environments.
Collapse
Affiliation(s)
- Corinna L. Kufner
- grid.38142.3c000000041936754XHarvard-Smithsonian Center for Astrophysics, Department of Astronomy, Harvard University, 60 Garden Street, Cambridge, MA 02138 USA
| | - Stefan Krebs
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Marlis Fischaleck
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Julia Philippou-Massier
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Helmut Blum
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Dominik B. Bucher
- grid.6936.a0000000123222966Chemistry Department, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Dieter Braun
- grid.5252.00000 0004 1936 973XSystems Biophysics, Ludwig Maximilians University Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Wolfgang Zinth
- grid.5252.00000 0004 1936 973XBiomolecular Optics and Center for Integrated Protein Science, Ludwig Maximilians University Munich, Oettingenstrasse 67, 80538 Munich, Germany
| | - Christof B. Mast
- grid.5252.00000 0004 1936 973XSystems Biophysics, Ludwig Maximilians University Munich, Amalienstr. 54, 80799 Munich, Germany
| |
Collapse
|
4
|
Blessing C, Apelt K, van den Heuvel D, Gonzalez-Leal C, Rother MB, van der Woude M, González-Prieto R, Yifrach A, Parnas A, Shah RG, Kuo TT, Boer DEC, Cai J, Kragten A, Kim HS, Schärer OD, Vertegaal ACO, Shah GM, Adar S, Lans H, van Attikum H, Ladurner AG, Luijsterburg MS. XPC-PARP complexes engage the chromatin remodeler ALC1 to catalyze global genome DNA damage repair. Nat Commun 2022; 13:4762. [PMID: 35963869 PMCID: PMC9376112 DOI: 10.1038/s41467-022-31820-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/29/2022] [Indexed: 11/24/2022] Open
Abstract
Cells employ global genome nucleotide excision repair (GGR) to eliminate a broad spectrum of DNA lesions, including those induced by UV light. The lesion-recognition factor XPC initiates repair of helix-destabilizing DNA lesions, but binds poorly to lesions such as CPDs that do not destabilize DNA. How difficult-to-repair lesions are detected in chromatin is unknown. Here, we identify the poly-(ADP-ribose) polymerases PARP1 and PARP2 as constitutive interactors of XPC. Their interaction results in the XPC-stimulated synthesis of poly-(ADP-ribose) (PAR) by PARP1 at UV lesions, which in turn enables the recruitment and activation of the PAR-regulated chromatin remodeler ALC1. PARP2, on the other hand, modulates the retention of ALC1 at DNA damage sites. Notably, ALC1 mediates chromatin expansion at UV-induced DNA lesions, leading to the timely clearing of CPD lesions. Thus, we reveal how chromatin containing difficult-to-repair DNA lesions is primed for repair, providing insight into mechanisms of chromatin plasticity during GGR. Cells employ global genome nucleotide excision repair to repair a broad spectrum of genomic DNA lesions. Here, the authors reveal how chromatin is primed for repair, providing insight into mechanisms of chromatin plasticity during DNA repair.
Collapse
Affiliation(s)
- Charlotte Blessing
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany.,International Max Planck Research School (IMPRS) for Molecular Life Sciences, Planegg-Martinsried, Germany
| | - Katja Apelt
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Claudia Gonzalez-Leal
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany.,International Max Planck Research School (IMPRS) for Molecular Life Sciences, Planegg-Martinsried, Germany
| | - Magdalena B Rother
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Melanie van der Woude
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, The Netherlands.,Genome Proteomics Laboratory, Andalusian Center For Molecular Biology and Regenerative Medicine (CABIMER), University of Seville, Seville, Spain.,Department of Cell Biology, University of Seville, Seville, Spain
| | - Adi Yifrach
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Avital Parnas
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rashmi G Shah
- Laboratory for Skin Cancer Research, CHU-Q: Laval University Hospital Research Centre of Quebec (CHUL site), Quebec City, Canada
| | - Tia Tyrsett Kuo
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany.,International Max Planck Research School (IMPRS) for Molecular Life Sciences, Planegg-Martinsried, Germany
| | - Daphne E C Boer
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Jin Cai
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany.,International Max Planck Research School (IMPRS) for Molecular Life Sciences, Planegg-Martinsried, Germany
| | - Angela Kragten
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Hyun-Suk Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Girish M Shah
- Laboratory for Skin Cancer Research, CHU-Q: Laval University Hospital Research Centre of Quebec (CHUL site), Quebec City, Canada
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Andreas G Ladurner
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany. .,International Max Planck Research School (IMPRS) for Molecular Life Sciences, Planegg-Martinsried, Germany. .,Eisbach Bio GmbH, Planegg-Martinsried, Germany.
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands.
| |
Collapse
|
5
|
Kim SH, Kim GH, Kemp MG, Choi JH. TREX1 degrades the 3' end of the small DNA oligonucleotide products of nucleotide excision repair in human cells. Nucleic Acids Res 2022; 50:3974-3984. [PMID: 35357486 PMCID: PMC9023299 DOI: 10.1093/nar/gkac214] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/02/2022] [Accepted: 03/18/2022] [Indexed: 01/01/2023] Open
Abstract
The nucleotide excision repair (NER) machinery removes UV photoproducts from DNA in the form of small, excised damage-containing DNA oligonucleotides (sedDNAs) ∼30 nt in length. How cells process and degrade these byproducts of DNA repair is not known. Using a small scale RNA interference screen in UV-irradiated human cells, we identified TREX1 as a major regulator of sedDNA abundance. Knockdown of TREX1 increased the level of sedDNAs containing the two major UV photoproducts and their association with the NER proteins TFIIH and RPA. Overexpression of wild-type but not nuclease-inactive TREX1 significantly diminished sedDNA levels, and studies with purified recombinant TREX1 showed that the enzyme efficiently degrades DNA located 3′ of the UV photoproduct in the sedDNA. Knockdown or overexpression of TREX1 did not impact the overall rate of UV photoproduct removal from genomic DNA or cell survival, which indicates that TREX1 function in sedDNA degradation does not impact NER efficiency. Taken together, these results indicate a previously unknown role for TREX1 in promoting the degradation of the sedDNA products of the repair reaction. Because TREX1 mutations and inefficient DNA degradation impact inflammatory and immune signaling pathways, the regulation of sedDNA degradation by TREX1 may contribute to photosensitive skin disorders.
