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Smerdon MJ, Wyrick JJ, Delaney S. A half century of exploring DNA excision repair in chromatin. J Biol Chem 2023; 299:105118. [PMID: 37527775 PMCID: PMC10498010 DOI: 10.1016/j.jbc.2023.105118] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023] Open
Abstract
DNA in eukaryotic cells is packaged into the compact and dynamic structure of chromatin. This packaging is a double-edged sword for DNA repair and genomic stability. Chromatin restricts the access of repair proteins to DNA lesions embedded in nucleosomes and higher order chromatin structures. However, chromatin also serves as a signaling platform in which post-translational modifications of histones and other chromatin-bound proteins promote lesion recognition and repair. Similarly, chromatin modulates the formation of DNA damage, promoting or suppressing lesion formation depending on the chromatin context. Therefore, the modulation of DNA damage and its repair in chromatin is crucial to our understanding of the fate of potentially mutagenic and carcinogenic lesions in DNA. Here, we survey many of the landmark findings on DNA damage and repair in chromatin over the last 50 years (i.e., since the beginning of this field), focusing on excision repair, the first repair mechanism studied in the chromatin landscape. For example, we highlight how the impact of chromatin on these processes explains the distinct patterns of somatic mutations observed in cancer genomes.
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Affiliation(s)
- Michael J Smerdon
- Biochemistry and Biophysics, School of Molecular Biosciences, Washington State University, Pullman, Washington, USA.
| | - John J Wyrick
- Genetics and Cell Biology, School of Molecular Biosciences, Washington State University, Pullman, Washington, USA
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, Rhode Island, USA
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Singh L, Nair L, Kumar D, Arora MK, Bajaj S, Gadewar M, Mishra SS, Rath SK, Dubey AK, Kaithwas G, Choudhary M, Singh M. Hypoxia induced lactate acidosis modulates tumor microenvironment and lipid reprogramming to sustain the cancer cell survival. Front Oncol 2023; 13:1034205. [PMID: 36761981 PMCID: PMC9906992 DOI: 10.3389/fonc.2023.1034205] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/04/2023] [Indexed: 01/26/2023] Open
Abstract
It is well known that solid hypoxic tumour cells oxidise glucose through glycolysis, and the end product of this pathway is fermented into lactate which accumulates in the tumour microenvironment (TME). Initially, it was proclaimed that cancer cells cannot use lactate; therefore, they dump it into the TME and subsequently augment the acidity of the tumour milieu. Furthermore, the TME acts as a lactate sink with stope variable amount of lactate in different pathophysiological condition. Regardless of the amount of lactate pumped out within TME, it disappears immediately which still remains an unresolved puzzle. Recent findings have paved pathway in exploring the main role of lactate acidosis in TME. Cancer cells utilise lactate in the de novo fatty acid synthesis pathway to initiate angiogenesis and invasiveness, and lactate also plays a crucial role in the suppression of immunity. Furthermore, lactate re-programme the lipid biosynthetic pathway to develop a metabolic symbiosis in normoxic, moderately hypoxic and severely hypoxic cancer cells. For instance: severely hypoxic cancer cells enable to synthesizing poly unsaturated fatty acids (PUFA) in oxygen scarcity secretes excess of lactate in TME. Lactate from TME is taken up by the normoxic cancer cells whereas it is converted back to PUFAs after a sequence of reactions and then liberated in the TME to be utilized in the severely hypoxic cancer cells. Although much is known about the role of lactate in these biological processes, the exact molecular pathways that are involved remain unclear. This review attempts to understand the molecular pathways exploited by lactate to initiate angiogenesis, invasiveness, suppression of immunity and cause re-programming of lipid synthesis. This review will help the researchers to develop proper understanding of lactate associated bimodal regulations of TME.
