1
|
Shilkin ES, Petrova DV, Novikova AA, Boldinova EO, Zharkov DO, Makarova AV. Methylation and hydroxymethylation of cytosine alter activity and fidelity of translesion DNA polymerases. DNA Repair (Amst) 2024; 141:103712. [PMID: 38959714 DOI: 10.1016/j.dnarep.2024.103712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/24/2024] [Accepted: 06/11/2024] [Indexed: 07/05/2024]
Abstract
Epigenetic cytosine methylation covers most of genomic CpG dinucleotides in human cells. In addition to common deamination-mediated mutagenesis at CpG sites, an alternative deamination-independent pathway associated with DNA polymerase activity was previously described. This mutagenesis is characterized by the TCG→TTG mutational signature and is believed to arise from dAMP misincorporation opposite 5-methylcytosine (mC) or its oxidized derivative 5-hydroxymethylcytosine (hmC) by B-family replicative DNA polymerases with disrupted proofreading 3→5'-exonuclease activity. In addition to being less stable and pro-mutagenic themselves, cytosine modifications also increase the risk of adjacent nucleotides damage, including the formation of 8-oxo-2'-deoxyguanosine (8-oxoG), a well-known mutagenic lesion. The effect of cytosine methylation on error-prone DNA polymerases lacking proofreading activity and involved in repair and DNA translesion synthesis remains unexplored. Here we analyze the efficiency and fidelity of translesion Y-family polymerases (Pol κ, Pol η, Pol ι and REV1) and primase-polymerase PrimPol opposite mC and hmC as well as opposite 8-oxoG adjacent to mC in the TCG context. We demonstrate that epigenetic cytosine modifications suppress Pol ι and REV1 activities and lead to increasing dAMP misincorporation by PrimPol, Pol κ and Pol ι in vitro. Cytosine methylation also increases misincorporation of dAMP opposite the adjacent 8-oxoG by PrimPol, decreases the TLS activity of Pol η opposite the lesion but increases dCMP incorporation opposite 8-oxoG by REV1. Altogether, these data suggest that methylation and hydroxymethylation of cytosine alter activity and fidelity of translesion DNA polymerases.
Collapse
Affiliation(s)
- Evgeniy S Shilkin
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow 123182, Russia; Institute of Gene Biology of Russian Academy of Sciences, Moscow 119334, Russia
| | - Daria V Petrova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 63009, Russia
| | - Anna A Novikova
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow 123182, Russia; Institute of Gene Biology of Russian Academy of Sciences, Moscow 119334, Russia
| | - Elizaveta O Boldinova
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow 123182, Russia; Institute of Gene Biology of Russian Academy of Sciences, Moscow 119334, Russia
| | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 63009, Russia.
| | - Alena V Makarova
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow 123182, Russia; Institute of Gene Biology of Russian Academy of Sciences, Moscow 119334, Russia.
| |
Collapse
|
2
|
Hsu CW, Conrad JW, Sowers ML, Baljinnyam T, Herring JL, Hackfeld LC, Hatch SS, Sowers LC. A combinatorial system to examine the enzymatic repair of multiply damaged DNA substrates. Nucleic Acids Res 2022; 50:7406-7419. [PMID: 35776119 PMCID: PMC9303388 DOI: 10.1093/nar/gkac530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/18/2022] [Accepted: 06/07/2022] [Indexed: 12/03/2022] Open
Abstract
DNA damage drives genetic mutations that underlie the development of cancer in humans. Multiple pathways have been described in mammalian cells which can repair this damage. However, most work to date has focused upon single lesions in DNA. We present here a combinatorial system which allows assembly of duplexes containing single or multiple types of damage by ligating together six oligonucleotides containing damaged or modified bases. The combinatorial system has dual fluorescent labels allowing examination of both strands simultaneously, in order to study interactions or competition between different DNA repair pathways. Using this system, we demonstrate how repair of oxidative damage in one DNA strand can convert a mispaired T:G deamination intermediate into a T:A mutation. We also demonstrate that slow repair of a T:G mispair, relative to a U:G mispair, by the human methyl-binding domain 4 DNA glycosylase provides a competitive advantage to competing repair pathways, and could explain why CpG dinucleotides are hotspots for C to T mutations in human tumors. Data is also presented that suggests repair of closely spaced lesions in opposing strands can be repaired by a combination of short and long-patch base excision repair and simultaneous repair of multiply damage sites can potentially lead to lethal double strand breaks.
Collapse
Affiliation(s)
- Chia Wei Hsu
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.,MD-PhD Combined Degree Program, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - James W Conrad
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Mark L Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.,MD-PhD Combined Degree Program, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Tuvshintugs Baljinnyam
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Jason L Herring
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Linda C Hackfeld
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Sandra S Hatch
- Department of Radiation Oncology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.,Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lawrence C Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.,Department of Internal Medicine, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| |
Collapse
|
3
|
DNA Methylation Biomarkers for Prediction of Response to Platinum-Based Chemotherapy: Where Do We Stand? Cancers (Basel) 2022; 14:cancers14122918. [PMID: 35740584 PMCID: PMC9221086 DOI: 10.3390/cancers14122918] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/10/2022] [Accepted: 06/11/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Platinum-based agents are one of the most widely used chemotherapy drugs for various types of cancer. However, one of the main challenges in the application of platinum drugs is resistance, which is currently being widely investigated. Epigenetic DNA methylation-based biomarkers are promising to aid in the selection of patients, helping to foresee their platinum therapy response in advance. These biomarkers enable minimally invasive patient sample collection, short analysis, and good sensitivity. Hence, improved methodologies for the detection and quantification of DNA methylation biomarkers will facilitate their use in the choice of an optimal treatment strategy. Abstract Platinum-based chemotherapy is routinely used for the treatment of several cancers. Despite all the advances made in cancer research regarding this therapy and its mechanisms of action, tumor resistance remains a major concern, limiting its effectiveness. DNA methylation-based biomarkers may assist in the selection of patients that may benefit (or not) from this type of treatment and provide new targets to circumvent platinum chemoresistance, namely, through demethylating agents. We performed a systematic search of studies on biomarkers that might be predictive of platinum-based chemotherapy resistance, including in vitro and in vivo pre-clinical models and clinical studies using patient samples. DNA methylation biomarkers predictive of response to platinum remain mostly unexplored but seem promising in assisting clinicians in the generation of more personalized follow-up and treatment strategies. Improved methodologies for their detection and quantification, including non-invasively in liquid biopsies, are additional attractive features that can bring these biomarkers into clinical practice, fostering precision medicine.
Collapse
|
4
|
Pokusaeva VO, Diez AR, Espinar L, Pérez AT, Filion GJ. Strand asymmetry influences mismatch resolution during a single-strand annealing. Genome Biol 2022; 23:93. [PMID: 35414014 PMCID: PMC9001825 DOI: 10.1186/s13059-022-02665-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/30/2022] [Indexed: 02/08/2023] Open
Abstract
Background Biases of DNA repair can shape the nucleotide landscape of genomes at evolutionary timescales. The molecular mechanisms of those biases are still poorly understood because it is difficult to isolate the contributions of DNA repair from those of DNA damage. Results Here, we develop a genome-wide assay whereby the same DNA lesion is repaired in different genomic contexts. We insert thousands of barcoded transposons carrying a reporter of DNA mismatch repair in the genome of mouse embryonic stem cells. Upon inducing a double-strand break between tandem repeats, a mismatch is generated if the break is repaired through single-strand annealing. The resolution of the mismatch showed a 60–80% bias in favor of the strand with the longest 3′ flap. The location of the lesion in the genome and the type of mismatch had little influence on the bias. Instead, we observe a complete reversal of the bias when the longest 3′ flap is moved to the opposite strand by changing the position of the double-strand break in the reporter. Conclusions These results suggest that the processing of the double-strand break has a major influence on the repair of mismatches during a single-strand annealing. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02665-3.
Collapse
Affiliation(s)
- Victoria O Pokusaeva
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Present Address: Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, Austria
| | - Aránzazu Rosado Diez
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Present Address: H12O-CNIO Lung Cancer Clinical Research Unit, i + 12 Research Institute, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Lorena Espinar
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Albert Torelló Pérez
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Guillaume J Filion
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain. .,University Pompeu Fabra (UPF), Barcelona, Spain. .,Present Address: Department Biological Sciences, University of Toronto Scarborough, Toronto, Canada.
| |
Collapse
|
5
|
Ehrlich M. Risks and rewards of big-data in epigenomics research: an interview with Melanie Ehrlich. Epigenomics 2022; 14:351-358. [PMID: 35255735 DOI: 10.2217/epi-2022-0056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Melanie Ehrlich, PhD, is a professor in the Tulane Cancer Center, the Tulane Center for Medical Bioinformatics and Genomics and the Hayward Human Genetics Program at Tulane Medical School, New Orleans, LA. She obtained her PhD in molecular biology in 1971 from the State University of New York at Stony Brook and completed postdoctoral research at Albert Einstein College of Medicine in 1972. She has been working on various aspects of epigenetics, starting with DNA methylation, since 1973. Her group made many first findings about DNA methylation (see below). For example, in 1982 and 1983, in collaboration with Charles Gehrke at the University of Missouri, she was the first to report tissue-specific and cancer-specific differences in overall DNA methylation in humans. In 1985, Xian-Yang Zhang and Richard Wang in her lab discovered a class of human DNA sequences specifically hypomethylated in sperm. In 1998, her group was the first to describe extensive losses of DNA methylation in pericentromeric and centromeric DNA repeats in human cancer. Her lab's many publications on the prevalence of both DNA hypermethylation and hypomethylation in the same cancers brought needed balance to our understanding of the epigenetics of cancer and to its clinical implications [1]. Besides working on cancer epigenetics, her research group has helped elucidate cytogenetic and gene expression abnormalities in the immunodeficiency, centromeric and facial anomalies (ICF) syndrome, a rare recessive disease often caused by mutations in DNMT3B. Her group also studied the epigenetics and transcriptomics of facioscapulohumeral muscular dystrophy (FSHD), whose disease locus is a tandem 3.3-kb repeat at subtelomeric 4q (that happens to be hypomethylated in ICF DNA [2]). Her study of FSHD has taken her in the direction of muscle (skeletal muscle, heart and aorta) epigenetics [3-6]. Recently, she has led research that applies epigenetics much more rigorously than usual to the evaluation of genetic variants from genome-wide association studies (GWAS) of osteoporosis and obesity. In continued collaboration with Sriharsa Pradhan at New England Biolabs and Michelle Lacey at Tulane University, she has compared 5-hydroxymethylcytosine and 5-methylcytosine clustering in various human tissues [7] and is studying myoblast methylomes that they generated by a new high-resolution enzymatic technique (enzymatic methyl-seq).