Collapse
Affiliation(s)
- Seon Hee Kim
- Biometrology Group, Division of Chemical and Biological Metrology, Korea Research Institute of Standards and Science, Daejeon 305-340, Republic of Korea.,Department of Bio-Analytical Science, University of Science & Technology, Daejeon 305-340, Republic of Korea
| | - Geun Hoe Kim
- Biometrology Group, Division of Chemical and Biological Metrology, Korea Research Institute of Standards and Science, Daejeon 305-340, Republic of Korea.,Department of Bio-Analytical Science, University of Science & Technology, Daejeon 305-340, Republic of Korea
| | - Michael G Kemp
- Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, OH 45435, USA.,Dayton Veterans Administration Medical Center, Dayton, OH 45428, USA
| | - Jun-Hyuk Choi
- Biometrology Group, Division of Chemical and Biological Metrology, Korea Research Institute of Standards and Science, Daejeon 305-340, Republic of Korea.,Department of Bio-Analytical Science, University of Science & Technology, Daejeon 305-340, Republic of Korea
| |
Collapse
|
6
|
Wu S, Huang Y, Selby CP, Gao M, Sancar A, Hu J. A new technique for genome-wide mapping of nucleotide excision repair without immunopurification of damaged DNA. J Biol Chem 2022; 298:101863. [PMID: 35339490 PMCID: PMC9034098 DOI: 10.1016/j.jbc.2022.101863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 12/03/2022] Open
Abstract
Nucleotide excision repair functions to protect genome integrity, and ongoing studies using excision repair sequencing (XR-seq) have contributed to our understanding of how cells prioritize repair across the genome. In this method, the products of excision repair bearing damaged DNA are captured, sequenced, and then mapped genome-wide at single-nucleotide resolution. However, reagent requirements and complex procedures have limited widespread usage of this technique. In addition to the expense of these reagents, it has been hypothesized that the immunoprecipitation step using antibodies directed against damaged DNA may introduce bias in different sequence contexts. Here, we describe a newly developed adaptation called dA-tailing and adaptor ligation (ATL)–XR-seq, a relatively simple XR-seq method that avoids the use of immunoprecipitation targeting damaged DNA. ATL-XR-seq captures repair products by 3′-dA-tailing and 5′-adapter ligation instead of the original 5′- and 3′-dual adapter ligation. This new approach avoids adapter dimer formation during subsequent PCR, omits inefficient and time-consuming purification steps, and is very sensitive. In addition, poly(dA) tail length heterogeneity can serve as a molecular identifier, allowing more repair hotspots to be mapped. Importantly, a comparison of both repair mapping methods showed that no major bias is introduced by the anti-UV damage antibodies used in the original XR-seq procedure. Finally, we also coupled the described dA-tailing approach with quantitative PCR in a new method to quantify repair products. These new methods provide powerful and user-friendly tools to qualitatively and quantitatively measure excision repair.
Collapse
Affiliation(s)
- Sizhong Wu
- Shanghai Fifth People's Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yanchao Huang
- Shanghai Fifth People's Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Christopher P Selby
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599-7260, USA
| | - Meng Gao
- Shanghai Fifth People's Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599-7260, USA.
| | - Jinchuan Hu
- Shanghai Fifth People's Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
| |
Collapse
|
7
|
van Toorn M, Turkyilmaz Y, Han S, Zhou D, Kim HS, Salas-Armenteros I, Kim M, Akita M, Wienholz F, Raams A, Ryu E, Kang S, Theil AF, Bezstarosti K, Tresini M, Giglia-Mari G, Demmers JA, Schärer OD, Choi JH, Vermeulen W, Marteijn JA. Active DNA damage eviction by HLTF stimulates nucleotide excision repair. Mol Cell 2022; 82:1343-1358.e8. [PMID: 35271816 PMCID: PMC9473497 DOI: 10.1016/j.molcel.2022.02.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/15/2021] [Accepted: 02/10/2022] [Indexed: 10/18/2022]
Abstract
Nucleotide excision repair (NER) counteracts the onset of cancer and aging by removing helix-distorting DNA lesions via a "cut-and-patch"-type reaction. The regulatory mechanisms that drive NER through its successive damage recognition, verification, incision, and gap restoration reaction steps remain elusive. Here, we show that the RAD5-related translocase HLTF facilitates repair through active eviction of incised damaged DNA together with associated repair proteins. Our data show a dual-incision-dependent recruitment of HLTF to the NER incision complex, which is mediated by HLTF's HIRAN domain that binds 3'-OH single-stranded DNA ends. HLTF's translocase motor subsequently promotes the dissociation of the stably damage-bound incision complex together with the incised oligonucleotide, allowing for an efficient PCNA loading and initiation of repair synthesis. Our findings uncover HLTF as an important NER factor that actively evicts DNA damage, thereby providing additional quality control by coordinating the transition between the excision and DNA synthesis steps to safeguard genome integrity.
Collapse
Affiliation(s)
- Marvin van Toorn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Yasemin Turkyilmaz
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Sueji Han
- Center for Bioanalysis, Korea Research Institute of Standards and Science, Daejeon 305-340, Republic of Korea; Department of Bio-Analytical Science, University of Science & Technology, Daejeon 305-350, Republic of Korea
| | - Di Zhou
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Hyun-Suk Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Irene Salas-Armenteros
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Mihyun Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea; Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Masaki Akita
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Franziska Wienholz
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Anja Raams
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Eunjin Ryu
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea; Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Arjan F Theil
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Karel Bezstarosti
- Proteomics Centre, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Maria Tresini
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Giuseppina Giglia-Mari
- Institut NeuroMyoGène (INMG), CNRS UMR 5310, INSERM U1217, Université de Lyon, Université Claude Bernard Lyon1, 16 rue Dubois, 69622 Villeurbanne Cedex, France
| | - Jeroen A Demmers
- Proteomics Centre, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea; Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jun-Hyuk Choi
- Center for Bioanalysis, Korea Research Institute of Standards and Science, Daejeon 305-340, Republic of Korea; Department of Bio-Analytical Science, University of Science & Technology, Daejeon 305-350, Republic of Korea
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands.
| |
Collapse
|
8
|
Liu G, Liu X, Yang Y. Comparative transcriptome analysis of miRNA in hydronephrosis male children caused by ureteropelvic junction obstruction with or without renal functional injury. PeerJ 2022; 10:e12962. [PMID: 35237468 PMCID: PMC8884061 DOI: 10.7717/peerj.12962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 01/27/2022] [Indexed: 01/11/2023] Open
Abstract
MicroRNAs (miRNAs or miRs) are non-coding RNAs that contribute to pathological processes of various kidney diseases. Renal function injury represents a final common outcome of congenital obstructive nephropathy and has attracted a great deal of attention. However the molecular mechanisms are still not fully established. In this study, we compared transcriptome sequencing data of miRNAs of renal tissues from congenital hydronephrosis children with or without renal functional injury, in order to better understand whether microRNAs could play important roles in renal functional injury after ureteropelvic junction obstruction. A total of 22 microRNAs with significant changes in their expression were identified. Five microRNAs were up-regulated and 17 microRNAs were down-regulated in the renal tissues of the hydronephrosis patients with renal function injury compared with those without renal function injury. MicroRNA target genes were predicted by three major online miRNA target prediction algorithms, and all these mRNAs were used to perform the gene ontology analysis and Kyoto Encyclopedia of Gene and Genomes pathway analysis. Then, twelve candidate human and rat homologous miRNAs were selected for validation using RT-qPCR in vitro and in vivo; only miR-187-3p had a trend identical to that detected by the sequencing results among the human tissues, in vivo and in vitro experimental models. In addition, we found that the change of miR-187-3p in vivo was consistent with results in vitro models and showed a decrease trend in time dependence. These results provided a detailed catalog of candidate miRNAs to investigate their regulatory role in renal injury of congenital hydronephrosis, indicating that they may serve as candidate biomarkers or therapeutic targets in the future.
