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Khoshkhoo S, Lal D, Walsh CA. Application of single cell genomics to focal epilepsies: A call to action. Brain Pathol 2021; 31:e12958. [PMID: 34196990 PMCID: PMC8412079 DOI: 10.1111/bpa.12958] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 12/24/2022] Open
Abstract
Focal epilepsies are the largest epilepsy subtype and associated with significant morbidity. Somatic variation is a newly recognized genetic mechanism underlying a subset of focal epilepsies, but little is known about the processes through which somatic mosaicism causes seizures, the cell types carrying the pathogenic variants, or their developmental origin. Meanwhile, the inception of single cell biology has completely revolutionized the study of neurological diseases and has the potential to answer some of these key questions. Focusing on single cell genomics, transcriptomics, and epigenomics in focal epilepsy research, circumvents the averaging artifact associated with studying bulk brain tissue and offers the kind of granularity that is needed for investigating the consequences of somatic mosaicism. Here we have provided a brief overview of some of the most developed single cell techniques and the major considerations around applying them to focal epilepsy research.
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Affiliation(s)
- Sattar Khoshkhoo
- Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.,Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dennis Lal
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Cologne Center for Genomics, University of Cologne, Cologne, Germany.,Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.,Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
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2
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Karemaker ID, Vermeulen M. Single-Cell DNA Methylation Profiling: Technologies and Biological Applications. Trends Biotechnol 2018; 36:952-965. [PMID: 29724495 DOI: 10.1016/j.tibtech.2018.04.002] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/05/2018] [Accepted: 04/06/2018] [Indexed: 12/18/2022]
Abstract
DNA methylation is an epigenetic modification that plays an important role in gene expression regulation, development, and disease. Recent technological innovations have spurred the development of methods that enable us to study the occurrence and biology of this mark at the single-cell level. Apart from answering fundamental biological questions about heterogeneous systems or rare cell types, low-input methods also bring clinical applications within reach. Ultimately, integrating these data with other single-cell data sets will allow deciphering multiple layers of gene expression regulation within each individual cell. Here, we review the approaches that have been developed to facilitate single-cell DNA methylation profiling, their biological applications, and how these will further our understanding of the biology of DNA methylation.
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Affiliation(s)
- Ino D Karemaker
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands.
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3
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Tang Q, Cai A, Bian K, Chen F, Delaney JC, Adusumalli S, Bach AC, Akhlaghi F, Cho BP, Li D. Characterization of Byproducts from Chemical Syntheses of Oligonucleotides Containing 1-Methyladenine and 3-Methylcytosine. ACS OMEGA 2017; 2:8205-8212. [PMID: 29214236 PMCID: PMC5709782 DOI: 10.1021/acsomega.7b01482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 11/01/2017] [Indexed: 06/07/2023]
Abstract
Oligonucleotides serve as important tools for biological, chemical, and medical research. The preparation of oligonucleotides through automated solid-phase synthesis is well-established. However, identification of byproducts generated from DNA synthesis, especially from oligonucleotides containing site-specific modifications, is sometimes challenging. Typical high-performance liquid chromatography (HPLC), mass spectrometry (MS), and gel electrophoresis methods alone are not sufficient for characterizing unexpected byproducts, especially for those having identical or very similar molecular weight (MW) to the products. We used a rigorous quality control procedure to characterize byproducts generated during oligonucleotide syntheses: (1) purify oligonucleotides by different HPLC systems; (2) determine exact MW by high-resolution MS; (3) locate modification position by MS/MS or exonuclease digestion with matrix-assisted laser desorption ionization-time of flight analysis; and (4) conduct, where applicable, enzymatic assays. We applied these steps to characterize byproducts in the syntheses of oligonucleotides containing biologically important methyl DNA adducts 1-methyladenine (m1A) and 3-methylcytosine (m3C). In m1A synthesis, we differentiated a regioisomeric byproduct 6-methyladenine, which possesses a MW identical to uncharged m1A. As for m3C, we identified a deamination byproduct 3-methyluracil, which is only 1 Da greater than uncharged m3C in the ∼4900 Da context. The detection of these byproducts would be very challenging if the abovementioned procedure was not adopted.