Collapse
Affiliation(s)
- Melanie Ehrlich
- Tulane Cancer Center, Center for Medical Bioinformatics & Genomics, & Hayward Genetics Center, Tulane University, New Orleans, LA 70112, USA
| |
Collapse
|
6
|
Hsu CW, Sowers ML, Baljinnyam T, Herring JL, Hackfeld LC, Tang H, Zhang K, Sowers LC. Measurement of deaminated cytosine adducts in DNA using a novel hybrid thymine DNA glycosylase. J Biol Chem 2022; 298:101638. [PMID: 35085553 PMCID: PMC8861164 DOI: 10.1016/j.jbc.2022.101638] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 01/16/2023] Open
Abstract
The hydrolytic deamination of cytosine and 5-methylcytosine drives many of the transition mutations observed in human cancer. The deamination-induced mutagenic intermediates include either uracil or thymine adducts mispaired with guanine. While a substantial array of methods exist to measure other types of DNA adducts, the cytosine deamination adducts pose unusual analytical problems, and adequate methods to measure them have not yet been developed. We describe here a novel hybrid thymine DNA glycosylase (TDG) that is comprised of a 29-amino acid sequence from human TDG linked to the catalytic domain of a thymine glycosylase found in an archaeal thermophilic bacterium. Using defined-sequence oligonucleotides, we show that hybrid TDG has robust mispair-selective activity against deaminated U:G and T:G mispairs. We have further developed a method for separating glycosylase-released free bases from oligonucleotides and DNA followed by GC-MS/MS quantification. Using this approach, we have measured for the first time the levels of total uracil, U:G, and T:G pairs in calf thymus DNA. The method presented here will allow the measurement of the formation, persistence, and repair of a biologically important class of deaminated cytosine adducts.
Collapse
Affiliation(s)
- Chia Wei Hsu
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA,MD-PhD Combined Degree Program, University of Texas Medical Branch, Galveston, Texas, USA
| | - Mark L. Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA,MD-PhD Combined Degree Program, University of Texas Medical Branch, Galveston, Texas, USA
| | - Tuvshintugs Baljinnyam
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jason L. Herring
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Linda C. Hackfeld
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Hui Tang
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Kangling Zhang
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Lawrence C. Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA,Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, USA,For correspondence: Lawrence C. Sowers
| |
Collapse
|
7
|
Baum C, Lin YC, Fomenkov A, Anton BP, Chen L, Yan B, Evans TC, Roberts RJ, Tolonen AC, Ettwiller L. Rapid identification of methylase specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes. Nucleic Acids Res 2021; 49:e113. [PMID: 34417598 PMCID: PMC8565308 DOI: 10.1093/nar/gkab705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/29/2021] [Accepted: 08/16/2021] [Indexed: 11/21/2022] Open
Abstract
DNA methylation is widespread amongst eukaryotes and prokaryotes to modulate gene expression and confer viral resistance. 5-Methylcytosine (m5C) methylation has been described in genomes of a large fraction of bacterial species as part of restriction-modification systems, each composed of a methyltransferase and cognate restriction enzyme. Methylases are site-specific and target sequences vary across organisms. High-throughput methods, such as bisulfite-sequencing can identify m5C at base resolution but require specialized library preparations and single molecule, real-time (SMRT) sequencing usually misses m5C. Here, we present a new method called RIMS-seq (rapid identification of methylase specificity) to simultaneously sequence bacterial genomes and determine m5C methylase specificities using a simple experimental protocol that closely resembles the DNA-seq protocol for Illumina. Importantly, the resulting sequencing quality is identical to DNA-seq, enabling RIMS-seq to substitute standard sequencing of bacterial genomes. Applied to bacteria and synthetic mixed communities, RIMS-seq reveals new methylase specificities, supporting routine study of m5C methylation while sequencing new genomes.
Collapse
Affiliation(s)
- Chloé Baum
- New England Biolabs, Inc. 240 County Road Ipswich, MA 01938, USA.,Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Évry, France
| | - Yu-Cheng Lin
- New England Biolabs, Inc. 240 County Road Ipswich, MA 01938, USA
| | - Alexey Fomenkov
- New England Biolabs, Inc. 240 County Road Ipswich, MA 01938, USA
| | - Brian P Anton
- New England Biolabs, Inc. 240 County Road Ipswich, MA 01938, USA
| | - Lixin Chen
- New England Biolabs, Inc. 240 County Road Ipswich, MA 01938, USA
| | - Bo Yan
- 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
| | | | - Andrew C Tolonen
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Évry, France
| | | |
Collapse
|
8
|
Evaluation of the Properties of the DNA Methyltransferase from Aeropyrum pernix K1. Microbiol Spectr 2021; 9:e0018621. [PMID: 34585946 PMCID: PMC8557920 DOI: 10.1128/spectrum.00186-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Little is known regarding the DNA methyltransferases (MTases) in hyperthermophilic archaea. In this study, we focus on an MTase from Aeropyrum pernix K1, a hyperthermophilic archaeon that is found in hydrothermal vents and whose optimum growth temperature is 90°C to 95°C. From genomic sequence analysis, A. pernix K1 has been predicted to have a restriction-modification system (R-M system). The restriction endonuclease from A. pernix K1 (known as ApeKI from New England BioLabs Inc. [catalog code R06435]) has been described previously, but the properties of the MTase from A. pernix K1 (M.ApeKI) have not yet been clarified. Thus, we demonstrated the properties of M.ApeKI. In this study, M.ApeKI was expressed in Escherichia coli strain JM109 and affinity purified using its His tag. The recognition sequence of M.ApeKI was determined by methylation activity and bisulfite sequencing (BS-seq). High-performance liquid chromatography (HPLC) was used to detect the position of the methyl group in methylated cytosine. As a result, it was clarified that M.ApeKI adds the methyl group at the C-5 position of the second cytosine in 5'-GCWGC-3'. Moreover, we also determined that the MTase optimum temperature was over 70°C and that it is strongly tolerant to high temperatures. M.ApeKI is the first highly thermostable DNA (cytosine-5)-methyltransferase to be evaluated by experimental evidence. IMPORTANCE In general, thermophilic bacteria with optimum growth temperatures over or equal to 60°C have been predicted to include only N4-methylcytosine or N6-methyladenine as methylated bases in their DNA, because 5-methylcytosine is susceptible to deamination by heat. However, from this study, A. pernix K1, with an optimum growth temperature at 95°C, was demonstrated to produce a DNA (cytosine-5)-methyltransferase. Thus, A. pernix K1 presumably has 5-methylcytosine in its DNA and may produce an original repair system for the expected C-to-T mutations. M.ApeKI was demonstrated to be tolerant to high temperatures; thus, we expect that M.ApeKI may be valuable for the development of a novel analysis system or epigenetic editing tool.
Collapse
|
9
|
Matoulek D, Borůvková V, Ocalewicz K, Symonová R. GC and Repeats Profiling along Chromosomes-The Future of Fish Compositional Cytogenomics. Genes (Basel) 2020; 12:50. [PMID: 33396302 PMCID: PMC7823971 DOI: 10.3390/genes12010050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 12/14/2022] Open
Abstract
The study of fish cytogenetics has been impeded by the inability to produce G-bands that could assign chromosomes to their homologous pairs. Thus, the majority of karyotypes published have been estimated based on morphological similarities of chromosomes. The reason why chromosome G-banding does not work in fish remains elusive. However, the recent increase in the number of fish genomes assembled to the chromosome level provides a way to analyse this issue. We have developed a Python tool to visualize and quantify GC percentage (GC%) of both repeats and unique DNA along chromosomes using a non-overlapping sliding window approach. Our tool profiles GC% and simultaneously plots the proportion of repeats (rep%) in a color scale (or vice versa). Hence, it is possible to assess the contribution of repeats to the total GC%. The main differences are the GC% of repeats homogenizing the overall GC% along fish chromosomes and a greater range of GC% scattered along fish chromosomes. This may explain the inability to produce G-banding in fish. We also show an occasional banding pattern along the chromosomes in some fish that probably cannot be detected with traditional qualitative cytogenetic methods.