Collapse
Affiliation(s)
- Ge Liu
- Urology Division, Pediatric Surgery Department, Shengjing Hospital of China Medical University, Shenyang, Liaoning, People’s Republic of China
| | - Xin Liu
- Urology Division, Pediatric Surgery Department, Shengjing Hospital of China Medical University, Shenyang, Liaoning, People’s Republic of China
| | - Yi Yang
- Urology Division, Pediatric Surgery Department, Shengjing Hospital of China Medical University, Shenyang, Liaoning, People’s Republic of China
| |
Collapse
|
9
|
Li W, Sancar A. Methodologies for detecting environmentally induced DNA damage and repair. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:664-679. [PMID: 32083352 PMCID: PMC7442611 DOI: 10.1002/em.22365] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 02/08/2020] [Accepted: 02/16/2020] [Indexed: 05/07/2023]
Abstract
Environmental DNA damaging agents continuously challenge the integrity of the genome by introducing a variety of DNA lesions. The DNA damage caused by environmental factors will lead to mutagenesis and subsequent carcinogenesis if they are not removed efficiently by repair pathways. Methods for detection of DNA damage and repair can be applied to identify, visualize, and quantify the DNA damage formation and repair events, and they enable us to illustrate the molecular mechanisms of DNA damage formation, DNA repair pathways, mutagenesis, and carcinogenesis. Ever since the discovery of the double helical structure of DNA in 1953, a great number of methods have been developed to detect various types of DNA damage and repair. Rapid advances in sequencing technologies have facilitated the emergence of a variety of novel methods for detecting environmentally induced DNA damage and repair at the genome-wide scale during the last decade. In this review, we provide a historical overview of the development of various damage detection methods. We also highlight the current methodologies to detect DNA damage and repair, especially some next generation sequencing-based methods.
Collapse
Affiliation(s)
- Wentao Li
- Correspondence to: Wentao Li and Aziz Sancar, Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599. and
| | - Aziz Sancar
- Correspondence to: Wentao Li and Aziz Sancar, Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599. and
| |
Collapse
|
10
|
Choi JH, Han S, Kemp MG. Detection of the small oligonucleotide products of nucleotide excision repair in UVB-irradiated human skin. DNA Repair (Amst) 2019; 86:102766. [PMID: 31838380 DOI: 10.1016/j.dnarep.2019.102766] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/26/2019] [Accepted: 12/04/2019] [Indexed: 11/29/2022]
Abstract
UVB radiation results in the formation of potentially mutagenic photoproducts in the DNA of epidermal skin cells. In vitro approaches have demonstrated that the nucleotide excision repair (NER) machinery removes UV photoproducts from DNA in the form of small (∼30-nt-long), excised, damage-containing DNA oligonucleotides (sedDNAs). Though this process presumably takes place in human skin exposed to UVB radiation, sedDNAs have not previously been detected in human skin. Using surgically discarded human skin, we have optimized the detection of the sedDNA products of NER from small amounts of human epidermal tissue ex vivo within minutes of UVB exposure and after UVB doses that normally lead to minimal erythema. Moreover, sedDNA generation was inhibited by treatment of skin explants with spironolactone, which depletes the epidermis of the essential NER protein XPB to mimic the skin of xeroderma pigmentosum patients. Time course experiments revealed that a partially degraded form of the sedDNAs could be readily detected even 12 hours following UVB exposure, which indicates that these repair products are relatively stable in human skin epidermis. Together, these data suggest that sedDNA detection may be a useful assay for determining how genetic, environmental, and other factors influence NER activity in human skin epidermis and whether abnormal sedDNA processing contributes to photosensitive skin disorders.
Collapse
Affiliation(s)
- Jun-Hyuk Choi
- Center for Bioanalysis, Korea Research Institute of Standards and Science, Republic of Korea; Department of Bio-Analytical Science, University of Science & Technology, Republic of Korea
| | - Sueji Han
- Center for Bioanalysis, Korea Research Institute of Standards and Science, Republic of Korea; Department of Bio-Analytical Science, University of Science & Technology, Republic of Korea
| | - Michael G Kemp
- Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, OH 45435, United States.
| |
Collapse
|
11
|
Abstract
The nucleotide excision repair (NER) system removes a variety of types of helix-distorting lesions from DNA through a dual incision mechanism, in which the damaged nucleotide bases are excised in the form of a small, excised, damage-containing single-stranded DNA oligonucleotide (sedDNA). Damage removal leaves a gap in the DNA template that must then be filled in by the action of a DNA polymerase and ligated to the downstream phosphodiester backbone in the DNA to complete the repair reaction. Defects in damage removal, sedDNA processing, or gap filling have the potential to be mutagenic and lethal to cells, and thus several human pathologies, including cancer and aging, are associated with defects in NER. This review summarizes our current understanding of NER with a focus on the enzymes that excise sedDNAs and restore the duplex DNA to its native state in human cells.
Collapse
Affiliation(s)
- Michael G Kemp
- Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, OH, United States.
| |
Collapse
|
12
|
Zatopek KM, Potapov V, Maduzia LL, Alpaslan E, Chen L, Evans TC, Ong JL, Ettwiller LM, Gardner AF. RADAR-seq: A RAre DAmage and Repair sequencing method for detecting DNA damage on a genome-wide scale. DNA Repair (Amst) 2019; 80:36-44. [PMID: 31247470 DOI: 10.1016/j.dnarep.2019.06.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/13/2019] [Accepted: 06/19/2019] [Indexed: 12/19/2022]
Abstract
RAre DAmage and Repair sequencing (RADAR-seq) is a highly adaptable sequencing method that enables the identification and detection of rare DNA damage events for a wide variety of DNA lesions at single-molecule resolution on a genome-wide scale. In RADAR-seq, DNA lesions are replaced with a patch of modified bases that can be directly detected by Pacific Biosciences Single Molecule Real-Time (SMRT) sequencing. RADAR-seq enables dynamic detection over a wide range of DNA damage frequencies, including low physiological levels. Furthermore, without the need for DNA amplification and enrichment steps, RADAR-seq provides sequencing coverage of damaged and undamaged DNA across an entire genome. Here, we use RADAR-seq to measure the frequency and map the location of ribonucleotides in wild-type and RNaseH2-deficient E. coli and Thermococcus kodakarensis strains. Additionally, by tracking ribonucleotides incorporated during in vivo lagging strand DNA synthesis, we determined the replication initiation point in E. coli, and its relation to the origin of replication (oriC). RADAR-seq was also used to map cyclobutane pyrimidine dimers (CPDs) in Escherichia coli (E. coli) genomic DNA exposed to UV-radiation. On a broader scale, RADAR-seq can be applied to understand formation and repair of DNA damage, the correlation between DNA damage and disease initiation and progression, and complex biological pathways, including DNA replication.
Collapse
Affiliation(s)
- Kelly M Zatopek
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938 USA
| | - Vladimir Potapov
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938 USA
| | - Lisa L Maduzia
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938 USA
| | - Ece Alpaslan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938 USA
| | - Lixin Chen
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938 USA
| | - Thomas C Evans
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938 USA
| | - Jennifer L Ong
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938 USA.
| | | | - Andrew F Gardner
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938 USA.
| |
Collapse
|
13
|
Shafirovich V, Kropachev K, Kolbanovskiy M, Geacintov NE. Excision of Oxidatively Generated Guanine Lesions by Competing Base and Nucleotide Excision Repair Mechanisms in Human Cells. Chem Res Toxicol 2019; 32:753-761. [PMID: 30688445 PMCID: PMC6465092 DOI: 10.1021/acs.chemrestox.8b00411] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The interchange between different repair mechanisms in human cells has long been a subject of interest. Here, we provide a direct demonstration that the oxidatively generated guanine lesions spiroiminodihydantoin (Sp) and 5-guanidinohydantoin (Gh) embedded in double-stranded DNA are substrates of both base excision repair (BER) and nucleotide excision repair (NER) mechanisms in intact human cells. Site-specifically modified, 32P-internally labeled double-stranded DNA substrates were transfected into fibroblasts or HeLa cells, and the BER and/or NER mono- and dual incision products were quantitatively recovered after 2-8 h incubation periods and lysis of the cells. DNA duplexes bearing single benzo[ a]pyrene-derived guanine adduct were employed as positive controls of NER. The NER activities, but not the BER activities, were abolished in XPA-/- cells, while the BER yields were strongly reduced in NEIL1-/- cells. Co-transfecting different concentrations of analogous DNA sequences bearing the BER substrates 5-hydroxyuracil diminish the BER yields of Sp lesions and enhance the yields of NER products. These results are consistent with a model based on the local availability of BER and NER factors in human cells and their competitive binding to the same Sp or Gh BER/NER substrates.
