1
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Li Y, Liang ZY, Wang HL. N6-methyl-2'-deoxyadenosine promotes self-renewal of BFU-E progenitor in erythropoiesis. iScience 2023; 26:106924. [PMID: 37283807 PMCID: PMC10239700 DOI: 10.1016/j.isci.2023.106924] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/08/2023] [Accepted: 05/15/2023] [Indexed: 06/08/2023] Open
Abstract
Red blood cells supply the oxygen required for all human cells and are in demand for emerging blood-loss therapy. Here we identified N6-methyl-2'-deoxyadenosine (6mdA) as an agonist that promotes the hyperproliferation of burst-forming unit erythroid (BFU-E) progenitor cells. In addition, 6mdA represses the apoptosis of erythroid progenitor cells (EPCs). Combined use of with SCF and EPO enabled cultures of isolated BFU-E to be expanded up to 5,000-fold. Transcriptome analysis showed that 6mdA upregulates the expression of the EPC-associated factors c-Kit, Myb, and Gata2 and downregulates that of the erythroid maturation-related transcription factors Gata1, Spi1, and Klf1. Mechanistic studies suggested that 6mdA enhances and prolongs the activation of erythropoiesis-associated master gene c-Kit and its downstream signaling, leading to expansion and accumulation of EPCs. Collectively, we demonstrate that 6mdA can efficiently stimulate the EPC hyperproliferation and provide a new regenerative medicine recipe to improve ex vivo generation of red blood cells.
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Affiliation(s)
- Yao Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zi-Yu Liang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hai-Lin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Environment and Health, Jianghan University, Wuhan, Hubei 430056, China
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2
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Boulias K, Greer EL. Means, mechanisms and consequences of adenine methylation in DNA. Nat Rev Genet 2022; 23:411-428. [PMID: 35256817 PMCID: PMC9354840 DOI: 10.1038/s41576-022-00456-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2022] [Indexed: 12/29/2022]
Abstract
N6-methyl-2'-deoxyadenosine (6mA or m6dA) has been reported in the DNA of prokaryotes and eukaryotes ranging from unicellular protozoa and algae to multicellular plants and mammals. It has been proposed to modulate DNA structure and transcription, transmit information across generations and have a role in disease, among other functions. However, its existence in more recently evolved eukaryotes remains a topic of debate. Recent technological advancements have facilitated the identification and quantification of 6mA even when the modification is exceptionally rare, but each approach has limitations. Critical assessment of existing data, rigorous design of future studies and further development of methods will be required to confirm the presence and biological functions of 6mA in multicellular eukaryotes.
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3
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O’Brown ZK, Greer EL. N6-methyladenine: A Rare and Dynamic DNA Mark. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:177-210. [DOI: 10.1007/978-3-031-11454-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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4
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Li X, Zhang Z, Luo X, Schrier J, Yang AD, Wu TP. The exploration of N6-deoxyadenosine methylation in mammalian genomes. Protein Cell 2021; 12:756-768. [PMID: 34405377 PMCID: PMC8464638 DOI: 10.1007/s13238-021-00866-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/12/2021] [Indexed: 11/11/2022] Open
Abstract
N6-methyladenine (N6-mA, m6dA, or 6mA), a prevalent DNA modification in prokaryotes, has recently been identified in higher eukaryotes, including mammals. Although 6mA has been well-studied in prokaryotes, the function and regulatory mechanism of 6mA in eukaryotes are still poorly understood. Recent studies indicate that 6mA can serve as an epigenetic mark and play critical roles in various biological processes, from transposable-element suppression to environmental stress response. Here, we review the significant advances in methodology for 6mA detection and major progress in understanding the regulation and function of this non-canonical DNA methylation in eukaryotes, predominantly mammals.