Collapse
Affiliation(s)
- Dominik Matoulek
- Faculty of Science, University of Hradec Kralove, 500 03 Hradec Králové, Czech Republic; (D.M.); (V.B.)
| | - Veronika Borůvková
- Faculty of Science, University of Hradec Kralove, 500 03 Hradec Králové, Czech Republic; (D.M.); (V.B.)
| | - Konrad Ocalewicz
- Department of Marine Biology and Ecology, Institute of Oceanography, Faculty of Oceanography and Geography, University of Gdansk, 80-309 Gdansk, Poland;
| | - Radka Symonová
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 80333 Freising, Germany
| |
Collapse
|
10
|
Iyer GR, Hasan Q. Alteration of methylation status in archival DNA samples: A qualitative assessment by methylation specific polymerase chain reaction. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:837-842. [PMID: 32649027 DOI: 10.1002/em.22398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/25/2020] [Accepted: 07/05/2020] [Indexed: 06/11/2023]
Abstract
DNA methylation is an epigenetic mechanism that regulates gene expression, which also facilitates genomic imprinting. Genomic imprinting is responsible for differential expression of genes based on parent of origin. Altered methylation of parental alleles results in imprinting disorders diagnosed by methylation specific polymerase chain reaction (MS-PCR) technique. With increasing evidence of genes under epigenetic influence, methylation studies are extensively performed on archival samples. To evaluate effect of storage and storage conditions on DNA methylation, a systematic MS-PCR based analysis was planned on an imprinted gene, SNRPN, located on chromosome 15q11.2. It was assessed by MS-PCR on fresh, 4 -20, and -80°C stored DNA samples for different time periods for systematic evaluation of methylation status. Technical factors like type of sample processing, method of DNA isolation, primer region polymorphism, sample heterogeneity were also evaluated. DNA methylation was observed to be altered for SNRPN gene after storage at -80°C from 2 months onwards. Long-term storage of DNA at -80°C results in altered DNA methylation status. This may lead to false MS-PCR diagnosis of imprinting disorders. Our proof of concept study should be followed with quantitative validation since the findings have critical implications in the present era of biobanking.
Collapse
Affiliation(s)
- Gayatri Rangarajan Iyer
- Department of Genetics & Molecular Medicine, Kamineni Hospitals, LB Nagar, Hyderabad, India
- Department of Genetics, Osmania University, Tarnaka, Hyderabad, India
| | - Qurratulain Hasan
- Department of Genetics & Molecular Medicine, Kamineni Hospitals, LB Nagar, Hyderabad, India
| |
Collapse
|
11
|
Hwang T, Reh S, Dunbayev Y, Zhong Y, Takata Y, Shen J, McBride KM, Murnane JP, Bhak J, Lee S, Wood RD, Takata KI. Defining the mutation signatures of DNA polymerase θ in cancer genomes. NAR Cancer 2020; 2:zcaa017. [PMID: 32885167 PMCID: PMC7454005 DOI: 10.1093/narcan/zcaa017] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/03/2020] [Accepted: 08/06/2020] [Indexed: 01/25/2023] Open
Abstract
DNA polymerase theta (POLQ)-mediated end joining (TMEJ) is a distinct pathway for mediating DNA double-strand break (DSB) repair. TMEJ is required for the viability of BRCA-mutated cancer cells. It is crucial to identify tumors that rely on POLQ activity for DSB repair, because such tumors are defective in other DSB repair pathways and have predicted sensitivity to POLQ inhibition and to cancer therapies that produce DSBs. We define here the POLQ-associated mutation signatures in human cancers, characterized by short insertions and deletions in a specific range of microhomologies. By analyzing 82 COSMIC (Catalogue of Somatic Mutations in Cancer) signatures, we found that BRCA-mutated cancers with a higher level of POLQ expression have a greatly enhanced representation of the small insertion and deletion signature 6, as well as single base substitution signature 3. Using human cancer cells with disruptions of POLQ, we further show that TMEJ dominates end joining of two separated DSBs (distal EJ). Templated insertions with microhomology are enriched in POLQ-dependent distal EJ. The use of this signature analysis will aid in identifying tumors relying on POLQ activity.
Collapse
Affiliation(s)
- Taejoo Hwang
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Shelley Reh
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Yerkin Dunbayev
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Yi Zhong
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Yoko Takata
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Jianjun Shen
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Kevin M McBride
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - John P Murnane
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jong Bhak
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Semin Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Richard D Wood
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Kei-Ichi Takata
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| |
Collapse
|
12
|
Youk J, An Y, Park S, Lee JK, Ju YS. The genome-wide landscape of C:G > T:A polymorphism at the CpG contexts in the human population. BMC Genomics 2020; 21:270. [PMID: 32228436 PMCID: PMC7106825 DOI: 10.1186/s12864-020-6674-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/13/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The C:G > T:A substitution at the CpG dinucleotide contexts is the most frequent substitution type in genome evolution. The mutational process is obviously ongoing in the human germline; however, its impact on common and rare genomic polymorphisms has not been comprehensively investigated yet. Here we observed the landscape and dynamics of C:G > T:A substitutions from population-scale human genome sequencing datasets including ~ 4300 whole-genomes from the 1000 Genomes and the pan-cancer analysis of whole genomes (PCAWG) Project and ~ 60,000 whole-exomes from the Exome Aggregation Consortium (ExAC) database. RESULTS Of the 28,084,558 CpG sites in the human reference genome, 26.0% show C:G > T:A substitution in the dataset. Remarkably, CpGs in CpG islands (CGIs) have a much lower frequency of such mutations (5.6%). Interestingly, the mutation frequency of CGIs is not uniform with a significantly higher C:G > T:A substitution rate for intragenic CGIs compared to other types. For non-CGI CpGs, the mutation rate was positively correlated with the distance from the nearest CGI up to 2 kb. Finally, we found the impact of negative selection for coding CpG mutations resulting in amino acid change. CONCLUSIONS This study provides the first unbiased rate of C:G > T:A substitution at the CpG dinucleotide contexts, using population-scale human genome sequencing data. Our findings provide insights into the dynamics of the mutation acquisition in the human genome.
Collapse
Affiliation(s)
- Jeonghwan Youk
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yohan An
- Biomedical Science and Engineering Interdisciplinary Program, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Seongyeol Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - June-Koo Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea. .,Biomedical Science and Engineering Interdisciplinary Program, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| |
Collapse
|
13
|
Cytosine Methylation Affects the Mutability of Neighboring Nucleotides in Germline and Soma. Genetics 2020; 214:809-823. [PMID: 32079595 DOI: 10.1534/genetics.120.303028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/12/2020] [Indexed: 02/07/2023] Open
Abstract
Methylated cytosines deaminate at higher rates than unmethylated cytosines, and the lesions they produce are repaired less efficiently. As a result, methylated cytosines are mutational hotspots. Here, combining rare polymorphism and base-resolution methylation data in humans, Arabidopsis thaliana, and rice (Oryza sativa), we present evidence that methylation state affects mutation dynamics not only at the focal cytosine but also at neighboring nucleotides. In humans, contrary to prior suggestions, we find that nucleotides in the close vicinity (±3 bp) of methylated cytosines mutate less frequently. Reduced mutability around methylated CpGs is also observed in cancer genomes, considering single nucleotide variants alongside tissue-of-origin-matched methylation data. In contrast, methylation is associated with increased neighborhood mutation risk in A. thaliana and rice. The difference in neighborhood mutation risk is less pronounced further away from the focal CpG and modulated by regional GC content. Our results are consistent with a model where altered risk at neighboring bases is linked to lesion formation at the focal CpG and subsequent long-patch repair. Our findings indicate that cytosine methylation has a broader mutational footprint than is commonly assumed.
Collapse
|
14
|
Koliadenko V, Wilanowski T. Additional functions of selected proteins involved in DNA repair. Free Radic Biol Med 2020; 146:1-15. [PMID: 31639437 DOI: 10.1016/j.freeradbiomed.2019.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/16/2019] [Accepted: 10/16/2019] [Indexed: 12/30/2022]
Abstract
Protein moonlighting is a phenomenon in which a single polypeptide chain can perform a number of different unrelated functions. Here we present our analysis of moonlighting in the case of selected DNA repair proteins which include G:T mismatch-specific thymine DNA glycosylase (TDG), methyl-CpG-binding domain protein 4 (MBD4), apurinic/apyrimidinic endonuclease 1 (APE1), AlkB homologs, poly (ADP-ribose) polymerase 1 (PARP-1) and single-strand selective monofunctional uracil DNA glycosylase 1 (SMUG1). Most of their additional functions are not accidental and clear patterns are emerging. Participation in RNA metabolism is not surprising as bases occurring in RNA are the same or very similar to those in DNA. Other common additional function involves regulation of transcription. This is not unexpected as these proteins bind to specific DNA regions for DNA repair, hence they can also be recruited to regulate transcription. Participation in demethylation and replication of DNA appears logical as well. Some of the multifunctional DNA repair proteins play major roles in many diseases, including cancer. However, their moonlighting might prove a major difficulty in the development of new therapies because it will not be trivial to target a single protein function without affecting its other functions that are not related to the disease.