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Affiliation(s)
- Lakhveer Singh
- School of Pharmaceutical & Population Health Informatics, DIT University, Dehradun, India
| | - Lakshmi Nair
- Department of Pharmaceutical Science, Assam University (A Central University), Silchar, Assam, India
| | - Dinesh Kumar
- Department of Pharmaceutical Sciences, Central University of Haryana, Mahendergarh, Haryana, India
| | - Mandeep Kumar Arora
- School of Pharmaceutical & Population Health Informatics, DIT University, Dehradun, India
| | - Sakshi Bajaj
- Chaudhary Devi Lal College of Pharmacy, Yamuna Nagar, India
| | - Manoj Gadewar
- School of Medical and Allied Sciences, KR Mangalam University, Gurgaon, India
| | | | - Santosh Kumar Rath
- School of Pharmaceutical & Population Health Informatics, DIT University, Dehradun, India
| | - Amit Kumar Dubey
- School of Pharmaceutical & Population Health Informatics, DIT University, Dehradun, India
| | - Gaurav Kaithwas
- Department of Pharmaceutical Science, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Manjusha Choudhary
- University Institute of Pharmaceutical Sciences, Kurukshetra University, Kurukshetra, India,*Correspondence: Manjusha Choudhary, ; Manjari Singh,
| | - Manjari Singh
- Department of Pharmaceutical Science, Assam University (A Central University), Silchar, Assam, India,*Correspondence: Manjusha Choudhary, ; Manjari Singh,
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Paillé A, Charton R, Dholandre Q, Conconi A. The Efficiency of Global Genome-Nucleotide Excision Repair is Linked to the Fraction of Open rRNA Gene Chromatin, in Yeast. Photochem Photobiol 2021; 98:696-706. [PMID: 34921417 DOI: 10.1111/php.13580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/13/2021] [Indexed: 11/29/2022]
Abstract
The yeast rDNA locus is a suitable model to study nucleotide excision repair (NER) in chromatin. A portion of rRNA genes is transcribed and largely depleted of nucleosomes, the remaining genes are not transcribed and folded in nucleosomes. In G1-arrested cells, most rRNA genes do not have nucleosomes. TC-NER removes UV-induced DNA lesions from the transcribed strand of active genes. GG-NER is less efficient and removes DNA lesions from the nontranscribed strand of active genes and from the inactive genome. Different from mammalian cells, in yeast, the rRNA gene-transcribed strand is repaired by RNA polymerase-I-dependent TC-NER. The opposite nontranscribed strand is repaired faster than both strands of inactive rRNA genes. In log-phase cells, RNA polymerase-I are dislodged from the damaged transcribed strand and partially replaced by nucleosomes. Contrary to log-phase cells, in G1-phase cells few, if any, histones are deposited on the open rRNA genes during NER. In this study, we compared GG-NER efficiency in the rRNA gene coding region: without nucleosomes, partially loaded or wholly loaded with nucleosomes. The results indicate that in log-phase cells histones obstruct GG-NER, whereas in G1-phase cells GG-NER is as efficient as TC-NER.
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Affiliation(s)
- Audrey Paillé
- Département de Microbiologie et Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada
| | - Romain Charton
- Département de Microbiologie et Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada
| | - Quentin Dholandre
- Département de Microbiologie et Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada
| | - Antonio Conconi
- Département de Microbiologie et Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada
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Mechanistic insights in transcription-coupled nucleotide excision repair of ribosomal DNA. Proc Natl Acad Sci U S A 2018; 115:E6770-E6779. [PMID: 29967171 DOI: 10.1073/pnas.1716581115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nucleotide excision repair (NER) guarantees genome integrity against UV light-induced DNA damage. After UV irradiation, cells have to cope with a general transcriptional block. To ensure UV lesions repair specifically on transcribed genes, NER is coupled with transcription in an extremely organized pathway known as transcription-coupled repair. In highly metabolic cells, more than 60% of total cellular transcription results from RNA polymerase I activity. Repair of the mammalian transcribed ribosomal DNA has been scarcely studied. UV lesions severely block RNA polymerase I activity and the full transcription-coupled repair machinery corrects damage on actively transcribed ribosomal DNAs. After UV irradiation, RNA polymerase I is more bound to the ribosomal DNA and both are displaced to the nucleolar periphery. Importantly, the reentry of RNA polymerase I and the ribosomal DNA is dependent on the presence of UV lesions on DNA and independent of transcription restart.