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Affiliation(s)
- Xuwen Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zijian Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xinlong Luo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jacob Schrier
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Andrew D Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Tao P Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Huffington Center on Aging, Baylor College of Medicine, Houston, TX, 77030, USA. .,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
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5
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Musheev MU, Baumgärtner A, Krebs L, Niehrs C. The origin of genomic N6-methyl-deoxyadenosine in mammalian cells. Nat Chem Biol 2020; 16:630-634. [DOI: 10.1038/s41589-020-0504-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 02/18/2020] [Indexed: 11/09/2022]
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6
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O'Brown ZK, Boulias K, Wang J, Wang SY, O'Brown NM, Hao Z, Shibuya H, Fady PE, Shi Y, He C, Megason SG, Liu T, Greer EL. Sources of artifact in measurements of 6mA and 4mC abundance in eukaryotic genomic DNA. BMC Genomics 2019; 20:445. [PMID: 31159718 PMCID: PMC6547475 DOI: 10.1186/s12864-019-5754-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 04/30/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Directed DNA methylation on N6-adenine (6mA), N4-cytosine (4mC), and C5-cytosine (5mC) can potentially increase DNA coding capacity and regulate a variety of biological functions. These modifications are relatively abundant in bacteria, occurring in about a percent of all bases of most bacteria. Until recently, 5mC and its oxidized derivatives were thought to be the only directed DNA methylation events in metazoa. New and more sensitive detection techniques (ultra-high performance liquid chromatography coupled with mass spectrometry (UHPLC-ms/ms) and single molecule real-time sequencing (SMRTseq)) have suggested that 6mA and 4mC modifications could be present in a variety of metazoa. RESULTS Here, we find that both of these techniques are prone to inaccuracies, which overestimate DNA methylation concentrations in metazoan genomic DNA. Artifacts can arise from methylated bacterial DNA contamination of enzyme preparations used to digest DNA and contaminating bacterial DNA in eukaryotic DNA preparations. Moreover, DNA sonication introduces a novel modified base from 5mC that has a retention time near 4mC that can be confused with 4mC. Our analyses also suggest that SMRTseq systematically overestimates 4mC in prokaryotic and eukaryotic DNA and 6mA in DNA samples in which it is rare. Using UHPLC-ms/ms designed to minimize and subtract artifacts, we find low to undetectable levels of 4mC and 6mA in genomes of representative worms, insects, amphibians, birds, rodents and primates under normal growth conditions. We also find that mammalian cells incorporate exogenous methylated nucleosides into their genome, suggesting that a portion of 6mA modifications could derive from incorporation of nucleosides from bacteria in food or microbiota. However, gDNA samples from gnotobiotic mouse tissues found rare (0.9-3.7 ppm) 6mA modifications above background. CONCLUSIONS Altogether these data demonstrate that 6mA and 4mC are rarer in metazoa than previously reported, and highlight the importance of careful sample preparation and measurement, and need for more accurate sequencing techniques.
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Affiliation(s)
- Zach K O'Brown
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Konstantinos Boulias
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jie Wang
- Department of Biochemistry and Biostatistics, University at Buffalo Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, 14203, USA
| | - Simon Yuan Wang
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Natasha M O'Brown
- Department of Neurobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Ziyang Hao
- Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Hiroki Shibuya
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.,Present address: Department of Chemistry and Molecular Biology, University of Gothenburg, SE-40530, Gothenburg, Sweden
| | - Paul-Enguerrand Fady
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Yang Shi
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA.,Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Chuan He
- Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Sean G Megason
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Tao Liu
- Department of Biochemistry and Biostatistics, University at Buffalo Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, 14203, USA
| | - Eric L Greer
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA. .,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
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7
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Parashar NC, Parashar G, Nayyar H, Sandhir R. N 6-adenine DNA methylation demystified in eukaryotic genome: From biology to pathology. Biochimie 2017; 144:56-62. [PMID: 29074394 DOI: 10.1016/j.biochi.2017.10.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 10/17/2017] [Indexed: 01/16/2023]
Abstract
N6-methyl-2'-deoxyadenosine (m6dA) is a well characterized DNA modification in prokaryotes. Its existence in eukaryotic DNA remained doubtful until recently. Evidence suggests that the m6dA levels decrease with the increasing complexity of eukaryotic genomes. Analysis of m6dA levels in genome of lower eukaryotes reveals its role in gene regulation, nucleosome positioning and early development. In higher eukaryotes m6dA is enriched in nongenic region compared to genic region, preferentially in chromosome X and 13 suggesting a chromosome bias. High levels of m6dA during embryogenesis as compared to adult tissues are indicative of its importance during development and possible association with regeneration capabilities. Further, decreased levels of m6dA in diabetic patients has been correlated with expression of Fat mass and obesity-associated (FTO) which acts as m6A demethylase. m6dA levels have also been reported to be decreased in different types of cancers. The present review highlights the role of m6dA modification in eukaryotic genomes and its functional importance in regulation of physiological and pathological processes.