Collapse
Affiliation(s)
- Vladimir Shafirovich
- Chemistry Department, New York University, 31 Washington Place, New York, NY 10003-5180, USA
| | - Konstantin Kropachev
- Chemistry Department, New York University, 31 Washington Place, New York, NY 10003-5180, USA
| | - Marina Kolbanovskiy
- Chemistry Department, New York University, 31 Washington Place, New York, NY 10003-5180, USA
| | - Nicholas E. Geacintov
- Chemistry Department, New York University, 31 Washington Place, New York, NY 10003-5180, USA
| |
Collapse
|
14
|
Feinberg T, Wieland LS, Miller LE, Munir K, Pollin TI, Shuldiner AR, Amoils S, Gallagher L, Bahr-Robertson M, D'Adamo CR. Polyherbal dietary supplementation for prediabetic adults: study protocol for a randomized controlled trial. Trials 2019; 20:24. [PMID: 30616613 PMCID: PMC6323847 DOI: 10.1186/s13063-018-3032-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 11/01/2018] [Indexed: 12/15/2022] Open
Abstract
Background Prediabetes describes a state of hyperglycemia outside of normal limits that does not meet the criteria for diabetes diagnosis, is generally symptomless, and affects an estimated 38% of adults in the United States. Prediabetes typically precedes the diagnosis of type 2 diabetes, which accounts for increased morbidity and mortality. Although the use of dietary and herbal supplements is popular worldwide, and a variety of single herbal medicines have been examined for glycemic management, the potential of increasingly common polyherbal formulations to return glycemic parameters to normal ranges among adults with prediabetes remains largely unexplored. The purpose of this study is to evaluate the efficacy of a commercially available, polyherbal dietary supplement on glycemic and lipid parameters in prediabetic individuals. Methods In this multi-site, double-blinded, randomized controlled clinical trial, 40 participants with prediabetes will be randomized to either a daily oral polyherbal dietary supplement (GlucoSupreme™ Herbal; Designs for Health®, Suffield, CT, USA; containing cinnamon bark (Cinnamomum cassia), banaba leaf (Lagerstroemia speciosa standardized to 1% corosolic acid), kudzu root (Pueraria lobata standardized to 40% isoflavones), fenugreek seed (Trigonella foenum-graceum standardized to 60% saponins), gymnema leaf (Gymnema sylvestre standardized to 25% gymnemic acid), American ginseng root (Panax quinquefolius standardized to 5% ginsenosides), and berberine HCl derived from bark (Berberis aristata)) or placebo for 12 weeks. Short-, medium-, and comparatively long-term markers of glycemic control (blood glucose and fasting insulin, fructosamine, and glycated hemoglobin/A1c, respectively), and other glycemic parameters (GlycoMark, β-cell function, and insulin sensitivity/resistance) will be obtained. Lipid profile (total cholesterol, LDL, HDL, and triglycerides), inflammation (hs-CRP), progression to type 2 diabetes mellitus, as well as safety indices (ALT, AST) will be obtained. An intention-to-treat analysis will be used to assess changes in study outcomes. Discussion Treatment options for adults with prediabetes are currently limited. This study aims to evaluate the safety and efficacy of a commercially available dietary supplement in the popular, but as yet insufficiently studied, category of polyherbal formulas for the management of glycemic parameters and other biomarkers associated with prediabetes. Trial registration ClinicalTrials.gov, ID: NCT03388762. Retrospectively registered on 4 January 2018. Electronic supplementary material The online version of this article (10.1186/s13063-018-3032-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Termeh Feinberg
- University of Maryland School of Medicine Center for Integrative Medicine, Baltimore, MD, USA. .,Yale University School of Medicine Center for Medical Informatics, New Haven, CT, USA.
| | - L Susan Wieland
- University of Maryland School of Medicine Center for Integrative Medicine, Baltimore, MD, USA
| | | | - Kashif Munir
- University of Maryland School of Medicine Center for Diabetes and Endocrinology, Baltimore, MD, USA
| | - Toni I Pollin
- University of Maryland School of Medicine Department of Medicine, Baltimore, MD, USA
| | - Alan R Shuldiner
- University of Maryland School of Medicine Department of Medicine, Baltimore, MD, USA
| | - Steve Amoils
- Alliance Integrative Medicine, Cincinatti, OH, USA
| | | | - Mary Bahr-Robertson
- University of Maryland School of Medicine Center for Integrative Medicine, Baltimore, MD, USA
| | - Christopher R D'Adamo
- University of Maryland School of Medicine Center for Integrative Medicine, Baltimore, MD, USA
| |
Collapse
|
15
|
Mandemaker IK, Geijer ME, Kik I, Bezstarosti K, Rijkers E, Raams A, Janssens RC, Lans H, Hoeijmakers JH, Demmers JA, Vermeulen W, Marteijn JA. DNA damage-induced replication stress results in PA200-proteasome-mediated degradation of acetylated histones. EMBO Rep 2018; 19:embr.201745566. [PMID: 30104204 PMCID: PMC6172457 DOI: 10.15252/embr.201745566] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 07/06/2018] [Accepted: 07/16/2018] [Indexed: 12/21/2022] Open
Abstract
Histone acetylation influences protein interactions and chromatin accessibility and plays an important role in the regulation of transcription, replication, and DNA repair. Conversely, DNA damage affects these crucial cellular processes and induces changes in histone acetylation. However, a comprehensive overview of the effects of DNA damage on the histone acetylation landscape is currently lacking. To quantify changes in histone acetylation, we developed an unbiased quantitative mass spectrometry analysis on affinity‐purified acetylated histone peptides, generated by differential parallel proteolysis. We identify a large number of histone acetylation sites and observe an overall reduction of acetylated histone residues in response to DNA damage, indicative of a histone‐wide loss of acetyl modifications. This decrease is mainly caused by DNA damage‐induced replication stress coupled to specific proteasome‐dependent loss of acetylated histones. Strikingly, this degradation of acetylated histones is independent of ubiquitylation but requires the PA200‐proteasome activator, a complex that specifically targets acetylated histones for degradation. The uncovered replication stress‐induced degradation of acetylated histones represents an important chromatin‐modifying response to cope with replication stress.