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Guintini L, Tremblay M, Toussaint M, D'Amours A, Wellinger RE, Wellinger RJ, Conconi A. Repair of UV-induced DNA lesions in natural Saccharomyces cerevisiae telomeres is moderated by Sir2 and Sir3, and inhibited by yKu-Sir4 interaction. Nucleic Acids Res 2017; 45:4577-4589. [PMID: 28334768 PMCID: PMC5416773 DOI: 10.1093/nar/gkx123] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 02/10/2017] [Indexed: 01/28/2023] Open
Abstract
Ultraviolet light (UV) causes DNA damage that is removed by nucleotide excision repair (NER). UV-induced DNA lesions must be recognized and repaired in nucleosomal DNA, higher order structures of chromatin and within different nuclear sub-compartments. Telomeric DNA is made of short tandem repeats located at the ends of chromosomes and their maintenance is critical to prevent genome instability. In Saccharomyces cerevisiae the chromatin structure of natural telomeres is distinctive and contingent to telomeric DNA sequences. Namely, nucleosomes and Sir proteins form the heterochromatin like structure of X-type telomeres, whereas a more open conformation is present at Y’-type telomeres. It is proposed that there are no nucleosomes on the most distal telomeric repeat DNA, which is bound by a complex of proteins and folded into higher order structure. How these structures affect NER is poorly understood. Our data indicate that the X-type, but not the Y’-type, sub-telomeric chromatin modulates NER, a consequence of Sir protein-dependent nucleosome stability. The telomere terminal complex also prevents NER, however, this effect is largely dependent on the yKu–Sir4 interaction, but Sir2 and Sir3 independent.
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Affiliation(s)
- Laetitia Guintini
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke J1E 4K8, Canada
| | - Maxime Tremblay
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke J1E 4K8, Canada
| | - Martin Toussaint
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke J1E 4K8, Canada
| | - Annie D'Amours
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke J1E 4K8, Canada
| | - Ralf E Wellinger
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla, CSIC, Avda Américo Vespucio s/n, Sevilla 41092, Spain
| | - Raymund J Wellinger
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke J1E 4K8, Canada
| | - Antonio Conconi
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke J1E 4K8, Canada
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Peyresaubes F, Zeledon C, Guintini L, Charton R, Muguet A, Conconi A. RNA Polymerase-I-Dependent Transcription-coupled Nucleotide Excision Repair of UV-Induced DNA Lesions at Transcription Termination Sites, in Saccharomyces cerevisiae. Photochem Photobiol 2017; 93:363-374. [PMID: 27935059 DOI: 10.1111/php.12690] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 11/16/2016] [Indexed: 11/28/2022]
Abstract
If not repaired, ultraviolet light-induced DNA damage can lead to genome instability. Nucleotide excision repair (NER) of UV photoproducts is generally fast in the coding region of genes, where RNA polymerase-II (RNAP2) arrest at damage sites and trigger transcription-coupled NER (TC-NER). In Saccharomyces cerevisiae, there is RNA polymerase-I (RNAP1)-dependent TC-NER, but this process remains elusive. Therefore, we wished to characterize TC-NER efficiency in different regions of the rDNA locus: where RNAP1 are present at high density and start transcription elongation, where the elongation rate is slow, and in the transcription terminator where RNAP1 pause, accumulate and then are released. The Rpa12 subunit of RNAP1 and the Nsi1 protein participate in transcription termination, and NER efficiency was compared between wild type and cells lacking Rpa12 or Nsi1. The presence of RNAP1 was determined by chromatin endogenous cleavage and chromatin immunoprecipitation, and repair was followed at nucleotide precision with an assay that is based on the blockage of Taq polymerase by UV photoproducts. We describe that TC-NER, which is modulated by the RNAP1 level and elongation rate, ends at the 35S rRNA gene transcription termination site.