Collapse
Affiliation(s)
- Vlada Koliadenko
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096, Warsaw, Poland
| | - Tomasz Wilanowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096, Warsaw, Poland.
| |
Collapse
|
15
|
Jin L, Qin G, Zhao C, Yu X, Lu J, Meng H. The deamination mechanism of the 5,6-dihydro-6-hydro-6-hydroxylcytosine and 5,6-dihydro-5-methyl-6-hydroxylcytosine under typical bisulfite conditions. Mol Phys 2019. [DOI: 10.1080/00268976.2018.1541105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Lingxia Jin
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, People’s Republic of China
| | - Gongwei Qin
- Bioresources Key Laboratory of Shaanxi Province, College of Biological Science and Technology, Shaanxi University of Technology, Hanzhong, People’s Republic of China
| | - Caibin Zhao
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, People’s Republic of China
| | - Xiaohu Yu
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, People’s Republic of China
| | - Jiufu Lu
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, People’s Republic of China
| | - Hao Meng
- College of Physics and Telecom Engineering, Shaanxi University of Technology, Hanzhong, People’s Republic of China
| |
Collapse
|
16
|
Genome-Wide Mutation Rate Response to pH Change in the Coral Reef Pathogen Vibrio shilonii AK1. mBio 2017; 8:mBio.01021-17. [PMID: 28830944 PMCID: PMC5565966 DOI: 10.1128/mbio.01021-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Recent application of mutation accumulation techniques combined with whole-genome sequencing (MA/WGS) has greatly promoted studies of spontaneous mutation. However, such explorations have rarely been conducted on marine organisms, and it is unclear how marine habitats have influenced genome stability. This report resolves the mutation rate and spectrum of the coral reef pathogen Vibrio shilonii, which causes coral bleaching and endangers the biodiversity maintained by coral reefs. We found that its mutation rate and spectrum are highly similar to those of other studied bacteria from various habitats, despite the saline environment. The mutational properties of this marine bacterium are thus controlled by other general evolutionary forces such as natural selection and genetic drift. We also found that as pH drops, the mutation rate decreases and the mutation spectrum is biased in the direction of generating G/C nucleotides. This implies that evolutionary features of this organism and perhaps other marine microbes might be altered by the increasingly acidic ocean water caused by excess CO2 emission. Nonetheless, further exploration is needed as the pH range tested in this study was rather narrow and many other possible mutation determinants, such as carbonate increase, are associated with ocean acidification. This study explored the pH dependence of a bacterial genome-wide mutation rate. We discovered that the genome-wide rates of appearance of most mutation types decrease linearly and that the mutation spectrum is biased in generating more G/C nucleotides with pH drop in the coral reef pathogen V. shilonii.
Collapse
|
17
|
Luk ADW, Lee PP, Mao H, Chan KW, Chen XY, Chen TX, He JX, Kechout N, Suri D, Tao YB, Xu YB, Jiang LP, Liew WK, Jirapongsananuruk O, Daengsuwan T, Gupta A, Singh S, Rawat A, Abdul Latiff AH, Lee ACW, Shek LP, Nguyen TVA, Chin TJ, Chien YH, Latiff ZA, Le TMH, Le NNQ, Lee BW, Li Q, Raj D, Barbouche MR, Thong MK, Ang MCD, Wang XC, Xu CG, Yu HG, Yu HH, Lee TL, Yau FYS, Wong WHS, Tu W, Yang W, Chong PCY, Ho MHK, Lau YL. Family History of Early Infant Death Correlates with Earlier Age at Diagnosis But Not Shorter Time to Diagnosis for Severe Combined Immunodeficiency. Front Immunol 2017; 8:808. [PMID: 28747913 PMCID: PMC5506088 DOI: 10.3389/fimmu.2017.00808] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 06/26/2017] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Severe combined immunodeficiency (SCID) is fatal unless treated with hematopoietic stem cell transplant. Delay in diagnosis is common without newborn screening. Family history of infant death due to infection or known SCID (FH) has been associated with earlier diagnosis. OBJECTIVE The aim of this study was to identify the clinical features that affect age at diagnosis (AD) and time to the diagnosis of SCID. METHODS From 2005 to 2016, 147 SCID patients were referred to the Asian Primary Immunodeficiency Network. Patients with genetic diagnosis, age at presentation (AP), and AD were selected for study. RESULTS A total of 88 different SCID gene mutations were identified in 94 patients, including 49 IL2RG mutations, 12 RAG1 mutations, 8 RAG2 mutations, 7 JAK3 mutations, 4 DCLRE1C mutations, 4 IL7R mutations, 2 RFXANK mutations, and 2 ADA mutations. A total of 29 mutations were previously unreported. Eighty-three of the 94 patients fulfilled the selection criteria. Their median AD was 4 months, and the time to diagnosis was 2 months. The commonest SCID was X-linked (n = 57). A total of 29 patients had a positive FH. Candidiasis (n = 27) and bacillus Calmette-Guérin (BCG) vaccine infection (n = 19) were the commonest infections. The median age for candidiasis and BCG infection documented were 3 months and 4 months, respectively. The median absolute lymphocyte count (ALC) was 1.05 × 109/L with over 88% patients below 3 × 109/L. Positive FH was associated with earlier AP by 1 month (p = 0.002) and diagnosis by 2 months (p = 0.008), but not shorter time to diagnosis (p = 0.494). Candidiasis was associated with later AD by 2 months (p = 0.008) and longer time to diagnosis by 0.55 months (p = 0.003). BCG infections were not associated with age or time to diagnosis. CONCLUSION FH was useful to aid earlier diagnosis but was overlooked by clinicians and not by parents. Similarly, typical clinical features of SCID were not recognized by clinicians to shorten the time to diagnosis. We suggest that lymphocyte subset should be performed for any infant with one or more of the following four clinical features: FH, candidiasis, BCG infections, and ALC below 3 × 109/L.
Collapse
Affiliation(s)
- Anderson Dik Wai Luk
- LKS Faculty of Medicine, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Pamela P. Lee
- LKS Faculty of Medicine, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Huawei Mao
- LKS Faculty of Medicine, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
- Shenzhen Primary Immunodeficiency Diagnostic and Therapeutic Laboratory, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Koon-Wing Chan
- LKS Faculty of Medicine, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | | | - Tong-Xin Chen
- Department of Allergy and Immunology, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Xin He
- Beijing Children’s Hospital, Capital Medical University, Beijing, China
| | | | - Deepti Suri
- Allergy Immunology Unit, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Yin Bo Tao
- Guangzhou Children’s Hospital, Guangzhou, China
| | - Yong Bin Xu
- Guang Zhou Women and Children’s Medical Center, Guangzhou, China
| | - Li Ping Jiang
- Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Woei Kang Liew
- KK Women’s and Children’s Hospital, Singapore, Singapore
| | | | | | - Anju Gupta
- Allergy Immunology Unit, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Surjit Singh
- Allergy Immunology Unit, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Amit Rawat
- Allergy Immunology Unit, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | | | | | | | | | - Tek Jee Chin
- Sarawak General Hospital Malaysia, Kuching, Malaysia
| | - Yin Hsiu Chien
- National Taiwan University Children’s Hospital, Taipei, Taiwan
| | | | | | | | - Bee Wah Lee
- National University of Singapore, Singapore, Singapore
| | - Qiang Li
- Sichuan Second West China Hospital, Sichuan, China
| | - Dinesh Raj
- Department of Paediatrics, Holy Family Hospital, New Delhi, India
| | - Mohamed-Ridha Barbouche
- Department of Immunology, Institut Pasteur de Tunis and University Tunis-El Manar, Tunis, Tunisia
| | - Meow-Keong Thong
- Faculty of Medicine, Department of Paediatrics, University of Malaya, Kuala Lumpur, Malaysia
| | | | | | - Chen Guang Xu
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hai Guo Yu
- Nanjing Children’s Hospital, Nanjing, China
| | - Hsin-Hui Yu
- National Taiwan University Children’s Hospital, Taipei, Taiwan
| | - Tsz Leung Lee
- LKS Faculty of Medicine, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | | | - Wilfred Hing-Sang Wong
- LKS Faculty of Medicine, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Wenwei Tu
- LKS Faculty of Medicine, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
- Shenzhen Primary Immunodeficiency Diagnostic and Therapeutic Laboratory, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Wangling Yang
- LKS Faculty of Medicine, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
- Shenzhen Primary Immunodeficiency Diagnostic and Therapeutic Laboratory, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Patrick Chun Yin Chong
- LKS Faculty of Medicine, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Marco Hok Kung Ho
- LKS Faculty of Medicine, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Yu Lung Lau
- LKS Faculty of Medicine, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
- Shenzhen Primary Immunodeficiency Diagnostic and Therapeutic Laboratory, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- *Correspondence: Yu Lung Lau,
| |
Collapse
|
18
|
Xu X, Watt DS, Liu C. Multifaceted roles for thymine DNA glycosylase in embryonic development and human carcinogenesis. Acta Biochim Biophys Sin (Shanghai) 2016; 48:82-9. [PMID: 26370152 DOI: 10.1093/abbs/gmv083] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 07/12/2015] [Indexed: 01/03/2023] Open
Abstract
Thymine DNA glycosylase (TDG) is a multifunctional protein that plays important roles in DNA repair, DNA demethylation, and transcriptional regulation. These diverse functions make TDG a unique enzyme in embryonic development and carcinogenesis. This review discusses the molecular function of TDG in human cancers and the previously unrecognized value of TDG as a potential target for drug therapy.
Collapse
Affiliation(s)
- Xuehe Xu
- Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky, Lexington, KY 40536-0509, USA
| | - David S Watt
- Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky, Lexington, KY 40536-0509, USA
| | - Chunming Liu
- Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky, Lexington, KY 40536-0509, USA
| |
Collapse
|
19
|
Mugal CF, Weber CC, Ellegren H. GC-biased gene conversion links the recombination landscape and demography to genomic base composition. Bioessays 2015; 37:1317-26. [DOI: 10.1002/bies.201500058] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Carina F. Mugal
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Claudia C. Weber
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
- Department of Biology; Center for Computational Genetics and Genomics; Temple University; Philadelphia PA USA
| | - Hans Ellegren
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| |
Collapse
|
20
|
Bellacosa A, Drohat AC. Role of base excision repair in maintaining the genetic and epigenetic integrity of CpG sites. DNA Repair (Amst) 2015; 32:33-42. [PMID: 26021671 DOI: 10.1016/j.dnarep.2015.04.011] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cytosine methylation at CpG dinucleotides is a central component of epigenetic regulation in vertebrates, and the base excision repair (BER) pathway is important for maintaining both the genetic stability and the methylation status of CpG sites. This perspective focuses on two enzymes that are of particular importance for the genetic and epigenetic integrity of CpG sites, methyl binding domain 4 (MBD4) and thymine DNA glycosylase (TDG). We discuss their capacity for countering C to T mutations at CpG sites, by initiating base excision repair of G · T mismatches generated by deamination of 5-methylcytosine (5mC). We also consider their role in active DNA demethylation, including pathways that are initiated by oxidation and/or deamination of 5mC.