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Affiliation(s)
- Qi Tang
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - Ang Cai
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - Ke Bian
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - Fangyi Chen
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - James C. Delaney
- Visterra
Inc., One Kendall Square, Cambridge, Massachusetts 02139, United States
| | - Sravani Adusumalli
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - Alvin C. Bach
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - Fatemeh Akhlaghi
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - Bongsup P. Cho
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - Deyu Li
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
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4
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Li D, Delaney JC, Page CM, Chen AS, Wong C, Drennan CL, Essigmann JM. Repair of DNA Alkylation Damage by the Escherichia coli Adaptive Response Protein AlkB as Studied by ESI-TOF Mass Spectrometry. J Nucleic Acids 2010; 2010:369434. [PMID: 21048928 PMCID: PMC2965429 DOI: 10.4061/2010/369434] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 09/15/2010] [Indexed: 11/20/2022] Open
Abstract
DNA alkylation can cause mutations, epigenetic changes, and even cell death. All living organisms have evolved enzymatic and non-enzymatic strategies for repairing such alkylation damage. AlkB, one of the Escherichia coli adaptive response proteins, uses an α-ketoglutarate/Fe(II)-dependent mechanism that, by chemical oxidation, removes a variety of alkyl lesions from DNA, thus affording protection of the genome against alkylation. In an effort to understand the range of acceptable substrates for AlkB, the enzyme was incubated with chemically synthesized oligonucleotides containing alkyl lesions, and the reaction products were analyzed by electrospray ionization time-of-flight (ESI-TOF) mass spectrometry. Consistent with the literature, but studied comparatively here for the first time, it was found that 1-methyladenine, 1,N (6)-ethenoadenine, 3-methylcytosine, and 3-ethylcytosine were completely transformed by AlkB, while 1-methylguanine and 3-methylthymine were partially repaired. The repair intermediates (epoxide and possibly glycol) of 3,N (4)-ethenocytosine are reported for the first time. It is also demonstrated that O (6)-methylguanine and 5-methylcytosine are refractory to AlkB, lending support to the hypothesis that AlkB repairs only alkyl lesions attached to the nitrogen atoms of the nucleobase. ESI-TOF mass spectrometry is shown to be a sensitive and efficient tool for probing the comparative substrate specificities of DNA repair proteins in vitro.
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Affiliation(s)
- Deyu Li
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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5
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Shrivastav N, Li D, Essigmann JM. Chemical biology of mutagenesis and DNA repair: cellular responses to DNA alkylation. Carcinogenesis 2009; 31:59-70. [PMID: 19875697 DOI: 10.1093/carcin/bgp262] [Citation(s) in RCA: 207] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The reaction of DNA-damaging agents with the genome results in a plethora of lesions, commonly referred to as adducts. Adducts may cause DNA to mutate, they may represent the chemical precursors of lethal events and they can disrupt expression of genes. Determination of which adduct is responsible for each of these biological endpoints is difficult, but this task has been accomplished for some carcinogenic DNA-damaging agents. Here, we describe the respective contributions of specific DNA lesions to the biological effects of low molecular weight alkylating agents.
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Affiliation(s)
- Nidhi Shrivastav
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Delaney JC, Essigmann JM. Mutagenesis, genotoxicity, and repair of 1-methyladenine, 3-alkylcytosines, 1-methylguanine, and 3-methylthymine in alkB Escherichia coli. Proc Natl Acad Sci U S A 2004; 101:14051-6. [PMID: 15381779 PMCID: PMC521119 DOI: 10.1073/pnas.0403489101] [Citation(s) in RCA: 192] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
AlkB repairs 1-alkyladenine and 3-methylcytosine lesions in DNA by directly reversing the base damage. Although repair studies with randomly alkylated substrates have been performed, the miscoding nature of these and related individually alkylated bases and the suppression of mutagenesis by AlkB within cells have not yet been explored. Here, we address the miscoding potential of 1-methyldeoxyadenosine (m1A), 3-methyldeoxycytidine (m3C), 3-ethyldeoxycytidine (e3C), 1-methyldeoxyguanosine (m1G), and 3-methyldeoxythymidine (m3T) by synthesizing single-stranded vectors containing each alkylated base, followed by vector passage through Escherichia coli. In SOS(-), AlkB-deficient cells, m1A was only 1% mutagenic; however, m3C and e3C were 30% mutagenic, rising to 70% in SOS(+) cells. In contrast, the mutagenicity of m1G and m3T in AlkB(-) cells dropped slightly when SOS polymerases were expressed (m1G from 80% to 66% and m3T from 60% to 53%). Mutagenicity was abrogated for m1A, m3C, and e3C in wild-type (AlkB(+)) cells, whereas m3T mutagenicity was only partially reduced. Remarkably, m1G mutagenicity was also eliminated in AlkB(+) cells, establishing it as a natural AlkB substrate. All lesions were blocks to replication in AlkB-deficient cells. The m1A, m3C, and e3C blockades were completely removed in wild-type cells; the m1G blockade was partially removed and that for m3T was unaffected by the presence of AlkB. All lesions demonstrated enhanced bypass when SOS polymerases were induced. This work provides direct evidence that AlkB suppresses both genotoxicity and mutagenesis by physiologically realistic low doses of 1-alkylpurine and 3-alkylpyrimidine DNA damage in vivo.