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Affiliation(s)
| | - Gaurav Parashar
- Laboratory of Epigenetics and Diseases, Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar (Mohali), Punjab, 160062, India
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Rajat Sandhir
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India.
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8
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Kalubi KN, Mehes-Smith M, Spiers G, Omri A. Variation in whole DNA methylation in red maple (Acer rubrum) populations from a mining region: association with metal contamination and cation exchange capacity (CEC) in podzolic soils. ECOTOXICOLOGY (LONDON, ENGLAND) 2017; 26:405-414. [PMID: 28204976 DOI: 10.1007/s10646-017-1773-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/02/2017] [Indexed: 06/06/2023]
Abstract
Although a number of publications have provided convincing evidence that abiotic stresses such as drought and high salinity are involved in DNA methylation reports on the effects of metal contamination, pH, and cation exchange on DNA modifications are limited. The main objective of the present study is to determine the relationship between metal contamination and Cation exchange capacity (CEC) on whole DNA modifications. Metal analysis confirms that nickel and copper are the main contaminants in sampled sites within the Greater Sudbury Region (Ontario, Canada) and liming has increased soil pH significantly even after 30 years following dolomitic limestone applications. The estimated CEC values varied significantly among sites, ranging between 1.8 and 10.5 cmol(+) kg-1, with a strong relationship being observed between CEC and pH (r = 0.96**). Cation exchange capacity, significantly lower in highly metal contaminated sites compared to both reference and less contaminated sites, was higher in the higher organic matter limed compared to unlimed sites. There was a significant variation in the level of cytosine methylation among the metal-contaminated sites. Significant and strong negative correlations between [5mdC]/[dG] and bioavailable nickel (r = -0.71**) or copper (r = -0.72**) contents were observed. The analysis of genomic DNA for adenine methylation in this study showed a very low level of [6N-mdA]/dT] in Acer rubrum plants analyzed ranging from 0 to 0.08%. Significant and very strong positive correlation was observed between [6N-mdA]/dT] and soil bioavailable nickel (r = 0.78**) and copper (r = 0.88**) content. This suggests that the increased bioavailable metal levels associated with contamination by nickel and copper particulates are associated with cytosine and adenine methylation.
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Affiliation(s)
- K N Kalubi
- Biomolecular Sciences Program, Laurentian University, Sudbury, ON, P3E 2C6, Canada
| | - M Mehes-Smith
- Department of Biology, Laurentian University, Sudbury, ON, P3E 2C6, Canada.
| | - G Spiers
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, P3E 2C6, Canada
| | - A Omri
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, P3E 2C6, Canada
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9
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Nitrogen acquisition in Agave tequilana from degradation of endophytic bacteria. Sci Rep 2014; 4:6938. [PMID: 25374146 PMCID: PMC4221784 DOI: 10.1038/srep06938] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 10/20/2014] [Indexed: 11/30/2022] Open
Abstract
Plants form symbiotic associations with endophytic bacteria within tissues of leaves, stems, and roots. It is unclear whether or how plants obtain nitrogen from these endophytic bacteria. Here we present evidence showing nitrogen flow from endophytic bacteria to plants in a process that appears to involve oxidative degradation of bacteria. In our experiments we employed Agave tequilana and its seed-transmitted endophyte Bacillus tequilensis to elucidate organic nitrogen transfer from 15N-labeled bacteria to plants. Bacillus tequilensis cells grown in a minimal medium with 15NH4Cl as the nitrogen source were watered onto plants growing in sand. We traced incorporation of 15N into tryptophan, deoxynucleosides and pheophytin derived from chlorophyll a. Probes for hydrogen peroxide show its presence during degradation of bacteria in plant tissues, supporting involvement of reactive oxygen in the degradation process. In another experiment to assess nitrogen absorbed as a result of endophytic colonization of plants we demonstrated that endophytic bacteria potentially transfer more nitrogen to plants and stimulate greater biomass in plants than heat-killed bacteria that do not colonize plants but instead degrade in the soil. Findings presented here support the hypothesis that some plants under nutrient limitation may degrade and obtain nitrogen from endophytic microbes.