Collapse
Affiliation(s)
- Alfonso Bellacosa
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, United States.
| | - Alexander C Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD 21201, United States.
| |
Collapse
|
21
|
Wyatt MD. Advances in understanding the coupling of DNA base modifying enzymes to processes involving base excision repair. Adv Cancer Res 2014; 119:63-106. [PMID: 23870509 DOI: 10.1016/b978-0-12-407190-2.00002-2] [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] [Indexed: 12/23/2022]
Abstract
This chapter describes some of the recent, exciting developments that have characterized and connected processes that modify DNA bases with DNA repair pathways. It begins with AID/APOBEC or TET family members that covalently modify bases within DNA. The modified bases, such as uracil or 5-formylcytosine, are then excised by DNA glycosylases including UNG or TDG to initiate base excision repair (BER). BER is known to preserve genome integrity by removing damaged bases. The newer studies underscore the necessity of BER following enzymes that deliberately damage DNA. This includes the role of BER in antibody diversification and more recently, its requirement for demethylation of 5-methylcytosine in mammalian cells. The recent advances have shed light on mechanisms of DNA demethylation, and have raised many more questions. The potential hazards of these processes have also been revealed. Dysregulation of the activity of base modifying enzymes, and resolution by unfaithful or corrupt means can be a driver of genome instability and tumorigenesis. The understanding of both DNA and histone methylation and demethylation is now revealing the true extent to which epigenetics influence normal development and cancer, an abnormal development.
Collapse
Affiliation(s)
- Michael D Wyatt
- Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, South Carolina, USA.
| |
Collapse
|
22
|
Stirzaker C, Taberlay PC, Statham AL, Clark SJ. Mining cancer methylomes: prospects and challenges. Trends Genet 2013; 30:75-84. [PMID: 24368016 DOI: 10.1016/j.tig.2013.11.004] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 11/22/2013] [Accepted: 11/26/2013] [Indexed: 12/31/2022]
Abstract
There are over 28 million CpG sites in the human genome. Assessing the methylation status of each of these sites will be required to understand fully the role of DNA methylation in health and disease. Genome-wide analysis, using arrays and high-throughput sequencing, has enabled assessment of large fractions of the methylome, but each protocol comes with unique advantages and disadvantages. Notably, except for whole-genome bisulfite sequencing, most commonly used genome-wide methods detect <5% of all CpG sites. Here, we discuss approaches for methylome studies and compare genome coverage of promoters, genes, and intergenic regions, and capacity to quantitate individual CpG methylation states. Finally, we examine the extent of published cancer methylomes that have been generated using genome-wide approaches.
Collapse
Affiliation(s)
- Clare Stirzaker
- Epigenetics Program, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Sydney 2010, NSW, Australia; St Vincent's Clinical School, University of NSW, Sydney 2010, NSW, Australia
| | - Phillippa C Taberlay
- Epigenetics Program, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Sydney 2010, NSW, Australia; St Vincent's Clinical School, University of NSW, Sydney 2010, NSW, Australia
| | - Aaron L Statham
- Epigenetics Program, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Sydney 2010, NSW, Australia
| | - Susan J Clark
- Epigenetics Program, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Sydney 2010, NSW, Australia; St Vincent's Clinical School, University of NSW, Sydney 2010, NSW, Australia.
| |
Collapse
|
23
|
Ramiro-Merina Á, Ariza RR, Roldán-Arjona T. Molecular characterization of a putative plant homolog of MBD4 DNA glycosylase. DNA Repair (Amst) 2013; 12:890-8. [PMID: 23994068 DOI: 10.1016/j.dnarep.2013.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 08/02/2013] [Accepted: 08/07/2013] [Indexed: 11/19/2022]
Abstract
Methyl-CpG-binding domain 4 (MBD4) DNA glycosylase is involved in excision of spontaneous deamination products of cytosine and 5-methylcytosine in animals, but it is unknown whether related proteins perform similar functions in plants. We report here the isolation and biochemical characterization of a putative MBD4 homolog from Arabidopsis thaliana, designated as MBD4L (MBD4-like). The plant enzyme lacks the MBD domain present in mammalian MBD4 proteins, but conserves a DNA glycosylase domain with critical residues for substrate recognition and catalysis, and it is more closely related to MBD4 homologs than to other members of the HhH-GPD superfamily. Arabidopsis MBD4L excises uracil and thymine opposite G, and the presence of halogen substituents at C5 of the target base greatly increases its excision efficiency. No significant activity is detected on cytosine derivatives such as 5-methylcytosine or 5-hydroxymethylcytosine. The enzyme binds to the abasic site product generated after excision, which decreases its catalytic turnover in vitro. Both the full-length protein and a N-terminal truncated version retaining the catalytic domain exhibit a preference for a CpG sequence context, where most plant DNA methylation is found. Our results suggest that an important function of Arabidopsis MBD4L is to protect the plant genome from the mutagenic consequences of cytosine and 5-methylcytosine deamination.
Collapse
Affiliation(s)
- Ángel Ramiro-Merina
- Department of Genetics, University of Córdoba/Maimónides Institute for Research in Biomedicine of Córdoba (IMIBIC)/Reina Sofía University Hospital, 14071 Córdoba, Spain
| | | | | |
Collapse
|
24
|
Abstract
Cancer arises as a consequence of cumulative disruptions to cellular growth control with Darwinian selection for those heritable changes that provide the greatest clonal advantage. These traits can be acquired and stably maintained by either genetic or epigenetic means. Here, we explore the ways in which alterations in the genome and epigenome influence each other and cooperate to promote oncogenic transformation. Disruption of epigenomic control is pervasive in malignancy and can be classified as an enabling characteristic of cancer cells, akin to genome instability and mutation.
Collapse
Affiliation(s)
- Hui Shen
- USC Epigenome Center, University of Southern California, Room G511B, 1450 Biggy Street, Los Angeles, CA 90089-9061, USA
| | | |
Collapse
|
25
|
Flores-Juárez CR, González-Jasso E, Antaramian A, Pless RC. Capacity of N4-methyl-2'-deoxycytidine 5'-triphosphate to sustain the polymerase chain reaction using various thermostable DNA polymerases. Anal Biochem 2013; 438:73-81. [PMID: 23548504 DOI: 10.1016/j.ab.2013.03.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 03/22/2013] [Accepted: 03/23/2013] [Indexed: 10/27/2022]
Abstract
The dCTP analog N4-methyl-2'-deoxycytidine 5'-triphosphate (N4medCTP) was evaluated for its performance in the polymerase chain reaction (PCR). Using the HotStart Taq DNA polymerase with a standard thermal protocol, test segments 85 or 200 bp long were amplified equally well using dCTP or N4medCTP:dCTP mixtures ranging in molar ratio from 3:1 to 10:1, while complete replacement of dCTP by N4medCTP gave clearly lower amplicon yields and higher Cq values. Comparable yields with N4medCTP or dCTP were achieved only by using a slowdown protocol. Post-PCR melting analyses showed decreasing Tm values for amplicons obtained with increasing N4medCTP:dCTP input ratios; for the 200-bp amplicon, complete replacement of dCTP by N4medCTP in the reaction reduced the Tm by 11 °C; for the 85-bp amplicon the Tm reduction was 7 °C. In experiments aiming at the 200-bp amplicon, Pfu exo(-) DNA polymerase did not sustain PCR when dCTP was fully replaced by N4medCTP, even with the slowdown protocol, except at elevated N4medCTP concentrations, and, compared to PCR conducted exclusively with dCTP, the use of N4medCTP:dCTP mixtures gave reduced yields and distinctly higher Cq values, regardless of the thermal program employed. PCR experiments with 9°N DNA polymerase using N4medCTP in the conventional thermal protocol failed to produce the 200-bp amplicon.