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Affiliation(s)
- François Peyresaubes
- Département de Microbiologie et Infectiologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Carlos Zeledon
- Département de Microbiologie et Infectiologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Laetitia Guintini
- Département de Microbiologie et Infectiologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Romain Charton
- Département de Microbiologie et Infectiologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Alexia Muguet
- Département de Microbiologie et Infectiologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Antonio Conconi
- Département de Microbiologie et Infectiologie, Université de Sherbrooke, Sherbrooke, QC, Canada
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Waters R, van Eijk P, Reed S. Histone modification and chromatin remodeling during NER. DNA Repair (Amst) 2015; 36:105-113. [DOI: 10.1016/j.dnarep.2015.09.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Peyresaubes F, D'Amours A, Leduc F, Grégoire MC, Boissonneault G, Conconi A. Immuno-capture of UVDE generated 3'-OH ends at UV photoproducts. DNA Repair (Amst) 2015; 36:156-161. [PMID: 26547444 DOI: 10.1016/j.dnarep.2015.09.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A strategy amenable to the genome-wide study of DNA damage and repair kinetics is described. The ultraviolet damage endonuclease (UVDE) generates 3'-OH ends at the two major UV induced DNA lesions, cyclobutane pyrimidine dimers (CPDs) and 6,4 pyrimidine-pyrimidone dimers (6,4 PPs), allowing for their capture after biotin end-labeling. qPCR amplification of biotinylated DNA enables parallel measuring of DNA damage in several loci, which can then be combined with high-throughput screening of cell survival to test genotoxic reagents. Alternatively, a library of captured sequences could be generated for a genome wide study of damage sites and large-scale assessment of repair kinetics in different regions of the genome, using next-generation sequencing. The assay is suitable to study any DNA lesion that can be converted into 3'-OH by UVDE, or other enzymes. Toward these goals, we compared UVDE with the classical T4 endonuclease V (T4V) assay. We showed that there is a linear correlation between UV dose, 3'-OH formation and capture by immunoprecipitation, together with its potential application for in vivo studies.
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Affiliation(s)
- François Peyresaubes
- Département de Microbiologie et Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Annie D'Amours
- Département de Microbiologie et Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; Département de Biochimie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Frédéric Leduc
- Département de Biochimie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Marie-Chantal Grégoire
- Département de Biochimie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Guylain Boissonneault
- Département de Biochimie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
| | - Antonio Conconi
- Département de Microbiologie et Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
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Charton R, Guintini L, Peyresaubes F, Conconi A. Repair of UV induced DNA lesions in ribosomal gene chromatin and the role of "Odd" RNA polymerases (I and III). DNA Repair (Amst) 2015; 36:49-58. [PMID: 26411875 DOI: 10.1016/j.dnarep.2015.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In fast growing eukaryotic cells, a subset of rRNA genes are transcribed at very high rates by RNA polymerase I (RNAPI). Nuclease digestion-assays and psoralen crosslinking have shown that they are open; that is, largely devoid of nucleosomes. In the yeast Saccharomyces cerevisae, nucleotide excision repair (NER) and photolyase remove UV photoproducts faster from open rRNA genes than from closed and nucleosome-loaded inactive rRNA genes. After UV irradiation, rRNA transcription declines because RNAPI halt at UV photoproducts and are then displaced from the transcribed strand. When the DNA lesion is quickly recognized by NER, it is the sub-pathway transcription-coupled TC-NER that removes the UV photoproduct. If dislodged RNAPI are replaced by nucleosomes before NER recognizes the lesion, then it is the sub-pathway global genome GG-NER that removes the UV photoproducts from the transcribed strand. Also, GG-NER maneuvers in the non-transcribed strand of open genes and in both strands of closed rRNA genes. After repair, transcription resumes and elongating RNAPI reopen the rRNA gene. In higher eukaryotes, NER in rRNA genes is inefficient and there is no evidence for TC-NER. Moreover, TC-NER does not occur in RNA polymerase III transcribed genes of both, yeast and human fibroblast.