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10
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Vanyushin BF, Ashapkin VV. DNA methylation in higher plants: past, present and future. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:360-8. [PMID: 21549230 DOI: 10.1016/j.bbagrm.2011.04.006] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 04/13/2011] [Accepted: 04/15/2011] [Indexed: 01/19/2023]
Abstract
A relatively high degree of nuclear DNA (nDNA) methylation is a specific feature of plant genomes. Targets for cytosine DNA methylation in plant genomes are CG, CHG and CHH (H is A, T, C) sequences. More than 30% total m(5)C in plant DNA is located in non-CG sites. DNA methylation in plants is species-, tissue-, organelle- and age-specific; it is involved in the control of all genetic functions including transcription, replication, DNA repair, gene transposition and cell differentiation. DNA methylation is engaged in gene silencing and parental imprinting, it controls expression of transgenes and foreign DNA in cell. Plants have much more complicated and sophisticated system of the multicomponent genome methylations compared to animals; DNA methylation in plant mitochondria is performed in other fashion as compared to that in nuclei. The nDNA methylation is carried out by cytosine DNA methyltransferases of, at least, three families. In contrast to animals the plants with the major maintenance methyltransferase MET1 (similar to animal Dnmt1) inactivated do survive. One and the same plant gene may be methylated at both adenine and cytosine residues; specific plant adenine DNA methyltransferase was described. Thus, two different systems of the genome modification based on methylation of cytosines and adenines seem to coexist in higher plants. This article is part of a Special Issue entitled: Epigenetic control of cellular and developmental processes in plants.
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Affiliation(s)
- Boris F Vanyushin
- A N Belozersky Institute of Physical and Chemical Biology, Moscow State University, Moscow, Russian Federation.
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11
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Ratel D, Ravanat JL, Charles MP, Platet N, Breuillaud L, Lunardi J, Berger F, Wion D. Undetectable levels of N6-methyl adenine in mouse DNA: Cloning and analysis of PRED28, a gene coding for a putative mammalian DNA adenine methyltransferase. FEBS Lett 2006; 580:3179-84. [PMID: 16684535 DOI: 10.1016/j.febslet.2006.04.074] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2006] [Revised: 04/25/2006] [Accepted: 04/26/2006] [Indexed: 10/24/2022]
Abstract
Three methylated bases, 5-methylcytosine, N4-methylcytosine and N6-methyladenine (m6A), can be found in DNA. However, to date, only 5-methylcytosine has been detected in mammalian genomes. To reinvestigate the presence of m6A in mammalian DNA, we used a highly sensitive method capable of detecting one N6-methyldeoxyadenosine per million nucleosides. Our results suggest that the total mouse genome contains, if any, less than 10(3) m6A. Experiments were next performed on PRED28, a putative mammalian N6-DNA methyltransferase. The murine PRED28 encodes two alternatively spliced RNA. However, although recombinant PRED28 proteins are found in the nucleus, no evidence for an adenine-methyltransferase activity was detected.
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Affiliation(s)
- David Ratel
- INSERM U318, UJFG, CHU Michallon, 38043 Grenoble, France
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12
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Abstract
Contrary to mammalian DNA, which is thought to contain only 5-methylcytosine (m5C), bacterial DNA contains two additional methylated bases, namely N6-methyladenine (m6A), and N4-methylcytosine (m4C). However, if the main function of m5C and m4C in bacteria is protection against restriction enzymes, the roles of m6A are multiple and include, for example, the regulation of virulence and the control of many bacterial DNA functions such as the replication, repair, expression and transposition of DNA. Interestingly, even if adenine methylation is usually considered a bacterial DNA feature, the presence of m6A has been found in protist and plant DNAs. Furthermore, indirect evidence suggests the presence of m6A in mammal DNA, raising the possibility that this base has remained undetected due to the low sensitivity of the analytical methods used. This highlights the importance of considering m6A as the sixth element of DNA.