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Affiliation(s)
- James C Delaney
- Department of Chemistry and Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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7
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Di Pietro MC, Vannoni D, Leoncini R, Liso G, Guerranti R, Marinello E. Determination of urinary methylated purine pattern by high-performance liquid chromatography. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 2001; 751:87-92. [PMID: 11232859 DOI: 10.1016/s0378-4347(00)00471-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe the group selective separation and quantification of unmodified and modified purines in human urine by high-performance reverse phase liquid chromatography. The pattern of oxypurines and methylated purines: hypoxanthine (Hx), xanthine (X), 1-methyl hypoxanthine (1-MHx), 1-methyl guanine (1-MG), 3-methyl guanine (3-MG), 7-methyl guanine (7-MG), 1-methyl xanthine (1-MX), 3-methyl xanthine (3-MX), 7-methyl xanthine (7-MX), 1,7-dimethyl guanine (1,7-dMG), 1,3-dimethyl xanthine (1,3-dMX), 1,7-dimethyl xanthine (3,7-dMX) and 1,3,7-trimethyl xanthine (1,3,7-tMX) were determined in a single run in urine of a healthy subject and a gout patient before and after treatment with allopurinol. This method may be useful to investigate the urinary pattern of methylated bases in diseases involving purine metabolism.
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Affiliation(s)
- M C Di Pietro
- Institute of Biochemistry and Enzymology, University of Siena, Italy
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8
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Mazin AL. Life span prediction from the rate of age-related DNA demethylation in normal and cancer cell lines. Exp Gerontol 1995; 30:475-84. [PMID: 8557095 DOI: 10.1016/0531-5565(95)00004-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A method has been proposed for the Hayflick Limit prediction by the analysis of the 5-methylcytosine content in DNA at earlier and later cell passages. The following facts were used as the basis of the method: (i) the rate of m5C loss from DNA remains approximately constant during cell divisions and it does not depend on the cell donor age; (ii) this rate is inversely proportional to the Hayflick Limit as well as to the life span of cell donor species; (iii) the period corresponded to loss of all m5C residues from the genome coincides with or somewhat exceeds the Hayflick Limit of normal cells. The prognosis of the Hayflick Limit has usually been found in good agreement with the experimental evidences for various human, hamster, and mouse cell lines. The method proposed may be used for early detection of precrisis and cancer cells. The age-related m5C loss may result from accumulation of the m5C-->T+C transitions occurring with DNA methylation in every cell division.
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Affiliation(s)
- A L Mazin
- Laboratory of Molecular Bases of Ontogenesis, A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov State University, Moscow
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9
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Shuker DE. Nucleic acid-carcinogen adducts in human dosimetry. ARCHIVES OF TOXICOLOGY. SUPPLEMENT. = ARCHIV FUR TOXIKOLOGIE. SUPPLEMENT 1989; 13:55-65. [PMID: 2673151 DOI: 10.1007/978-3-642-74117-3_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- D E Shuker
- International Agency for Research on Cancer, Lyon, France
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10
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Abstract
The rates of methylation of total cellular DNA and newly synthesized DNA were measured in four unrelated SV40-transformed human fibroblast lines and in four control parent fibroblast lines. Rates of methylation of total cellular DNA were decreased by a factor of 1.8-2.3 in the transformed cells relative to control cells. Methylation was largely (75%-87%) restricted to newly synthesized DNA in control and transformed fibroblasts, and methylation rates of newly synthesized DNA were diminished in transformed cells by 12- to 19-fold relative to control cells. Growth rates were similar in the normal and transformed cells. The cellular uptake of methionine and conversion to S-adenosylmethionine were similar in the normal and transformed cells, suggesting no major differences between the normal and transformed cells in the cellular transport of methionine, methionine S-adenosyltransferase activity, or the intracellular concentrations of methionine and S-adenosylmethionine. The diminished rates of DNA methylation that we have observed suggest a possible mechanism for altered gene expression and growth control in transformed cells.