Collapse
Affiliation(s)
- Imke K Mandemaker
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marit E Geijer
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Iris Kik
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Karel Bezstarosti
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Erikjan Rijkers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anja Raams
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Roel C Janssens
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jan Hj Hoeijmakers
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.,CECAD Forschungszentrum, Köln, Germany.,Princess Máxima Center for Pediatric Oncology, Bilthoven, The Netherlands
| | - Jeroen Aa Demmers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| |
Collapse
|
16
|
Khan AQ, Travers JB, Kemp MG. Roles of UVA radiation and DNA damage responses in melanoma pathogenesis. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2018; 59:438-460. [PMID: 29466611 PMCID: PMC6031472 DOI: 10.1002/em.22176] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/18/2018] [Accepted: 01/22/2018] [Indexed: 05/10/2023]
Abstract
The growing incidence of melanoma is a serious public health issue that merits a thorough understanding of potential causative risk factors, which includes exposure to ultraviolet radiation (UVR). Though UVR has been classified as a complete carcinogen and has long been recognized for its ability to damage genomic DNA through both direct and indirect means, the precise mechanisms by which the UVA and UVB components of UVR contribute to the pathogenesis of melanoma have not been clearly defined. In this review, we therefore highlight recent studies that have addressed roles for UVA radiation in the generation of DNA damage and in modulating the subsequent cellular responses to DNA damage in melanocytes, which are the cell type that gives rise to melanoma. Recent research suggests that UVA not only contributes to the direct formation of DNA lesions but also impairs the removal of UV photoproducts from genomic DNA through oxidation and damage to DNA repair proteins. Moreover, the melanocyte microenvironment within the epidermis of the skin is also expected to impact melanomagenesis, and we therefore discuss several paracrine signaling pathways that have been shown to impact the DNA damage response in UV-irradiated melanocytes. Lastly, we examine how alterations to the immune microenvironment by UVA-associated DNA damage responses may contribute to melanoma development. Thus, there appear to be multiple avenues by which UVA may elevate the risk of melanoma. Protective strategies against excess exposure to UVA wavelengths of light therefore have the potential to decrease the incidence of melanoma. Environ. Mol. Mutagen. 59:438-460, 2018. © 2018 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Aiman Q Khan
- Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, Ohio
| | - Jeffrey B Travers
- Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, Ohio
- Dayton Veterans Affairs Medical Center, Dayton, Ohio
| | - Michael G Kemp
- Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, Ohio
| |
Collapse
|
17
|
Simultaneous detection of nucleotide excision repair events and apoptosis-induced DNA fragmentation in genotoxin-treated cells. Sci Rep 2018; 8:2265. [PMID: 29396432 PMCID: PMC5797224 DOI: 10.1038/s41598-018-20527-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/18/2018] [Indexed: 01/27/2023] Open
Abstract
Novel in vivo excision assays for monitoring the excised oligonucleotide products of nucleotide excision repair in UV-irradiated cells have provided unprecedented views of the kinetics and genomic distribution of repair events. However, an unresolved issue is the fate of the excised oligonucleotide products of repair and their mechanism of degradation. Based on our observation that decreases in excised oligonucleotide abundance coincide with the induction of apoptotic signaling in UV-irradiated cells, we considered the possibility that caspase-mediated apoptotic signaling contributes to excised oligonucleotide degradation or to a general inhibition of the excision repair system. However, genetic and pharmacological approaches to inhibit apoptotic signaling demonstrated that caspase-mediated apoptotic signaling does not affect excision repair or excised oligonucleotide stability. Nonetheless, our assay for detecting soluble DNAs produced by repair also revealed the production of larger DNAs following DNA damage induction that was dependent on caspase activation. We therefore further exploited the versatility of this assay by showing that soluble DNAs produced by both nucleotide excision repair and apoptotic signaling can be monitored simultaneously with a diverse set of DNA damaging agents. Thus, our in vivo excision repair assay provides a sensitive measure of both repair kinetics and apoptotic signaling in genotoxin-treated cells.
Collapse
|
18
|
Abstract
The eukaryotic global genomic nucleotide excision repair (GG-NER) pathway is the major mechanism that removes most bulky and some nonbulky lesions from cellular DNA. There is growing evidence that certain DNA lesions are repaired slowly or are entirely resistant to repair in cells, tissues, and in cell extract model assay systems. It is well established that the eukaryotic DNA lesion-sensing proteins do not detect the damaged nucleotide, but recognize the distortions/destabilizations in the native DNA structure caused by the damaged nucleotides. In this article, the nature of the structural features of certain bulky DNA lesions that render them resistant to NER, or cause them to be repaired slowly, is compared to that of those that are good-to-excellent NER substrates. Understanding the structural features that distinguish NER-resistant DNA lesions from good NER substrates may be useful for interpreting the biological significance of biomarkers of exposure of human populations to genotoxic environmental chemicals. NER-resistant lesions can survive to replication and cause mutations that can initiate cancer and other diseases. Furthermore, NER diminishes the efficacy of certain chemotherapeutic drugs, and the design of more potent pharmaceuticals that resist repair can be advanced through a better understanding of the structural properties of DNA lesions that engender repair-resistance.
Collapse
Affiliation(s)
- Nicholas E. Geacintov
- Chemistry and Biology Departments, New York University, New York, New York 10003-5180, United States
| | - Suse Broyde
- Chemistry and Biology Departments, New York University, New York, New York 10003-5180, United States
| |
Collapse
|
19
|
Hu J, Selby CP, Adar S, Adebali O, Sancar A. Molecular mechanisms and genomic maps of DNA excision repair in Escherichia coli and humans. J Biol Chem 2017; 292:15588-15597. [PMID: 28798238 DOI: 10.1074/jbc.r117.807453] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Nucleotide excision repair is a major DNA repair mechanism in all cellular organisms. In this repair system, the DNA damage is removed by concerted dual incisions bracketing the damage and at a precise distance from the damage. Here, we review the basic mechanisms of excision repair in Escherichia coli and humans and the recent genome-wide mapping of DNA damage and repair in these organisms at single-nucleotide resolution.
Collapse
Affiliation(s)
- Jinchuan Hu
- From the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7260 and
| | - Christopher P Selby
- From the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7260 and
| | - Sheera Adar
- From the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7260 and.,the Department of Microbiology and Molecular Genetics, Hebrew University-Hadassah Medical School, Ein Kerem 71120, Jerusalem, Israel
| | - Ogun Adebali
- From the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7260 and
| | - Aziz Sancar
- From the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7260 and
| |
Collapse
|
20
|
Human genome-wide repair map of DNA damage caused by the cigarette smoke carcinogen benzo[a]pyrene. Proc Natl Acad Sci U S A 2017; 114:6752-6757. [PMID: 28607059 DOI: 10.1073/pnas.1706021114] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Benzo[a]pyrene (BaP), a polycyclic aromatic hydrocarbon, is the major cause of lung cancer. BaP forms covalent DNA adducts after metabolic activation and induces mutations. We have developed a method for capturing oligonucleotides carrying bulky base adducts, including UV-induced cyclobutane pyrimidine dimers (CPDs) and BaP diol epoxide-deoxyguanosine (BPDE-dG), which are removed from the genome by nucleotide excision repair. The isolated oligonucleotides are ligated to adaptors, and after damage-specific immunoprecipitation, the adaptor-ligated oligonucleotides are converted to dsDNA with an appropriate translesion DNA synthesis (TLS) polymerase, followed by PCR amplification and next-generation sequencing (NGS) to generate genome-wide repair maps. We have termed this method translesion excision repair-sequencing (tXR-seq). In contrast to our previously described XR-seq method, tXR-seq does not depend on repair/removal of the damage in the excised oligonucleotides, and thus it is applicable to essentially all DNA damages processed by nucleotide excision repair. Here we present the excision repair maps for CPDs and BPDE-dG adducts generated by tXR-Seq for the human genome. In addition, we report the sequence specificity of BPDE-dG excision repair using tXR-seq.