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Affiliation(s)
- Romain Charton
- Département de Microbiologie et Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Laetitia Guintini
- Département de Microbiologie et Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - François Peyresaubes
- Département de Microbiologie et Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Antonio Conconi
- Département de Microbiologie et Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
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Krasikova YS, Rechkunova NI, Maltseva EA, Anarbaev RO, Pestryakov PE, Sugasawa K, Min JH, Lavrik OI. Human and yeast DNA damage recognition complexes bind with high affinity DNA structures mimicking in size transcription bubble. J Mol Recognit 2014; 26:653-61. [PMID: 24277610 DOI: 10.1002/jmr.2308] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 07/26/2013] [Accepted: 08/06/2013] [Indexed: 02/05/2023]
Abstract
The human XPC-RAD23B complex and its yeast ortholog, Rad4-Rad23, are the primary initiators of global genome nucleotide excision repair. In this study, two types of DNA binding assays were used for the detailed analysis of interaction of these proteins with damaged DNA. An electrophoretic mobility shift assay revealed that human and yeast orthologs behave similarly in DNA binding. Quantitative analyses of XPC/Rad4 binding to the model DNA structures were performed using fluorescent depolarization measurements. The XPC-RAD23B and the Rad4-Rad23 proteins bind to the damaged 15 nt bubble-DNA structure mimicking in size the "transcription bubble" DNA intermediate with the highest affinity (KD values ~10(-10) M or less) that is reduced in the following order: damaged bubble > undamaged bubble > damaged duplex > undamaged duplex. The affinity of XPC/Rad4 for various DNAs was shown to correlate with DNA bending angle. The results obtained show clearly that more deviation from regular DNA structure leads to higher XPC/Rad4 affinity.
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Affiliation(s)
- Yuliya S Krasikova
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
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Abstract
DNA repair mechanisms are critical for maintaining the integrity of genomic DNA, and their loss is associated with cancer predisposition syndromes. Studies in Saccharomyces cerevisiae have played a central role in elucidating the highly conserved mechanisms that promote eukaryotic genome stability. This review will focus on repair mechanisms that involve excision of a single strand from duplex DNA with the intact, complementary strand serving as a template to fill the resulting gap. These mechanisms are of two general types: those that remove damage from DNA and those that repair errors made during DNA synthesis. The major DNA-damage repair pathways are base excision repair and nucleotide excision repair, which, in the most simple terms, are distinguished by the extent of single-strand DNA removed together with the lesion. Mistakes made by DNA polymerases are corrected by the mismatch repair pathway, which also corrects mismatches generated when single strands of non-identical duplexes are exchanged during homologous recombination. In addition to the true repair pathways, the postreplication repair pathway allows lesions or structural aberrations that block replicative DNA polymerases to be tolerated. There are two bypass mechanisms: an error-free mechanism that involves a switch to an undamaged template for synthesis past the lesion and an error-prone mechanism that utilizes specialized translesion synthesis DNA polymerases to directly synthesize DNA across the lesion. A high level of functional redundancy exists among the pathways that deal with lesions, which minimizes the detrimental effects of endogenous and exogenous DNA damage.