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11
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Wilson VL, Smith RA, Autrup H, Krokan H, Musci DE, Le NN, Longoria J, Ziska D, Harris CC. Genomic 5-methylcytosine determination by 32P-postlabeling analysis. Anal Biochem 1986; 152:275-84. [PMID: 3963364 DOI: 10.1016/0003-2697(86)90409-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A simple and sensitive method for the quantitation of 5-methyldeoxycytidine in DNA has been developed by the adaptation of the Randerath 32P-postlabeling technique. Nucleic acids were digested to 3'-monophosphate nucleotides, which were converted to 32P-labeled 3',5'-bisphosphate nucleotides, the 3'-phosphate was cleaved by the action of nuclease P1, and the resultant 5'-[32P]-monophosphate nucleotides were separated by two-dimensional thin-layer chromatography. Less than 1 microgram of DNA was required for the precise quantitation of 5-methyldeoxycytidine content to a detectable limit of 0.01% of the total cytidine residues methylated. The genomic 5-methyldeoxycytidine content may thus be quantitated in tissue samples, small or selective cell populations, senescing or terminally differentiating cells, or DNA from any source. We report here, for the first time, the genomic 5-methyldeoxycytidine content of normal human bronchial epithelial and normal human pulmonary mesothelial cells. The chromatographic separation of all of the normal and some of the rare monophosphate deoxyribonucleotides and ribonucleotides has been characterized. Thus, 5-bromodeoxyuridine and the RNA contamination of DNA or the DNA contamination of RNA can also be quantitated during the same analysis.
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12
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Butkus VV, Klimasauskas SJ, Janulaitis AA. Analysis of products of DNA modification by methylases: a procedure for the determination of 5- and N4-methylcytosines in DNA. Anal Biochem 1985; 148:194-8. [PMID: 2994519 DOI: 10.1016/0003-2697(85)90645-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Although many different methods are used for the identification of methylated heterocyclic bases in DNA not all of them possess the ability to discriminate N4-methylcytosine (m4C) and 5-methylcytosine (m5C). Therefore, some of the methods need additional reexamination. This paper reinvestigates some chromatographic systems (thin-layer chromatography, paper chromatography, electrophoresis) most widely used in the analysis of minor bases occurring in nucleic acids according to their ability to separate m4C and m5C. A simple procedure for the preparation of the sample and a chromatographic system for its analysis was developed. The recommended chromatographic systems may be used for the simultaneous separation of not only of m4C and m5C but also both methylated cytosines together with N6-methyladenine and 7-methylguanine.
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13
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Abstract
Eukaryotic genomes contain 5-methylcytosine (5mC) as a rare base.5mC arises by postsynthetic modification of cytosine and occurs, at least in animals, predominantly in the dinucleotide CpG. The base is not distributed randomly in these genomes but conforms to a pattern. This pattern varies between taxa but appears to be inherited in a semi-conservative fashion. At the level of the genome, gross changes in the level of DNA methylation have been noted. This has encouraged speculation that the modification may play a role in cellular differentiation. Tissue-specific patterns of DNA methylation, predicted by various models of differentiation, have been found for most vertebrate genes so far examined. A correlation has emerged between the undermethylation of these regions and their transcription, but this is not always the case. While data for eukaryotic viral sequences are less equivocal, studies of this kind cannot in isolation distinguish between undermethylation being a cause or a consequence of gene activity. If it were a cause, it is probable that the demethylation of specific CpG sites would be a necessary yet not a sufficient condition for transcription to occur. The introduction of artificially methylated DNA sequences into individual eukaryotic cells by microinjection or transformation may provide the means to elucidate these questions in the future. In the meantime, the study of eukaryotic DNA methylation promises to contribute much to our understanding of the regulation of gene expression in these organisms.
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14
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Achwal CW, Iyer CA, Chandra HS. Immunochemical evidence for the presence of 5mC, 6mA and 7mG in human, Drosophila and mealybug DNA. FEBS Lett 1983; 158:353-8. [PMID: 6409666 DOI: 10.1016/0014-5793(83)80612-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We have reported that production and characterization of antibodies highly specific to 5-methyl-cytosine (5mC) and the development of a sensitive immunochemical method for the detection of 5mC in DNA [FEBS Lett. (1982) 150, 469]. Extension of this method to two other modified bases, 6-methyladenine (6mA) and 7-methylguanine (7mG), is reported here. By use of this immunochemical approach, we are able to detect 5mC, 6mA and 7mG in human and Drosophila DNA and confirm their presence in the DNA of two mealybug species.