Collapse
|
21
|
Kemp MG. DNA damage-induced ATM- and Rad-3-related (ATR) kinase activation in non-replicating cells is regulated by the XPB subunit of transcription factor IIH (TFIIH). J Biol Chem 2017; 292:12424-12435. [PMID: 28592488 DOI: 10.1074/jbc.m117.788406] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/05/2017] [Indexed: 11/06/2022] Open
Abstract
The role of the DNA damage response protein kinase ataxia telangiectasia-mutated (ATM)- and Rad-3-related (ATR) in the cellular response to DNA damage during the replicative phase of the cell cycle has been extensively studied. However, little is known about ATR kinase function in cells that are not actively replicating DNA and that constitute most cells in the human body. Using small-molecule inhibitors of ATR kinase and overexpression of a kinase-inactive form of the enzyme, I show here that ATR promotes cell death in non-replicating/non-cycling cultured human cells exposed to N-acetoxy-2-acetylaminofluorene (NA-AAF), which generates bulky DNA adducts that block RNA polymerase movement. Immunoblot analyses of soluble protein extracts revealed that ATR and other cellular proteins containing SQ motifs become rapidly and robustly phosphorylated in non-cycling cells exposed to NA-AAF in a manner largely dependent on ATR kinase activity but independent of the essential nucleotide excision repair factor XPA. Although the topoisomerase I inhibitor camptothecin also activated ATR in non-cycling cells, other transcription inhibitors that do not directly damage DNA failed to do so. Interestingly, genetic and pharmacological inhibition of the XPB subunit of transcription factor IIH prevented the accumulation of the single-stranded DNA binding protein replication protein A (RPA) on damaged chromatin and severely abrogated ATR signaling in response to NA-AAF and camptothecin. Together, these results reveal a previously unknown role for transcription factor IIH in ATR kinase activation in non-replicating, non-cycling cells.
Collapse
Affiliation(s)
- Michael G Kemp
- Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, Ohio 45435.
| |
Collapse
|
22
|
Impact of Age and Insulin-Like Growth Factor-1 on DNA Damage Responses in UV-Irradiated Human Skin. Molecules 2017; 22:molecules22030356. [PMID: 28245638 PMCID: PMC5432641 DOI: 10.3390/molecules22030356] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 02/22/2017] [Accepted: 02/24/2017] [Indexed: 01/19/2023] Open
Abstract
The growing incidence of non-melanoma skin cancer (NMSC) necessitates a thorough understanding of its primary risk factors, which include exposure to ultraviolet (UV) wavelengths of sunlight and age. Whereas UV radiation (UVR) has long been known to generate photoproducts in genomic DNA that promote genetic mutations that drive skin carcinogenesis, the mechanism by which age contributes to disease pathogenesis is less understood and has not been sufficiently studied. In this review, we highlight studies that have considered age as a variable in examining DNA damage responses in UV-irradiated skin and then discuss emerging evidence that the reduced production of insulin-like growth factor-1 (IGF-1) by senescent fibroblasts in the dermis of geriatric skin creates an environment that negatively impacts how epidermal keratinocytes respond to UVR-induced DNA damage. In particular, recent data suggest that two principle components of the cellular response to DNA damage, including nucleotide excision repair and DNA damage checkpoint signaling, are both partially defective in keratinocytes with inactive IGF-1 receptors. Overcoming these tumor-promoting conditions in aged skin may therefore provide a way to lower aging-associated skin cancer risk, and thus we will consider how dermal wounding and related clinical interventions may work to rejuvenate the skin, re-activate IGF-1 signaling, and prevent the initiation of NMSC.
Collapse
|
23
|
Hu J, Adar S. The Cartography of UV-induced DNA Damage Formation and DNA Repair. Photochem Photobiol 2017; 93:199-206. [PMID: 27861959 DOI: 10.1111/php.12668] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/23/2016] [Indexed: 12/29/2022]
Abstract
DNA damage presents a barrier to DNA-templated biochemical processes, including gene expression and faithful DNA replication. Compromised DNA repair leads to mutations, enhancing the risk for genetic diseases and cancer development. Conventional experimental approaches to study DNA damage required a researcher to choose between measuring bulk damage over the entire genome, with little or no resolution regarding a specific location, and obtaining data specific to a locus of interest, without a global perspective. Recent advances in high-throughput genomic tools overcame these limitations and provide high-resolution measurements simultaneously across the genome. In this review, we discuss the available methods for measuring DNA damage and their repair, focusing on genomewide assays for pyrimidine photodimers, the major types of damage induced by ultraviolet irradiation. These new genomic assays will be a powerful tool in identifying key components of genome stability and carcinogenesis.
Collapse
Affiliation(s)
- Jinchuan Hu
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Sheera Adar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC
| |
Collapse
|
24
|
Song J, Kemp MG, Choi JH. Detection of the Excised, Damage-containing Oligonucleotide Products of Nucleotide Excision Repair in Human Cells. Photochem Photobiol 2016; 93:192-198. [PMID: 27634428 PMCID: PMC5315615 DOI: 10.1111/php.12638] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 08/10/2016] [Indexed: 11/29/2022]
Abstract
The human nucleotide excision repair system targets a wide variety of DNA adducts for removal from DNA, including photoproducts induced by UV wavelengths of sunlight. A key feature of nucleotide excision repair is its dual incision mechanism, which results in generation of a small, damage‐containing oligonucleotide approximately 24 to 32 nt in length. Detection of these excised oligonucleotides using cell‐free extracts and purified proteins with defined DNA substrates has provided a robust biochemical assay for excision repair activity in vitro. However, the relevance of a number of in vitro findings to excision repair in living cells in vivo has remained unresolved. Over the past few years, novel methods for detecting and isolating the excised oligonucleotide products of repair in vivo have therefore been developed. Here we provide a basic outline of a sensitive and versatile in vivo excision assay and discuss how the assay both confirms previous in vitro findings and offers a number of advantages over existing cell‐based DNA repair assays. Thus, the in vivo excision assay offers a powerful tool for readily monitoring the repair of DNA lesions induced by a large number of environmental carcinogens and anticancer compounds.
Collapse
Affiliation(s)
- Jimyeong Song
- Center for Bioanalysis, Korea Research Institute of Standards and Science, Daejeon, Korea.,Department of Bio-Analytical Science, University of Science & Technology, Daejeon, Korea
| | - Michael G Kemp
- Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, OH
| | - Jun-Hyuk Choi
- Center for Bioanalysis, Korea Research Institute of Standards and Science, Daejeon, Korea.,Department of Bio-Analytical Science, University of Science & Technology, Daejeon, Korea
| |
Collapse
|
25
|
Kemp MG, Hu J. PostExcision Events in Human Nucleotide Excision Repair. Photochem Photobiol 2016; 93:178-191. [PMID: 27645806 DOI: 10.1111/php.12641] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 08/26/2016] [Indexed: 12/27/2022]
Abstract
The nucleotide excision repair system removes a wide variety of DNA lesions from the human genome, including photoproducts induced by ultraviolet (UV) wavelengths of sunlight. A defining feature of nucleotide excision repair is its dual incision mechanism, in which two nucleolytic incision events on the damaged strand of DNA at sites bracketing the lesion generate a damage-containing DNA oligonucleotide and a single-stranded DNA gap approximately 30 nucleotides in length. Although the early events of nucleotide excision repair, which include lesion recognition and the dual incisions, have been explored in detail and are reasonably well understood, the fate of the single-stranded DNA gaps and excised oligonucleotide products of repair have not been as extensively examined. In this review, recent findings that address these less-explored aspects of nucleotide excision repair are discussed and support the concept that postincision gap and excised oligonucleotide processing are critical steps in the cellular response to DNA damage induced by UV light and other environmental carcinogens. Defects in these latter stages of repair lead to cell death and other DNA damage signaling responses and may therefore contribute to a number of human disease states associated with exposure to UV wavelengths of sunlight, including skin cancer, aging and autoimmunity.