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Tremblay M, Charton R, Wittner M, Levasseur G, Griesenbeck J, Conconi A. UV light-induced DNA lesions cause dissociation of yeast RNA polymerases-I and establishment of a specialized chromatin structure at rRNA genes. Nucleic Acids Res 2013; 42:380-95. [PMID: 24097442 PMCID: PMC3874186 DOI: 10.1093/nar/gkt871] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The cytotoxicity of UV light-induced DNA lesions results from their interference with transcription and replication. DNA lesions arrest elongating RNA polymerases, an event that triggers transcription-coupled nucleotide excision repair. Since arrested RNA polymerases reduce the accessibility of repair factors to DNA lesions, they might be displaced. The fate of arrested RNA polymerases-II at DNA lesions has been extensively studied, yielding partially contradictory results. Considerably less is known about RNA polymerases-I that transcribe nucleosomes-depleted rRNA genes at very high rate. To investigate the fate of arrested RNA polymerases-I at DNA lesions, chromatin-immunoprecipitation, electron microscopy, transcription run-on, psoralen-cross-linking and chromatin-endogenous cleavage were employed. We found that RNA polymerases-I density increased at the 5′-end of the gene, likely due to continued transcription initiation followed by elongation and pausing/release at the first DNA lesion. Most RNA polymerases-I dissociated downstream of the first DNA lesion, concomitant with chromatin closing that resulted from deposition of nucleosomes. Although nucleosomes were deposited, the high mobility group-box Hmo1 (component of actively transcribed rRNA genes) remained associated. After repair of DNA lesions, Hmo1 containing chromatin might help to restore transcription elongation and reopening of rRNA genes chromatin.
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Affiliation(s)
- Maxime Tremblay
- Département de Microbiologie et Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada and Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, 93053 Regensburg, Germany
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Lafrance-Vanasse J, Arseneault G, Cappadocia L, Legault P, Omichinski JG. Structural and functional evidence that Rad4 competes with Rad2 for binding to the Tfb1 subunit of TFIIH in NER. Nucleic Acids Res 2013; 41:2736-45. [PMID: 23295669 PMCID: PMC3575800 DOI: 10.1093/nar/gks1321] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
XPC/Rad4 (human/yeast) recruits transcription faction IIH (TFIIH) to the nucleotide excision repair (NER) complex through interactions with its p62/Tfb1 and XPB/Ssl2 subunits. TFIIH then recruits XPG/Rad2 through interactions with similar subunits and the two repair factors appear to be mutually exclusive within the NER complex. Here, we show that Rad4 binds the PH domain of the Tfb1 (Tfb1PH) with high affinity. Structural characterization of a Rad4–Tfb1PH complex demonstrates that the Rad4-binding interface is formed using a motif similar to one used by Rad2 to bind Tfb1PH. In vivo studies in yeast demonstrate that the N-terminal Tfb1-binding motif and C-terminal TFIIH-binding motif of Rad4 are both crucial for survival following exposure to UV irradiation. Together, these results support the hypothesis that XPG/Rad2 displaces XPC/Rad4 from the repair complex in part through interactions with the Tfb1/p62 subunit of TFIIH. The Rad4–Tfb1PH structure also provides detailed information regarding, not only the interplay of TFIIH recruitment to the NER, but also links the role of TFIIH in NER and transcription.
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Affiliation(s)
- Julien Lafrance-Vanasse
- Département de Biochimie, Université de Montréal C.P. 6128 Succursale Centre-Ville, Montréal, Québec, Canada H3C 3J7
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Waters R, Evans K, Bennett M, Yu S, Reed S. Nucleotide excision repair in cellular chromatin: studies with yeast from nucleotide to gene to genome. Int J Mol Sci 2012; 13:11141-11164. [PMID: 23109843 PMCID: PMC3472735 DOI: 10.3390/ijms130911141] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 08/22/2012] [Accepted: 08/24/2012] [Indexed: 11/16/2022] Open
Abstract
Here we review our development of, and results with, high resolution studies on global genome nucleotide excision repair (GGNER) in Saccharomyces cerevisiae. We have focused on how GGNER relates to histone acetylation for its functioning and we have identified the histone acetyl tranferase Gcn5 and acetylation at lysines 9/14 of histone H3 as a major factor in enabling efficient repair. We consider results employing primarily MFA2 as a model gene, but also those with URA3 located at subtelomeric sequences. In the latter case we also see a role for acetylation at histone H4. We then go on to outline the development of a high resolution genome-wide approach that enables one to examine correlations between histone modifications and the nucleotide excision repair (NER) of UV-induced cyclobutane pyrimidine dimers throughout entire genomes. This is an approach that will enable rapid advances in understanding the complexities of how compacted chromatin in chromosomes is processed to access DNA damage and then returned to its pre-damaged status to maintain epigenetic codes.