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16
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The mealybug chromosome system I: Unusual methylated bases and dinucleotides in DNA of aPlanococcus species. J Biosci 1982. [DOI: 10.1007/bf02704646] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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17
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Yuki H, Yajima T, Kawasaki H, Yamaji A. Analysis of 7-methylguanine in deoxyribonucleic acids by high-performance liquid chromatography. Anal Biochem 1979; 97:203-9. [PMID: 525786 DOI: 10.1016/0003-2697(79)90347-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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18
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Pollock JM, Swihart M, Taylor JH. Methylation of DNA in early development: 5-methyl cytosine content of DNA in sea urchin sperm and embryos. Nucleic Acids Res 1978; 5:4855-61. [PMID: 745996 PMCID: PMC342793 DOI: 10.1093/nar/5.12.4855] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
By separating formic acid hydrolysates with high pressure chromatography on an Aminex-10 column, we determined the ratio of 5-methyl cytosine to cytosine and other bases of DNA from sea urchin sperm and nuclei of embryos from early cleavage through pluteus stages. Contrary to several previous reports, we could not find any measurable changes in the methylation levels of embryonic nuclear DNAs at different stages of development. We also found no consistent differences between the methylation levels of sea urchin sperm and embryonic nuclei or the 5-methyl cytosine content of fish (Mugil cephalus) sperm and liver nuclei. While these measurements would not have detected subtle variations associated with differentiation, they would have indicated the gross changes previously reported for embryos or between sperm and somatic nuclei had those changes been present.
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19
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Sharma S, Biswal N. Studies on the in vivo methylation of replicating herpes simplex virus type 1 DNA. Virology 1977; 82:265-74. [PMID: 199990 DOI: 10.1016/0042-6822(77)90002-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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20
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Pegg AE. Formation and metabolism of alkylated nucleosides: possible role in carcinogenesis by nitroso compounds and alkylating agents. Adv Cancer Res 1977; 25:195-269. [PMID: 326002 DOI: 10.1016/s0065-230x(08)60635-1] [Citation(s) in RCA: 247] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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21
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Nikolskaya II, Lopatina NG, Debov SS. Methylated guanine derivative as a minor base in the DNA of phage DDVI Shigella disenteriae. BIOCHIMICA ET BIOPHYSICA ACTA 1976; 435:206-10. [PMID: 779843 DOI: 10.1016/0005-2787(76)90251-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
7-Methylguanine has been identified in the DNA of phage DDVI, which replicates in Escherichia coli B cells. The amount of this minor base is 0.27 mol per 100 mol of nucleotides. In the DNA of DDVI phage there is no 6-methylaminopurine which is usually a minor component in the DNA of E. coli B and phage T2, yet the DNA of DDVI phage is readily methylated during incubation in vitro with the B-specific methylase and adenosyl[3H]methionine with the label found only in 6-methylaminopurine. An extract of E. coli B cells infected with DDVI phage showed activity of a novel methylase which transfers the [3H]methyl group from S-adenosylmethionine to guanine, leading to the appearance of 7-methylguanine in the acceptor DNA.
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22
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Abstract
A DNA methylase has been purified 270-fold from HeLa cell nuclei by chromatography on DEAE-cellulose, phosphocellulose, and hydroxyapatite. The enzyme transfers methyl groups from S-adenosyl-L-methionine to cytosine residues in DNA. The sole product of the reaction has been identified as 5-methylcytosine. The enzyme is able to methylate homologous (HeLa) DNA, although to a lesser extent than heterologous DNA. This may be due to incomplete methylation of HeLa DNA synthesized in vivo. The HeLa enzyme can methylate single-stranded DNA, and does so to an extent three times greater than that of the corresponding double-stranded DNA. In single-stranded M. luteus DNA, at least 2.4% of the cytosine residues can be methylated in vitro by the enzyme. The enzyme also can methylate poly (dG-dC-dG-dC) and poly (dG, dC). Bilateral nearest neighbors to the 5-methylcytosine have been determined with M. luteus DNA in vitro and HeLa DNA in vivo. The 5' neighbor can be either G or C while the 3' neighbor is always G and this sequence is, thus, p(G/C)pmCpG.