Collapse
Affiliation(s)
- Michael G Kemp
- Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, OH
| | - Jinchuan Hu
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC
| |
Collapse
|
26
|
Discrimination of Kinetic Models by a Combination of Microirradiation and Fluorescence Photobleaching. Biophys J 2016; 109:1551-64. [PMID: 26488646 DOI: 10.1016/j.bpj.2015.08.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 08/10/2015] [Accepted: 08/11/2015] [Indexed: 11/23/2022] Open
Abstract
Fluorescence recovery after photobleaching (FRAP) is an excellent tool to measure the chemical rate constants of fluorescently labeled proteins in living cells. Usually FRAP experiments are conducted with the protein concentrations being in a steady state, i.e., when the association and dissociation of the proteins are equilibrated. This is a strong limitation because situations in which rate constants change with time are of great scientific interest. In this study, we present an approach in which FRAP is used shortly after DNA damage introducing laser microirradiation, which results in the recruitment of the DNA clamp protein proliferating cell nuclear antigen (PCNA) to DNA lesions. We establish different kinetic models that are compatible with the observed PCNA recruitment data if FRAP is not used. By using FRAP at different time points during protein accumulation, we can not only exclude two out of three models, but we can also determine the rate constants with increased reliability. This study thus demonstrates the feasibility of using FRAP during protein recruitment and its application in the discrimination of possible kinetic models.
Collapse
|
27
|
Sancar A. Mechanisms of DNA Repair by Photolyase and Excision Nuclease (Nobel Lecture). Angew Chem Int Ed Engl 2016; 55:8502-27. [PMID: 27337655 DOI: 10.1002/anie.201601524] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Indexed: 01/27/2023]
Abstract
Ultraviolet light damages DNA by converting two adjacent thymines into a thymine dimer which is potentially mutagenic, carcinogenic, or lethal to the organism. This damage is repaired by photolyase and the nucleotide excision repair system in E. coli by nucleotide excision repair in humans. The work leading to these results is presented by Aziz Sancar in his Nobel Lecture.
Collapse
Affiliation(s)
- Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.
| |
Collapse
|
28
|
Sancar A. Mechanismen der DNA-Reparatur durch Photolyasen und Exzisionsnukleasen (Nobel-Aufsatz). Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601524] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Aziz Sancar
- Department of Biochemistry and Biophysics; University of North Carolina School of Medicine; Chapel Hill North Carolina USA
| |
Collapse
|
29
|
Abstract
Plants use light for photosynthesis and for various signaling purposes. The UV wavelengths in sunlight also introduce DNA damage in the form of cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone photoproducts [(6-4)PPs] that must be repaired for the survival of the plant. Genome sequencing has revealed the presence of genes for both CPD and (6-4)PP photolyases, as well as genes for nucleotide excision repair in plants, such as Arabidopsis and rice. Plant photolyases have been purified, characterized, and have been shown to play an important role in plant survival. In contrast, even though nucleotide excision repair gene homologs have been found in plants, the mechanism of nucleotide excision repair has not been investigated. Here we used the in vivo excision repair assay developed in our laboratory to demonstrate that Arabidopsis removes CPDs and (6-4)PPs by a dual-incision mechanism that is essentially identical to the mechanism of dual incisions in humans and other eukaryotes, in which oligonucleotides with a mean length of 26-27 nucleotides are removed by incising ∼20 phosphodiester bonds 5' and 5 phosphodiester bonds 3' to the photoproduct.
Collapse
|
30
|
Kemp MG, Sancar A. ATR Kinase Inhibition Protects Non-cycling Cells from the Lethal Effects of DNA Damage and Transcription Stress. J Biol Chem 2016; 291:9330-42. [PMID: 26940878 DOI: 10.1074/jbc.m116.719740] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Indexed: 01/09/2023] Open
Abstract
ATR (ataxia telangiectasia and Rad-3-related) is a protein kinase that maintains genome stability and halts cell cycle phase transitions in response to DNA lesions that block DNA polymerase movement. These DNA replication-associated features of ATR function have led to the emergence of ATR kinase inhibitors as potential adjuvants for DNA-damaging cancer chemotherapeutics. However, whether ATR affects the genotoxic stress response in non-replicating, non-cycling cells is currently unknown. We therefore used chemical inhibition of ATR kinase activity to examine the role of ATR in quiescent human cells. Although ATR inhibition had no obvious effects on the viability of non-cycling cells, inhibition of ATR partially protected non-replicating cells from the lethal effects of UV and UV mimetics. Analyses of various DNA damage response signaling pathways demonstrated that ATR inhibition reduced the activation of apoptotic signaling by these agents in non-cycling cells. The pro-apoptosis/cell death function of ATR is likely due to transcription stress because the lethal effects of compounds that block RNA polymerase movement were reduced in the presence of an ATR inhibitor. These results therefore suggest that whereas DNA polymerase stalling at DNA lesions activates ATR to protect cell viability and prevent apoptosis, the stalling of RNA polymerases instead activates ATR to induce an apoptotic form of cell death in non-cycling cells. These results have important implications regarding the use of ATR inhibitors in cancer chemotherapy regimens.
Collapse
Affiliation(s)
- Michael G Kemp
- From the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
| | - Aziz Sancar
- From the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
| |
Collapse
|
31
|
Choi JH, Kim SY, Kim SK, Kemp MG, Sancar A. An Integrated Approach for Analysis of the DNA Damage Response in Mammalian Cells: NUCLEOTIDE EXCISION REPAIR, DNA DAMAGE CHECKPOINT, AND APOPTOSIS. J Biol Chem 2015; 290:28812-21. [PMID: 26438822 DOI: 10.1074/jbc.m115.690354] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Indexed: 11/06/2022] Open
Abstract
DNA damage by UV and UV-mimetic agents elicits a set of inter-related responses in mammalian cells, including DNA repair, DNA damage checkpoints, and apoptosis. Conventionally, these responses are analyzed separately using different methodologies. Here we describe a unified approach that is capable of quantifying all three responses in parallel using lysates from the same population of cells. We show that a highly sensitive in vivo excision repair assay is capable of detecting nucleotide excision repair of a wide spectrum of DNA lesions (UV damage, chemical carcinogens, and chemotherapeutic drugs) within minutes of damage induction. This method therefore allows for a real-time measure of nucleotide excision repair activity that can be monitored in conjunction with other components of the DNA damage response, including DNA damage checkpoint and apoptotic signaling. This approach therefore provides a convenient and reliable platform for simultaneously examining multiple aspects of the DNA damage response in a single population of cells that can be applied for a diverse array of carcinogenic and chemotherapeutic agents.