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Affiliation(s)
- Raymond Waters
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +44-29-2068-7336; Fax: +44-29-2074-4276
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Pelloux J, Tremblay M, Wellinger RJ, Conconi A. UV-induced DNA damage and DNA repair in ribosomal genes chromatin. Methods Mol Biol 2012; 809:303-320. [PMID: 22113285 DOI: 10.1007/978-1-61779-376-9_21] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Cyclobutane pyrimidine dimers (CPDs) and (6,4) pyrimidine-pyrimidone dimers are the major DNA lesions (or photoproducts) induced by ultraviolet light and are removed by the nucleotide excision repair (NER) pathway. If not repaired, DNA damage can lead to genome instability. The genome is organized into nuclear domains with distinct functions and chromatin structures. Although studies on NER in all chromosomal contexts are important to understand the mechanisms of genome maintenance, we focused on NER in the nucleolus. The attractive feature of the rDNA locus is its chromatin structure; not all rRNA genes are transcribed and both active (no nucleosomes) and inactive (nucleosomes) rRNA genes coexist in the nucleolus. These characteristics allow for direct comparison of NER in two very different chromatin structures. Yeast is used as a model system and the methods employed are as follows: nuclei isolation, restriction enzyme digestion of chromatin to release active rRNA genes, psoralen cross-linking, T4-endonuclease-V enzyme to detect CPDs and CPDs repair over relatively large stretches of DNA, and primer extension to follow DNA damage and repair at nucleotide level. Using this approach, we have shown that NER is faster in nonnucleosomes vs. nucleosomes rDNA, that the formation of CPDs promotes changes in the active rDNA chromatin, and that NER is coupled to rRNA genes transcription.
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Affiliation(s)
- Julie Pelloux
- Département de Microbiologie et Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC, Canada
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Toussaint M, Wellinger RJ, Conconi A. Differential participation of homologous recombination and nucleotide excision repair in yeast survival to ultraviolet light radiation. Mutat Res 2010; 698:52-9. [PMID: 20348017 DOI: 10.1016/j.mrgentox.2010.03.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 02/16/2010] [Accepted: 03/20/2010] [Indexed: 01/17/2023]
Abstract
AIMS The purpose of this research was to assess the ultraviolet light (UV) phenotype of yeast sirDelta cells vs. WT cells, and to determine whether de-silenced chromatin or the intrinsic pseudoploidy of sirDelta mutants contributes to their response to UV. Additional aims were to study the participation of HR and NER in promoting UV survival during the cell cycle, and to define the extent of the co-participation for both repair pathways. MAIN METHODS The sensitivity of yeast Saccharomyces cerevisiae to UV light was determined using a method based on automatic measurements of optical densities of very small (100mul) liquid cell cultures. KEY FINDINGS We show that pseudo-diploidy of sirDelta strains promotes resistance to UV irradiation and that HR is the main mechanism that is responsible for this phenotype. In addition, HR together with GG-NER renders cells in the G2-phase of the cell cycle more resistant to UV irradiation than cells in the G1-phase, which underscore the importance of HR when two copies of the chromosomes are present. Nevertheless, in asynchronously growing cells NER is the main repair pathway that responds to UV induced DNA damage. SIGNIFICANCE This study provides detailed and quantitative information on the co-participation of HR and NER in UV survival of yeast cells.