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23
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Nass MM. Differential methylation of mitochondrial and nuclear DNA in cultured mouse, hamster and virus-transformed hamster cells. In vivo and in vitro methylation. J Mol Biol 1973; 80:155-75. [PMID: 4361747 DOI: 10.1016/0022-2836(73)90239-8] [Citation(s) in RCA: 119] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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24
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Gorovsky MA, Hattman S, Pleger GL. ( 6 N)methyl adenine in the nuclear DNA of a eucaryote, Tetrahymena pyriformis. J Cell Biol 1973; 56:697-701. [PMID: 4631666 PMCID: PMC2108936 DOI: 10.1083/jcb.56.3.697] [Citation(s) in RCA: 125] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
DNA isolated from macronuclei of the ciliate, Tetrahymena pyriformis, has been found to contain [(6)N]methyl adenine (MeAde); this represents the first clear demonstration of significant amounts of MeAde in the DNA of a eucaryote. The amounts of macronuclear MeAde differed slightly between different strains of Tetrahymena, with approximately 0.65-0.80% of the adenine bases being methylated. The MeAde content of macronuclear DNA did not seem to vary in different physiological states. The level of MeAde in DNA isolated from micronuclei, on the other hand, was quite low (at least tenfold lower than in macronuclear DNA).
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Lawley PD, Crathorn AR, Shah SA, Smith BA. Biomethylation of deoxyribonucleic acid in cultured human tumour cells (HeLa). Methylated bases other than 5-methylcytosine not detected. Biochem J 1972; 128:133-8. [PMID: 5085550 PMCID: PMC1173577 DOI: 10.1042/bj1280133] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
1. Incorporation of methyl groups from [methyl-(14)C]methionine into DNA of dividing HeLa cells was investigated, essentially by the procedures of Culp, et al. (1970). 2. Contrary to the report of the latter, but in agreement with other work on biomethylation of mammalian DNA, 5-methylcytosine was the sole methylated base detected. 3. Chromatographic separations of 3-methylcytosine from 5-methylcytosine and purines are discussed.
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Fischer MH, Welker C, Waisman HA. Generalized growth retardation in rats induced by prenatal exposure to methylazoxymethyl acetate. TERATOLOGY 1972; 5:223-32. [PMID: 5063372 DOI: 10.1002/tera.1420050212] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Hattman S, Gold E, Plotnik A. Methylation of cytosine residues in DNA controlled by a drug resistance factor (host-induced modification-R factors-N 6 -methyladenine-5-methylcytosine). Proc Natl Acad Sci U S A 1972; 69:187-90. [PMID: 4550503 PMCID: PMC427572 DOI: 10.1073/pnas.69.1.187] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The proportion of 5-methylcytosine (5MeCyt) and 6-methylaminopurine (N(6)-methyladenine, 6MeAde) in bacteriophage P22 DNA was analyzed as a function of the host-specificity the phage carried. In the DNA of P22 grown in strains harboring the modifying drug-resistance-transfer-factor N-3, the 5MeCyt content was at least twice that after growth in strains lacking the factor. In contrast, the 6MeAde level of P22 DNA was unaffected by the presence or absence of the factor. The 6MeAde and 5MeCyt levels were unaffected by factors 222 and N-1, which do not modify phage DNA. The 5MeCyt/6MeAde ratio was only slightly higher in the DNA of Salmonella strains that had received the N-3 factor. After transfer of the N-3 factor to Escherichia coli strain B, which normally lacks 5MeCyt, a high content of 5MeCyt is observed. We conclude that the N-3 factor controls a DNA methylase specific for cytosine residues. If the N-3 host specificity is imparted by cytosine methylation, this would be the first instance where a biological role for 5MeCyt has been elucidated.
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Culp LA, Black PH. DNA synthesis in normal and virus-transformed mammalian cells after methionine deprivation. BIOCHIMICA ET BIOPHYSICA ACTA 1971; 247:220-32. [PMID: 4331337 DOI: 10.1016/0005-2787(71)90672-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Methylation of DNA in the intact animal and the effect of the carcinogens dimethylnitrosamine and ethionine. ACTA ACUST UNITED AC 1971. [DOI: 10.1016/0005-2787(71)90531-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Drahovský D, Morris NR. Mechanism of action of rat liver DNA methylase. I. Interaction with double-stranded methyl-acceptor DNA. J Mol Biol 1971; 57:475-89. [PMID: 4931679 DOI: 10.1016/0022-2836(71)90104-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Srivastava BI. Studies on methylation of nucleic acids in crown gall tumor tissue cultures of tobacco. LIFE SCIENCES. PT. 2: BIOCHEMISTRY, GENERAL AND MOLECULAR BIOLOGY 1970; 9:1315-20. [PMID: 5494943 DOI: 10.1016/0024-3205(70)90131-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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