Collapse
Affiliation(s)
- Jun-Hyuk Choi
- From the Center for Bioanalysis, Department of Metrology for Quality of Life, Korea Research Institute of Standards and Science, Daejeon 305-340, South Korea, the Department of Bio-Analytical Science, University of Science & Technology, Daejeon 305-350, South Korea, and
| | - So-Young Kim
- From the Center for Bioanalysis, Department of Metrology for Quality of Life, Korea Research Institute of Standards and Science, Daejeon 305-340, South Korea
| | - Sook-Kyung Kim
- From the Center for Bioanalysis, Department of Metrology for Quality of Life, Korea Research Institute of Standards and Science, Daejeon 305-340, South Korea, the Department of Bio-Analytical Science, University of Science & Technology, Daejeon 305-350, South Korea, and
| | - Michael G Kemp
- the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7260
| | - Aziz Sancar
- the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7260
| |
Collapse
|
32
|
Hu J, Adar S, Selby CP, Lieb JD, Sancar A. Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution. Genes Dev 2015; 29:948-60. [PMID: 25934506 PMCID: PMC4421983 DOI: 10.1101/gad.261271.115] [Citation(s) in RCA: 192] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hu et al. developed a method for genome-wide mapping of DNA excision repair named XR-seq (excision repair sequencing) and used it to produce stranded, nucleotide-resolution maps of repair of two UV-induced DNA damages in human cells. XR-seq and the resulting repair maps will facilitate studies of the effects of genomic location, chromatin context, transcription, and replication on DNA repair in human cells. We developed a method for genome-wide mapping of DNA excision repair named XR-seq (excision repair sequencing). Human nucleotide excision repair generates two incisions surrounding the site of damage, creating an ∼30-mer. In XR-seq, this fragment is isolated and subjected to high-throughput sequencing. We used XR-seq to produce stranded, nucleotide-resolution maps of repair of two UV-induced DNA damages in human cells: cyclobutane pyrimidine dimers (CPDs) and (6-4) pyrimidine–pyrimidone photoproducts [(6-4)PPs]. In wild-type cells, CPD repair was highly associated with transcription, specifically with the template strand. Experiments in cells defective in either transcription-coupled excision repair or general excision repair isolated the contribution of each pathway to the overall repair pattern and showed that transcription-coupled repair of both photoproducts occurs exclusively on the template strand. XR-seq maps capture transcription-coupled repair at sites of divergent gene promoters and bidirectional enhancer RNA (eRNA) production at enhancers. XR-seq data also uncovered the repair characteristics and novel sequence preferences of CPDs and (6-4)PPs. XR-seq and the resulting repair maps will facilitate studies of the effects of genomic location, chromatin context, transcription, and replication on DNA repair in human cells.
Collapse
Affiliation(s)
- Jinchuan Hu
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
| | - Sheera Adar
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Christopher P Selby
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
| | - Jason D Lieb
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA;
| |
Collapse
|
33
|
Kemp MG, Lindsey-Boltz LA, Sancar A. UV Light Potentiates STING (Stimulator of Interferon Genes)-dependent Innate Immune Signaling through Deregulation of ULK1 (Unc51-like Kinase 1). J Biol Chem 2015; 290:12184-94. [PMID: 25792739 PMCID: PMC4424351 DOI: 10.1074/jbc.m115.649301] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 03/19/2015] [Indexed: 01/04/2023] Open
Abstract
The mechanism by which ultraviolet (UV) wavelengths of sunlight trigger or exacerbate the symptoms of the autoimmune disorder lupus erythematosus is not known but may involve a role for the innate immune system. Here we show that UV radiation potentiates STING (stimulator of interferon genes)-dependent activation of the immune signaling transcription factor interferon regulatory factor 3 (IRF3) in response to cytosolic DNA and cyclic dinucleotides in keratinocytes and other human cells. Furthermore, we find that modulation of this innate immune response also occurs with UV-mimetic chemical carcinogens and in a manner that is independent of DNA repair and several DNA damage and cell stress response signaling pathways. Rather, we find that the stimulation of STING-dependent IRF3 activation by UV is due to apoptotic signaling-dependent disruption of ULK1 (Unc51-like kinase 1), a pro-autophagic protein that negatively regulates STING. Thus, deregulation of ULK1 signaling by UV-induced DNA damage may contribute to the negative effects of sunlight UV exposure in patients with autoimmune disorders.
Collapse
Affiliation(s)
- Michael G Kemp
- From the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
| | - Laura A Lindsey-Boltz
- From the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
| | - Aziz Sancar
- From the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
| |
Collapse
|
34
|
Kemp MG, Gaddameedhi S, Choi JH, Hu J, Sancar A. DNA repair synthesis and ligation affect the processing of excised oligonucleotides generated by human nucleotide excision repair. J Biol Chem 2014; 289:26574-26583. [PMID: 25107903 DOI: 10.1074/jbc.m114.597088] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Ultraviolet (UV) photoproducts are removed from genomic DNA by dual incisions in humans in the form of 24- to 32-nucleotide-long oligomers (canonical 30-mers) by the nucleotide excision repair system. How the small, excised, damage-containing DNA oligonucleotides (sedDNAs) are processed in cells following the dual incision event is not known. Here, we demonstrate that sedDNAs are localized to the nucleus in two biochemically distinct forms, which include chromatin-associated, transcription factor II H-bound complexes and more readily solubilized, RPA-bound complexes. Because the nuclear mobility and repair functions of transcription factor II H and RPA are influenced by post-incision gap-filling events, we examined how DNA repair synthesis and DNA ligation affect sedDNA processing. We found that although these gap filling activities are not essential for the dual incision/sedDNA generation event per se, the inhibition of DNA repair synthesis and ligation is associated with a decrease in UV photoproduct removal rate and an accumulation of RPA-sedDNA complexes in the cell. These findings indicate that sedDNA processing and association with repair proteins following the dual incisions may be tightly coordinated with gap filling during nucleotide excision repair in vivo.
Collapse
Affiliation(s)
- Michael G Kemp
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 and
| | - Shobhan Gaddameedhi
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 and
| | - Jun-Hyuk Choi
- Center for Bioanalysis, Department of Metrology for Quality of Life, Korea Research Institute of Standards and Science, Daejeon 305-340, South Korea
| | - Jinchuan Hu
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 and
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 and.
| |
Collapse
|
35
|
Lee MH, Wang L, Chang ZF. The contribution of mitochondrial thymidylate synthesis in preventing the nuclear genome stress. Nucleic Acids Res 2014; 42:4972-84. [PMID: 24561807 PMCID: PMC4005647 DOI: 10.1093/nar/gku152] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
In quiescent fibroblasts, the expression levels of cytosolic enzymes for thymidine triphosphate (dTTP) synthesis are down-regulated, causing a marked reduction in the dTTP pool. In this study, we provide evidence that mitochondrial thymidylate synthesis via thymidine kinase 2 (TK2) is a limiting factor for the repair of ultraviolet (UV) damage in the nuclear compartment in quiescent fibroblasts. We found that TK2 deficiency causes secondary DNA double-strand breaks formation in the nuclear genome of quiescent cells at the late stage of recovery from UV damage. Despite slower repair of quiescent fibroblast deficient in TK2, DNA damage signals eventually disappeared, and these cells were capable of re-entering the S phase after serum stimulation. However, these cells displayed severe genome stress as revealed by the dramatic increase in 53BP1 nuclear body in the G1 phase of the successive cell cycle. Here, we conclude that mitochondrial thymidylate synthesis via TK2 plays a role in facilitating the quality repair of UV damage for the maintenance of genome integrity in the cells that are temporarily arrested in the quiescent state.
Collapse
Affiliation(s)
- Ming-Hsiang Lee
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan (R.O.C.), Department of Anatomy, Physiology and Biochemistry, The Swedish University of Agricultural Sciences, Biomedical Center, S-751 23 Uppsala, Sweden and Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan (R.O.C.)
| | | | | |
Collapse
|