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Affiliation(s)
- Martin Toussaint
- Département de Microbiologie et d'Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
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Tremblay M, Toussaint M, D'Amours A, Conconi A. Nucleotide excision repair and photolyase repair of UV photoproducts in nucleosomes: assessing the existence of nucleosome and non-nucleosome rDNA chromatin in vivo. Biochem Cell Biol 2009; 87:337-46. [PMID: 19234545 DOI: 10.1139/o08-128] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The genome is organized into nuclear domains, which create microenvironments that favor distinct chromatin structures and functions (e.g., highly repetitive sequences, centromeres, telomeres, noncoding sequences, inactive genes, RNA polymerase II and III transcribed genes, and the nucleolus). Correlations have been drawn between gene silencing and proximity to a heterochromatic compartment. At the other end of the scale are ribosomal genes, which are transcribed at a very high rate by RNA polymerase I (~60% of total transcription), have a loose chromatin structure, and are clustered in the nucleolus. The rDNA sequences have 2 distinct structures: active rRNA genes, which have no nucleosomes; and inactive rRNA genes, which have nucleosomes. Like DNA transcription and replication, DNA repair is modulated by the structure of chromatin, and the kinetics of DNA repair vary among the nuclear domains. Although research on DNA repair in all chromosomal contexts is important to understand the mechanisms of genome maintenance, this review focuses on nucleotide excision repair and photolyase repair of UV photoproducts in the first-order packing of DNA in chromatin: the nucleosome. In addition, it summarizes the studies that have demonstrated the existence of the 2 rDNA chromatins, and the way this feature of the rDNA locus allows for direct comparison of DNA repair in 2 very different structures: nucleosome and non-nucleosome DNA.
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Affiliation(s)
- Maxime Tremblay
- Departement de Microbiologie et Infectiologie, Faculte de Medecine, Universite de Sherbrooke, Sherbrooke, QCJ1H5N4, Canada
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Lux ex tenebris: nucleotide resolution DNA repair and nucleosome mapping. Methods 2009; 48:23-34. [PMID: 19269326 DOI: 10.1016/j.ymeth.2009.02.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Accepted: 02/25/2009] [Indexed: 11/21/2022] Open
Abstract
In recent years a great deal of progress has been made in understanding how the various DNA repair mechanisms function when DNA is assembled into chromatin. In the case of nucleotide excision repair, a core group of DNA repair proteins is required in vitro to observe DNA repair activity in damaged DNA devoid of chromatin structure. This group of proteins is not sufficient to promote repair in the same DNA when assembled into nucleosomes; the first level of chromatin compaction. Clearly other factors are required for efficient DNA repair of chromatin. For some time chromatin has been considered a barrier to be overcome, and inhibitory to DNA metabolic processes including DNA repair. However, an emerging picture suggests a fascinating link at the interface of chromatin metabolism and DNA repair. In this view these two fundamental processes are mechanistically intertwined and function in concert to bring about regulated DNA repair throughout the genome. Light from the darkness has come as a result of many elegant studies performed by a number of research groups. Here we describe two techniques developed in our laboratories which we hope have contributed to our understanding in this arena.
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Waters R, Teng Y, Yu Y, Yu S, Reed SH. Tilting at windmills? The nucleotide excision repair of chromosomal DNA. DNA Repair (Amst) 2008; 8:146-52. [PMID: 19041427 DOI: 10.1016/j.dnarep.2008.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2008] [Indexed: 10/21/2022]
Abstract
A typical view of how DNA repair functions in chromatin usually depicts a struggle in which the DNA repair machinery battles to overcome the inhibitory effect of chromatin on the repair process. It may be that in this current interpretation the repair mechanisms are 'tilting at windmills', fighting an imaginary foe. An emerging picture suggests that we should not consider chromatin as an inhibitory force to be overcome like some quixotic giant by the DNA repair processes. Instead we should now recognize that DNA repair and chromatin metabolism are inextricably and mechanistically linked. Here we discuss the latest findings which are beginning to reveal how changes in chromatin dynamics integrate with the DNA repair process in response to UV induced DNA damage, with an emphasis on events in the yeast Saccharomyces cerevisiae.
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Affiliation(s)
- Raymond Waters
- Department of Pathology, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
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