Collapse
|
26
|
Jin L, Wang W, Hu D, Min S. Effects of Protonation and C5 Methylation on the Electrophilic Addition Reaction of Cytosine: A Computational Study. J Phys Chem B 2012; 117:3-12. [DOI: 10.1021/jp304282z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Lingxia Jin
- Key Laboratory for
Macromolecular Science of Shaanxi Province, School of
Chemistry and Chemical Engineering, Shaanxi Normal University, Xi′an 710062, China
- School of Chemical
and Environmental Sciences, Shaanxi University of Technology, Hanzhong 723001, China
| | - Wenliang Wang
- Key Laboratory for
Macromolecular Science of Shaanxi Province, School of
Chemistry and Chemical Engineering, Shaanxi Normal University, Xi′an 710062, China
| | - Daodao Hu
- Key Laboratory for
Macromolecular Science of Shaanxi Province, School of
Chemistry and Chemical Engineering, Shaanxi Normal University, Xi′an 710062, China
| | - Suotian Min
- School of Chemical
and Environmental Sciences, Shaanxi University of Technology, Hanzhong 723001, China
| |
Collapse
|
27
|
Morell C, Herrera B, Gutiérrez-Oliva S, Cerón ML, Grand A, Toro-Labbé A. A Relation between Different Scales of Electrophilicity: Are the Scales Consistent Along a Chemical Reaction? J Phys Chem A 2012; 116:7074-81. [DOI: 10.1021/jp209955c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christophe Morell
- CEA Grenoble -INAC/SCIB/LAN
(UMR-E n°3 CEA-UJF)), CEA-Grenoble, 17, rue des Martyrs, F-38054
Grenoble Cedex 9, France
| | - Bárbara Herrera
- Laboratorio de Química
Teórica Computacional (QTC), Facultad de Química, Pontifica Universidad Católica de Chile, Casilla
306, Correo 22, Santiago, Chile
| | - Soledad Gutiérrez-Oliva
- Laboratorio de Química
Teórica Computacional (QTC), Facultad de Química, Pontifica Universidad Católica de Chile, Casilla
306, Correo 22, Santiago, Chile
| | - Maria-Luisa Cerón
- Laboratorio de Química
Teórica Computacional (QTC), Facultad de Química, Pontifica Universidad Católica de Chile, Casilla
306, Correo 22, Santiago, Chile
| | - André Grand
- CEA Grenoble -INAC/SCIB/LAN
(UMR-E n°3 CEA-UJF)), CEA-Grenoble, 17, rue des Martyrs, F-38054
Grenoble Cedex 9, France
| | - Alejandro Toro-Labbé
- Laboratorio de Química
Teórica Computacional (QTC), Facultad de Química, Pontifica Universidad Católica de Chile, Casilla
306, Correo 22, Santiago, Chile
| |
Collapse
|
28
|
Containment of bioaerosol infection risk by the Xpert MTB/RIF assay and its applicability to point-of-care settings. J Clin Microbiol 2010; 48:3551-7. [PMID: 20720033 DOI: 10.1128/jcm.01053-10] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The recently introduced Xpert MTB/RIF assay (Xpert) has point-of-care potential, but its capacity for biohazard containment remained to be studied. We compared the bioaerosols generated by the Xpert assay to acid-fast bacillus (AFB) microscope slide smear preparation. The Xpert assay sample treatment reagent (SR) was also studied for its sterilizing capacity, stability, and effect on assay sensitivity after prolonged treatment. During the preparation of AFB smears, sputum samples spiked with Mycobacterium bovis BCG at 5 × 10(8) CFU/ml produced 16 and 325 CFU/m(3) air measured with an Andersen impactor or BioSampler, respectively. In contrast, neither the sample preparation steps for the Xpert assay nor its automated processing produced any culturable bioaerosols. In testing of SR sterilizing capacity, clinical sputum samples from strongly smear-positive tuberculosis patients treated with SR at a 2:1 ratio eliminated Mycobacterium tuberculosis growth in all but 1/39 or 3/45 samples cultured on solid or liquid medium, respectively. These few unsterilized samples had a mean 13.1-day delay in the time to positive culture. SR treatment at a 3:1 ratio eliminated growth in all samples. SR retained a greater than 6-log-unit killing capacity despite storage at temperatures spanning 4 to 45°C for at least 3 months. The effect of prolonged SR sample treatment was also studied. Spiked sputum samples could be incubated in SR for up to 3 days without affecting Xpert sensitivity for M. tuberculosis detection and up to 8 h without affecting specificity for rifampin resistance detection. These results suggest that benchtop use of the Xpert MTB/RIF assay limits infection risk to the user.
Collapse
|
29
|
Li JB, Gao Y, Aach J, Zhang K, Kryukov GV, Xie B, Ahlford A, Yoon JK, Rosenbaum AM, Zaranek AW, LeProust E, Sunyaev SR, Church GM. Multiplex padlock targeted sequencing reveals human hypermutable CpG variations. Genome Res 2009; 19:1606-15. [PMID: 19525355 DOI: 10.1101/gr.092213.109] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Utilizing the full power of next-generation sequencing often requires the ability to perform large-scale multiplex enrichment of many specific genomic loci in multiple samples. Several technologies have been recently developed but await substantial improvements. We report the 10,000-fold improvement of a previously developed padlock-based approach, and apply the assay to identifying genetic variations in hypermutable CpG regions across human chromosome 21. From approximately 3 million reads derived from a single Illumina Genome Analyzer lane, approximately 94% (approximately 50,500) target sites can be observed with at least one read. The uniformity of coverage was also greatly improved; up to 93% and 57% of all targets fell within a 100- and 10-fold coverage range, respectively. Alleles at >400,000 target base positions were determined across six subjects and examined for single nucleotide polymorphisms (SNPs), and the concordance with independently obtained genotypes was 98.4%-100%. We detected >500 SNPs not currently in dbSNP, 362 of which were in targeted CpG locations. Transitions in CpG sites were at least 13.7 times more abundant than non-CpG transitions. Fractions of polymorphic CpG sites are lower in CpG-rich regions and show higher correlation with human-chimpanzee divergence within CpG versus non-CpG sites. This is consistent with the hypothesis that methylation rate heterogeneity along chromosomes contributes to mutation rate variation in humans. Our success suggests that targeted CpG resequencing is an efficient way to identify common and rare genetic variations. In addition, the significantly improved padlock capture technology can be readily applied to other projects that require multiplex sample preparation.
Collapse
Affiliation(s)
- Jin Billy Li
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Labet V, Morell C, Cadet J, Eriksson LA, Grand A. Hydrolytic Deamination of 5-Methylcytosine in Protic Medium—A Theoretical Study. J Phys Chem A 2009; 113:2524-33. [DOI: 10.1021/jp808902j] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vanessa Labet
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E n°3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology, and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
| | - Christophe Morell
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E n°3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology, and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
| | - Jean Cadet
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E n°3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology, and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
| | - Leif A. Eriksson
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E n°3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology, and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
| | - André Grand
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E n°3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology, and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
| |
Collapse
|
31
|
Alvarez-Salgado F, Desvaux H, Boulard Y. NMR assessment of the global shape of a non-labelled DNA dodecamer containing a tandem of G-T mismatches. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2006; 44:1081-9. [PMID: 16972306 DOI: 10.1002/mrc.1902] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We have carried out a solution study of two non-labelled self-complementary DNA dodecamers d(GACTGTACAGTC)2 and d(GACTGTGCAGTC)2 by NMR, the second sequence composed of two G-T mismatches. Structures were determined using distances extracted from NOE effects alone or using both NOE and RDC constraints, measured in three different liquid crystalline media. We ensured that our data on the influence of the mesogen on the DNA structures, and the way in which the RDCs were incorporated as constraints in the protocol refinement, were consistent. We also tested the influence of different sets of RDCs and the best means of optimizing the calculation of D(a) and R. Resolution and accuracy of the ten best energy final structures were compared. The addition of a small set of RDC constraints significantly improves the final determined structures. We took advantage of the specificity of the RDC, i.e. it contains orientational information, and explored the global shape of the DNA duplexes; it was found that the duplexes do not have a large curvature. For the G-T base pair, we observed, in this particular sequence (tandem of G-T mismatches), a new pattern of base pairing, which involved the formation of a bifurcated hydrogen bond.
Collapse
Affiliation(s)
- Francisco Alvarez-Salgado
- Laboratoire du Contrôle du Cycle Cellulaire, DSV/DBJC, Service de Biochimie et de Génétique Moléculaire, CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France
| | | | | |
Collapse
|
32
|
Angelov A, Liebl W. Insights into extreme thermoacidophily based on genome analysis of Picrophilus torridus and other thermoacidophilic archaea. J Biotechnol 2006; 126:3-10. [PMID: 16621083 DOI: 10.1016/j.jbiotec.2006.02.017] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2005] [Revised: 01/11/2006] [Accepted: 02/17/2006] [Indexed: 12/01/2022]
Abstract
Thermoacidophiles are prokaryotic microorganisms with the stunning capability to survive and multiply at extremely low pH and simultaneously at high temperatures. The mechanisms by which these organisms, exclusively members of the Archaea, cope with their harsh surroundings are poorly understood. The genome sequences of several representatives of the thermoacidophilic genera Picrophilus, Thermoplasma and Sulfolobus have recently become available. Genome-wide comparison has revealed a number of features as possible facets of the overall acidophilic survival strategy of the most thermoacidophilic organisms known, such as a high ratio of secondary over primary transport systems, the composition of the respiratory chain, and the frequent genetic input via lateral gene transfer (LGT) during evolution.
Collapse
Affiliation(s)
- A Angelov
- Institute of Microbiology and Genetics, University of Goettingen, Grisebachstrasse 8, D-37077 Goettingen, Germany
| | | |
Collapse
|
33
|
Abstract
5-Methylcytosine in DNA is genetically unstable. Methylated CpG (mCpG) sequences frequently undergo mutation resulting in a general depletion of this dinucleotide sequence in mammalian genomes. In human genetic disease- and cancer-relevant genes, mCpG sequences are mutational hotspots. It is an almost universally accepted dogma that these mutations are caused by random deamination of 5-methylcytosines. However, it is plausible that mCpG transitions are not caused simply by spontaneous deamination of 5-methylcytosine in double-stranded DNA but by other processes including, for example, mCpG-specific base modification by endogenous or exogenous mutagens or, alternatively, by secondary factors operating at mCpG sequences and promoting deamination. We also discuss that mCpG sequences are favored targets for specific exogenous mutagens and carcinogens. When adjacent to another pyrimidine, 5-methylcytosine preferentially undergoes sunlight-induced pyrimidine dimer formation. Certain polycyclic aromatic hydrocarbons form guanine adducts and induce G to T transversion mutations with high selectivity at mCpG sequences.
