Chromosomal landscape of UV damage formation and repair at single-nucleotide resolution

Mao, Peng; Smerdon, Michael J.; Roberts, Steven A.; Wyrick, John J.

doi:10.1073/pnas.1606667113

Cited by 140 publications

(275 citation statements)

References 43 publications

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“…Comparing in vivo and in vitro damage formation at nucleosomes indicates nucleosome binding affords a small degree of protection from cisplatin damage formation. We do not observe the strong effect of nucleosome rotational setting on damage formation as was reported for CPDs in a recent highresolution study in yeast (25). This observation may be due to an inherent difference between cisplatin and UV damage formation, or between yeast and human nucleosome organization.…”

Section: Discussioncontrasting

confidence: 82%

“…Methods for mapping cisplatin (21) and UV (21-26) damage in yeast and human cells have been described. However, whereas CPDs can be mapped at high resolution (22,25), the utility of mapping of cisplatin has been limited because of the low resolution and the lack of strandedness. Moreover, these maps were not accompanied with the corresponding repair maps, which are necessary for making extrapolations vis a vis damage locationrepair-biological end points.…”

Section: Discussionmentioning

confidence: 99%

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Cisplatin DNA damage and repair maps of the human genome at single-nucleotide resolution

Lieb

Sancar

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

171

191

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Cisplatin is a major anticancer drug that kills cancer cells by damaging their DNA. Cancer cells cope with the drug by removal of the damages with nucleotide excision repair. We have developed methods to measure cisplatin adduct formation and its repair at single-nucleotide resolution. "Damage-seq" relies on the replication-blocking properties of the bulky base lesions to precisely map their location. "XR-seq" independently maps the removal of these damages by capturing and sequencing the excised oligomer released during repair. The damage and repair maps we generated reveal that damage distribution is essentially uniform and is dictated mostly by the underlying sequence. In contrast, cisplatin repair is heterogeneous in the genome and is affected by multiple factors including transcription and chromatin states. Thus, the overall effect of damages in the genome is primarily driven not by damage formation but by the repair efficiency. The combination of the Damageseq and XR-seq methods has the potential for developing novel cancer therapeutic strategies.] is a major frontline drug in the treatment of lung, colorectal, ovarian, and head-and-neck cancers (1) and has been used in the clinic since 1978. It kills cancer cells by damaging their DNA, mainly by forming Pt-d(GpG) and, to a lesser extent, Pt-d(ApG), Pt-d(GpXpG) intrastrand diadduct, and at lower frequency, Pt-G-G interstrand cross-links (2-4). The cisplatin-induced damage is repaired by nucleotide excision repair (5-8). In excision repair, the damage in DNA is excised from the genome as a single-stranded oligomer of ∼30 nt. The single-stranded gap in the genome is filled in by DNA polymerases and ligated, resulting in error-free repair. Although cisplatin is effective in the treatment of the indicated types of cancers, in some of the cases, drug resistance is observed. The cause of the resistance is multifactorial, and DNA repair is considered to be one of the contributing factors, although the degree to which DNA repair contributes to resistance is still unclear. Here, we describe the development of methods to measure cisplatin adduct formation and repair at single-nucleotide resolution. Using these methods, named "Damage-seq" and "eXcision Repairseq" (XR-seq), we have generated single-nucleotide resolution maps for both the damage induced by cisplatin and its removal by nucleotide excision repair (9, 10). Our method should be applicable for studying drug resistance and for optimization of cancer chemotherapy regimens. ResultsIn this work, we present the cisplatin damage and repair maps for the entire genome of the human lymphocyte cell line GM12878. This cell line was chosen because it has been extensively characterized by the ENCODE project (11). Similar experiments with oxaliplatin, a third generation derivative of cisplatin, yielded similar results and are presented in SI Appendix, SI Materials and Methods. All experiments were performed with two biological replicates.Cisplatin DNA Damage Map. We developed the method of Damage-seq based on the fact th...

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Section: Discussioncontrasting

confidence: 82%

Section: Discussionmentioning

confidence: 99%

Cisplatin DNA damage and repair maps of the human genome at single-nucleotide resolution

Lieb

Sancar

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

171

191

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“…10,25 These latter observations are consistent with the XPC binding results. However, in intact cells, the binding of XPC to the CPD lesion is primarily mediated by the DNA damage binding protein DDB2 that is part of the UV-DDB1/2 complex, 28−30 although the repair of CPD in intact cells is still significantly slower than the removal of the 6–4 lesions that are directly recognized by XPC. 23,26,30 While the thymine dimer T^T CPD opposite its canonical adenine (AA) bases in the complementary strand is NER-resistant, it becomes an excellent substrate of NER when these AA bases are replaced by “mismatched” GG.…”

Section: Recognition Of Dna Damage and Initiation Of Gg-nermentioning

confidence: 99%

Repair-Resistant DNA Lesions

Geacintov

Broyde

2017

Chem. Res. Toxicol.

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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.

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“…BPDE preferentially forms bulky covalent DNA adducts at N2 position of guanines and causes mutations if these BPDE-deoxyguanosines (BPDE-dGs) are not efficiently eliminated by nucleotide excision repair (3). Various methods of varying resolutions have been developed for mapping DNA damage and repair genome-wide (4)(5)(6)(7)(8)(9). We previously reported a method, termed excision repair-sequencing (XR-seq), for mapping nucleotide excision repair (6).…”

mentioning

confidence: 99%

Human genome-wide repair map of DNA damage caused by the cigarette smoke carcinogen benzo[a]pyrene

Adebali

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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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. N ucleotide excision repair is a versatile repair pathway that removes a variety of DNA damages, including UV-and benzo[a]pyrene (BaP)-induced DNA damages. BaP, a widespread carcinogen, is the major cause of lung cancer (1). It is produced by incomplete combustion of organic materials and converted to the ultimate mutagen, BaP diol epoxide (BPDE), through enzymatic metabolism (2). BPDE preferentially forms bulky covalent DNA adducts at N2 position of guanines and causes mutations if these BPDE-deoxyguanosines (BPDE-dGs) are not efficiently eliminated by nucleotide excision repair (3). Various methods of varying resolutions have been developed for mapping DNA damage and repair genome-wide (4-9). We previously reported a method, termed excision repair-sequencing (XR-seq), for mapping nucleotide excision repair (6). This method has been used to generate excision repair maps for UV-induced cyclobutane pyrimidine dimers (CPDs) and (6-4)pyrimidine-pyrimidone photoproducts [(6-4)PPs], as well as cisplatin and oxaliplatin-induced Pt-d(GpG) diadducts for the human genome and CPDs for the Escherichia coli genome (10-12).Although the XR-seq method has been quite useful in determining the effects of various factors, such as genetic background, transcription, posttranscriptional histone modification, and chromatin states, on the timing and efficiency of repair (13), the method in its original form requires the reversal of damage in the excised oligonucleotide (26-27 mers in humans and 12-13 mers in E. coli) by enzymatic or chemical means before it can be processed for nextgeneration sequencing (NGS) and generation of repair maps. As such, this method has limitations, because it is not possible to reverse, either enzymatically or chemically, most DNA lesions removed f...

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Chromosomal landscape of UV damage formation and repair at single-nucleotide resolution

Cited by 140 publications

References 43 publications

Cisplatin DNA damage and repair maps of the human genome at single-nucleotide resolution

Cisplatin DNA damage and repair maps of the human genome at single-nucleotide resolution

Repair-Resistant DNA Lesions

Human genome-wide repair map of DNA damage caused by the cigarette smoke carcinogen benzo[a]pyrene

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