Collapse
Affiliation(s)
- G P Pfeifer
- Division of Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA.
| |
Collapse
|
34
|
Hayatsu H. Bisulfite Modification of Cytosine and 5-Methylcytosine as used in Epigenetic Studies. Genes Environ 2006. [DOI: 10.3123/jemsge.28.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
|
35
|
Fujimoto K, Matsuda S, Yoshimura Y, Matsumura T, Hayashi M, Saito I. Site-specific transition of cytosine to uracil via reversible DNA photoligation. Chem Commun (Camb) 2006:3223-5. [PMID: 17028750 DOI: 10.1039/b605289d] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report that deamination coupled with 5-carboxyvinyldeoxyuridine-mediated photobranching causes the heat-induced transition of cytosine to uracil with high efficiency without any side reaction.
Collapse
Affiliation(s)
- Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa 923-1292, Japan.
| | | | | | | | | | | |
Collapse
|
36
|
Fütterer O, Angelov A, Liesegang H, Gottschalk G, Schleper C, Schepers B, Dock C, Antranikian G, Liebl W. Genome sequence of Picrophilus torridus and its implications for life around pH 0. Proc Natl Acad Sci U S A 2004; 101:9091-6. [PMID: 15184674 PMCID: PMC428478 DOI: 10.1073/pnas.0401356101] [Citation(s) in RCA: 154] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2004] [Indexed: 11/18/2022] Open
Abstract
The euryarchaea Picrophilus torridus and Picrophilus oshimae are able to grow around pH 0 at up to 65 degrees C, thus they represent the most thermoacidophilic organisms known. Several features that may contribute to the thermoacidophilic survival strategy of P. torridus were deduced from analysis of its 1.55-megabase genome. P. torridus has the smallest genome among nonparasitic aerobic microorganisms growing on organic substrates and simultaneously the highest coding density among thermoacidophiles. An exceptionally high ratio of secondary over ATP-consuming primary transport systems demonstrates that the high proton concentration in the surrounding medium is extensively used for transport processes. Certain genes that may be particularly supportive for the extreme lifestyle of P. torridus appear to have been internalized into the genome of the Picrophilus lineage by horizontal gene transfer from crenarchaea and bacteria. Finally, it is noteworthy that the thermoacidophiles from phylogenetically distant branches of the Archaea apparently share an unexpectedly large pool of genes.
Collapse
Affiliation(s)
- O Fütterer
- Institut of Microbiology and Genetics, University of Goettingen, Grisebachstrasse 8, D-37075 Goettingen, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Lee I, Dombkowski AA, Athey BD. Guidelines for incorporating non-perfectly matched oligonucleotides into target-specific hybridization probes for a DNA microarray. Nucleic Acids Res 2004; 32:681-90. [PMID: 14757833 PMCID: PMC373323 DOI: 10.1093/nar/gkh196] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sequence-specific oligonucleotide probes play a crucial role in hybridization techniques including PCR, DNA microarray and RNA interference. Once the entire genome becomes the search space for target genes/genomic sequences, however, cross-hybridization to non-target sequences becomes a problem. Large gene families with significant similarity among family members, such as the P450s, are particularly problematic. Additionally, accurate single nucleotide polymorphism (SNP) detection depends on probes that can distinguish between nearly identical sequences. Conventional oligonucleotide probes that are perfectly matched to target genes/genomic sequences are often unsuitable in such cases. Carefully designed mismatches can be used to decrease cross-hybridization potential, but implementing all possible mismatch probes is impractical. Our study provides guidelines for designing non-perfectly matched DNA probes to target DNA sequences as desired throughout the genome. These guidelines are based on the analysis of hybridization data between perfectly matched and non-perfectly matched DNA sequences (single-point or double-point mutated) calculated in silico. Large changes in hybridization temperature predicted by these guidelines for non-matched oligonucleotides fit independent experimental data very well. Applying the guidelines to find oligonucleotide microarray probes for P450 genes, we confirmed the ability of our point mutation method to differentiate the individual genes in terms of thermodynamic calculations of hybridization and sequence similarity.
Collapse
Affiliation(s)
- Inhan Lee
- Michigan Center for Biological Information and Department of Psychiatry, University of Michigan, 3600 Green Court, Suite 700, Ann Arbor, MI 48105, USA.
| | | | | |
Collapse
|
38
|
Kim AS, Thilly WG. Ligation of high-melting-temperature 'clamp' sequence extends the scanning range of rare point-mutational analysis by constant denaturant capillary electrophoresis (CDCE) to most of the human genome. Nucleic Acids Res 2003; 31:e97. [PMID: 12907749 PMCID: PMC169989 DOI: 10.1093/nar/gng099] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Mutations cause or influence the prevalence of many diseases. In human tissues, somatic point mutations have been observed at fractions at or below 4/10,000 and 5/100,000 in mitochondrial and nuclear DNA, respectively. In human populations, fractions for the multiple alleles that code for recessive deleterious syndromes are not expected to exceed 5 x 10(-4). Both nuclear and mitochondrial point mutations have been measured in human cells and tissues at fractions approaching 10(-6) using constant denaturant capillary electrophoresis (CDCE) coupled with high-fidelity PCR (hifiPCR). However, this approach is only applicable to those target sequences (approximately 100 bp) juxtaposed with a 'clamp', a higher-melting-temperature sequence, in genomic DNA; such naturally clamped targets represent approximately 9% of the human genome. To open up most of the human genome to rare point-mutational analysis, a high-efficiency DNA ligation procedure was recently developed so that a clamp could be attached to any target of interest. We coupled this ligation procedure with prior CDCE/hifiPCR and achieved a sensitivity of 2 x 10(-5) in human cells for the first time using an externally attached clamp. At this sensitivity, somatic mutations, each representing an anatomically distinct cluster of cells (turnover unit) derived from a mutant stem cell, may be detected in a series of tissue samples, each containing as many as 5 x 10(4) turnover units. Additionally, rare inherited mutations may be scanned in pooled DNA samples, each derived from as many as 10(5) persons.
Collapse
Affiliation(s)
- Andrea S Kim
- Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | | |
Collapse
|
39
|
|
40
|
Isaacs RJ, Rayens WS, Spielmann HP. Structural differences in the NOE-derived structure of G-T mismatched DNA relative to normal DNA are correlated with differences in (13)C relaxation-based internal dynamics. J Mol Biol 2002; 319:191-207. [PMID: 12051946 DOI: 10.1016/s0022-2836(02)00265-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Detailed description of the characteristics of mismatched DNA that are distinct from normal DNA is vital to the understanding of how mismatch repair proteins are able to recognize and repair these DNA lesions. To this end, we have used nuclear Overhauser effect spectroscopy (NOESY)-based distance restraints and (13)C relaxation measurements to solve the solution structures and measure some of the internal dynamics of the G-T mismatched DNA oligomer d(CCATGCGTGG)(2) (GT) and its parent DNA sequence d(CCACGCGTGG)(2) (GC). In GT, the mismatched G7 is structurally perturbed much more than the mismatched T4 relative to their corresponding bases in GC. The degree of G7 displacement differs from previous high-resolution structures of G-T mismatch-containing B-DNA, suggesting a dependence of G-T mismatch-induced structural perturbation on sequence context. The internal dynamics of GC and GT differ on multiple timescales. The mismatched G7 of GT contains spins that decrease significantly in order in GT compared to GC, while spins in C6, T8, and A3 have significantly higher order in GT compared to GC. Linear correlations between helical parameters of GC and GT and the order of C-1' and aromatic methine carbon atoms relate differences in internal dynamics to the structures quantitatively. The dynamic differences between the normal and mismatched DNA signify changes in local flexibility that may be exploited by the mismatch repair system to bind mismatched DNA preferentially while ignoring normal DNA.
Collapse
Affiliation(s)
- Richard J Isaacs
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536-0084, USA
| | | | | |
Collapse
|
41
|
Chan MF, van Amerongen R, Nijjar T, Cuppen E, Jones PA, Laird PW. Reduced rates of gene loss, gene silencing, and gene mutation in Dnmt1-deficient embryonic stem cells. Mol Cell Biol 2001; 21:7587-600. [PMID: 11604495 PMCID: PMC99930 DOI: 10.1128/mcb.21.22.7587-7600.2001] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Tumor suppressor gene inactivation is a crucial event in oncogenesis. Gene inactivation mechanisms include events resulting in loss of heterozygosity (LOH), gene mutation, and transcriptional silencing. The contribution of each of these different pathways varies among tumor suppressor genes and by cancer type. The factors that influence the relative utilization of gene inactivation pathways are poorly understood. In this study, we describe a detailed quantitative analysis of the three major gene inactivation mechanisms for a model gene at two different genomic integration sites in mouse embryonic stem (ES) cells. In addition, we targeted the major DNA methyltransferase gene, Dnmt1, to investigate the relative contribution of DNA methylation to these various competing gene inactivation pathways. Our data show that gene loss is the predominant mode of inactivation of a herpes simplex virus thymidine kinase neomycin phosphotransferase reporter gene (HSV-TKNeo) at the two integration sites tested and that this event is significantly reduced in Dnmt1-deficient cells. Gene silencing by promoter methylation requires Dnmt1, suggesting that the expression of Dnmt3a and Dnmt3b alone in ES cells is insufficient to achieve effective gene silencing. We used a novel assay to show that missense mutation rates are also substantially reduced in Dnmt1-deficient cells. This is the first direct demonstration that DNA methylation affects point mutation rates in mammalian cells. Surprisingly, the fraction of CpG transition mutations was not reduced in Dnmt1-deficient cells. Finally, we show that methyl group-deficient growth conditions do not cause an increase in missense mutation rates in Dnmt1-proficient cells, as predicted by methyltransferase-mediated mutagenesis models. We conclude that Dnmt1 deficiency and the accompanying genomic DNA hypomethylation result in a reduction of three major pathways of gene inactivation in our model system.
Collapse
Affiliation(s)
- M F Chan
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, 90089-9176, USA
| | | | | | | | | | | |
Collapse
|
42
|
Karino N, Ueno Y, Matsuda A. Synthesis and properties of oligonucleotides containing 5-formyl-2'-deoxycytidine: in vitro DNA polymerase reactions on DNA templates containing 5-formyl-2'-deoxycytidine. Nucleic Acids Res 2001; 29:2456-63. [PMID: 11410651 PMCID: PMC55734 DOI: 10.1093/nar/29.12.2456] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Oligodeoxynucleotides (ODNs) containing 5-formyl-2'-deoxycytidine (fC) were synthesized by the phosphoramidite method and subsequent oxidation with sodium periodate. The stabilities of duplexes containing A, G, C or T opposite fC were studied by thermal denaturation. It was found that fC:A, fC:C or fC:T base pairs significantly reduce the thermal stabilities of duplexes. Next, single nucleotide insertion reactions were performed using ODNs containing fC as templates and the Klenow fragment of Escherichia coli DNA polymerase I. It was found that: (i) insertion of dGMP opposite fC appears to be less efficient relative to insertion opposite 5-methyl-2'-deoxycytidine (mC); (ii) dAMP is misincorporated more frequently opposite fC than mC, although the frequency of misincorporation seems to be dependent on the sequence; (iii) TMP is misincorporated more frequently opposite fC than mC. These results suggest that fC may induce the transition mutation C.G-->T.A and the transversion mutation C.G-->A.T during DNA synthesis.
Collapse
Affiliation(s)
- N Karino
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | | | | |
Collapse
|
43
|
Su S, Gao YG, Robinson H, Liaw YC, Edmondson SP, Shriver JW, Wang AH. Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs. J Mol Biol 2000; 303:395-403. [PMID: 11031116 DOI: 10.1006/jmbi.2000.4112] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Sso7d and Sac7d are two small chromatin proteins from the hyperthermophilic archaeabacterium Sulfolobus solfataricus and Sulfolobus acidocaldarius, respectively. The crystal structures of Sso7d-GTGATCGC, Sac7d-GTGATCGC and Sac7d-GTGATCAC have been determined and refined at 1.45 A, 2.2 A and 2.2 A, respectively, to investigate the DNA binding property of Sso7d/Sac7d in the presence of a T-G mismatch base-pair. Detailed structural analysis revealed that the intercalation site includes the T-G mismatch base-pair and Sso7d/Sac7d bind to that mismatch base-pair in a manner similar to regular DNA. In the Sso7d-GTGATCGC complex, a new inter-strand hydrogen bond between T2O4 and C14N4 is formed and well-order bridging water molecules are found. The results suggest that the less stable DNA stacking site involving a T-G mismatch may be a preferred site for protein side-chain intercalation.
Collapse
Affiliation(s)
- S Su
- Center for Biophysics and COmputational BIology, University of Illinois at Urbana-Champaign, 61801, USA
| | | | | | | | | | | | | |
Collapse
|
44
|
Machwe A, Orren DK, Bohr VA. Accelerated methylation of ribosomal RNA genes during the cellular senescence of Werner syndrome fibroblasts. FASEB J 2000; 14:1715-24. [PMID: 10973920 DOI: 10.1096/fj.99-0926com] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Ribosomal DNA (rDNA) metabolism has been implicated in cellular and organismal aging. The role of rDNA in premature and normal human aging was investigated by measuring rDNA gene copy number, the level of rDNA methylation, and rRNA expression during the in vitro senescence of primary fibroblasts from normal (young and old) donors and from Werner syndrome (WS) patients. In comparison to their normal counterparts, WS fibroblasts grew slowly and reached senescence after fewer doublings. The rDNA copy number did not change significantly throughout the life span of both normal and WS fibroblasts. However, in senescent WS and normal old fibroblasts, we detected rDNA species with unusually slow electrophoretic mobility. Cellular aging in Saccharomyces cerevisiae is accompanied by the formation and accumulation of rDNA circles. Our analysis revealed that the rDNA species observed in this study were longer, linear rDNA molecules attributable to the inhibition of ECO:RI cleavage by methylation. Furthermore, isoschizomeric restriction analysis confirmed that in vitro senescence of fibroblasts is accompanied by significant increases in cytosine methylation within rDNA genes. This increased methylation is maximal during the abbreviated life span of WS fibroblasts. Despite increased methylation of rDNA in senescent cells, the steady-state levels of 28S rRNA remained constant over the life span of both normal and WS fibroblasts.
Collapse
Affiliation(s)
- A Machwe
- Laboratory of Molecular Genetics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | | | | |
Collapse
|
45
|
Affiliation(s)
- G P Pfeifer
- Department of Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA.
| | | | | |
Collapse
|
46
|
Abstract
The occurrence of tumor-specific mutational spectra in the p53 mutation database provides indirect evidence that implicates certain exogenous and possibly endogenous mutagenic events in human carcinogenesis. In some cases, the distribution of DNA damage along the p53 gene caused by environmental carcinogens can be correlated with the mutational spectra, i.e. hotspots and types of mutations of certain cancers, most notably for nonmelanoma skin cancers and lung cancers in smokers. This concept has been validated by experiments with sunlight and cigarette smoke components representing the polycyclic aromatic hydrocarbon class of carcinogens. A disproportionally high number of mutations in p53 (and other genes) are found at methylated CpG dinucleotides. These sequences are particularly prone to mutagenesis involving endogenous events as well as modification by exogenous carcinogens.
Collapse
Affiliation(s)
- G P Pfeifer
- Department of Biology, Beckman Research Institute of the City of Hope, 1450 East Duarte Road, Duarte, CA 91010, USA.
| |
Collapse
|
47
|
Murata-Kamiya N, Kamiya H, Karino N, Ueno Y, Kaji H, Matsuda A, Kasai H. Formation of 5-formyl-2'-deoxycytidine from 5-methyl-2'-deoxycytidine in duplex DNA by Fenton-type reactions and gamma-irradiation. Nucleic Acids Res 1999; 27:4385-90. [PMID: 10536146 PMCID: PMC148720 DOI: 10.1093/nar/27.22.4385] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
5-methyl-2'-deoxycytidine (5-Me-dC) is formed by the enzymatic methylation of dC, primarily in CpG sequences in DNA, and is involved in the regulation of gene expression. In the present study, 5-Me-dC and double-stranded DNA fragments containing 5-Me-dC were either gamma-irradiated or aerobically treated with Fenton-type reagents, Fe(II)-EDTA, Fe(II)-nitrilotriacetic acid, Fe(III)-EDTA-H(2)O(2)-catechol or ascorbic acid-H(2)O(2) under neutral conditions. The formation of 5-formyl-2'-deoxycytidine (5-CHO-dC) was observed upon treatment of both 5-Me-dC and DNA fragments containing 5-Me-dC. The yields of 5-CHO-dC from 5-Me-dC and those of 5-formyl-2'-deoxyuridine from dT were comparable. These results suggest that 5-Me-dC in DNA is as susceptible to oxidation as dT in cells, and raise the possibility that 5-CHO-dC may contribute to the high mutagenic rate observed in CpG sequences in genomic DNA.
Collapse
Affiliation(s)
- N Murata-Kamiya
- Department of Health Policy and Management, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Kitakyushu, Japan
| | | | | | | | | | | | | |
Collapse
|
48
|
Abstract
It is now generally accepted that the presence of 5-methylcytosine (5mC) in human DNA has both a genetic and an epigenetic effect on cellular development, differentiation and transformation. First, 5mC is more unstable than its unmethylated counterpart cytosine. Hydrolytic deamination of 5mC leads to a G/T mismatch and subsequently, if unrepaired, to a C-->T transition mutation. Sites of DNA methylation are mutational hotspots in many human tumors. Second, DNA methylation of promoter regions is often correlated with the down regulation of the corresponding gene. Both of these effects have fundamental consequences for basic functions of the cell like cellular differentiation, the development of cancer and possibly other diseases, and on the evolutionary process. Recent hypotheses also propose a role for methylation in the process of aging. In this review we will describe recent findings and hypotheses about the function of 5mC in DNA with the focus on its involvement in human carcinogenesis.
Collapse
Affiliation(s)
- C Schmutte
- Thomas Jefferson University, Kimmel Cancer Center, Philadelphia, PA 19107, USA
| | | |
Collapse
|
49
|
Nyce JW. Drug-induced DNA hypermethylation: a potential mediator of acquired drug resistance during cancer chemotherapy. Mutat Res 1997; 386:153-61. [PMID: 9113116 DOI: 10.1016/s1383-5742(96)00051-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- J W Nyce
- Department of Molecular Pharmacology and Therapeutics, EpiGenesis Pharmaceuticals, Greenville, NC 27858, USA
| |
Collapse
|
50
|
Cadet J, Berger M, Douki T, Ravanat JL. Oxidative damage to DNA: formation, measurement, and biological significance. Rev Physiol Biochem Pharmacol 1997; 131:1-87. [PMID: 9204689 DOI: 10.1007/3-540-61992-5_5] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- J Cadet
- Départament de Recherche Fondamentale sur la Matière Condensée, Commissariat à l'Energie Atomique/Grenoble, France
| | | | | | | |
Collapse
|