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Affiliation(s)
- David Ratel
- Neurosciences précliniques
INSERM : U318Université Joseph Fourier - Grenoble ICHU Grenoble 38043 Grenoble Cedex 9,FR
| | | | - François Berger
- Neurosciences précliniques
INSERM : U318Université Joseph Fourier - Grenoble ICHU Grenoble 38043 Grenoble Cedex 9,FR
| | - Didier Wion
- Neurosciences précliniques
INSERM : U318Université Joseph Fourier - Grenoble ICHU Grenoble 38043 Grenoble Cedex 9,FR
- * Correspondence should be adressed to: Didier Wion
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13
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Abstract
DNA in plants is highly methylated, containing 5-methylcytosine (m5C) and N6-methyladenine (m6A); m5C is located mainly in symmetrical CG and CNG sequences but it may occur also in other non-symmetrical contexts. m6A but not m5C was found in plant mitochondrial DNA. DNA methylation in plants is species-, tissue-, organelle- and age-specific. It is controlled by phytohormones and changes on seed germination, flowering and under the influence of various pathogens (viral, bacterial, fungal). DNA methylation controls plant growth and development, with particular involvement in regulation of gene expression and DNA replication. DNA replication is accompanied by the appearance of under-methylated, newly formed DNA strands including Okazaki fragments; asymmetry of strand DNA methylation disappears until the end of the cell cycle. A model for regulation of DNA replication by methylation is suggested. Cytosine DNA methylation in plants is more rich and diverse compared with animals. It is carried out by the families of specific enzymes that belong to at least three classes of DNA methyltransferases. Open reading frames (ORF) for adenine DNA methyltransferases are found in plant and animal genomes, and a first eukaryotic (plant) adenine DNA methyltransferase (wadmtase) is described; the enzyme seems to be involved in regulation of the mitochondria replication. Like in animals, DNA methylation in plants is closely associated with histone modifications and it affects binding of specific proteins to DNA and formation of respective transcription complexes in chromatin. The same gene (DRM2) in Arabidopsis thaliana is methylated both at cytosine and adenine residues; thus, at least two different, and probably interdependent, systems of DNA modification are present in plants. Plants seem to have a restriction-modification (R-M) system. RNA-directed DNA methylation has been observed in plants; it involves de novo methylation of almost all cytosine residues in a region of siRNA-DNA sequence identity; therefore, it is mainly associated with CNG and non-symmetrical methylations (rare in animals) in coding and promoter regions of silenced genes. Cytoplasmic viral RNA can affect methylation of homologous nuclear sequences and it maybe one of the feedback mechanisms between the cytoplasm and the nucleus to control gene expression.
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Affiliation(s)
- B F Vanyushin
- Belozersky Institute of Physical and Chemical Biology, Lomonosov Moscow State University, Russia.
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15
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Komyod W, Bauer UM, Heinrich PC, Haan S, Behrmann I. Are STATS arginine-methylated? J Biol Chem 2005; 280:21700-5. [PMID: 15826948 DOI: 10.1074/jbc.c400606200] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transcription factors of the STAT (signal transducer and activator of transcription) family are important in signal transduction of cytokines. They are subject to post-translational modification by phosphorylation on tyrosine and serine residues. Recent evidence suggested that STATs are methylated on a conserved arginine residue within the N-terminal region. STAT arginine methylation has been described to be important for STAT function and loss of arginine methylation was discussed to be involved in interferon resistance of cancer cells. Here we provide several independent lines of evidence indicating that the issue of arginine methylation of STATs has to be reassessed. First, we show that treatment of melanoma and fibrosarcoma cells with inhibitors used to suppress methylation (N-methyl-2-deoxyadenosine, adenosine, dl-homocysteine) had profound and rapid effects on phosphorylation of STAT1 and STAT3 but also on p38 and Erk signaling cascades which are known to cross-talk with the Jak/STAT pathway. Second, we show that anti-methylarginine antibodies did not precipitate specifically STAT1 or STAT3. Third, we show that mutation of Arg(31) to Lys led to destabilization of STAT1 and STAT3, implicating an important structural role of Arg(31). Finally, purified catalytically active protein arginine methyltransferases (PRMT1, -2, -3, -4, and -6) did not methylate STAT proteins, and cotransfection with PRMT1 did not affect STAT1-controlled reporter gene activity. Taken together, our data suggest the absence of arginine methylation of STAT1 and STAT3.
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Affiliation(s)
- Waraporn Komyod
- Institut für Biochemie, Universitätsklinikum der Rheinisch-Westfälischen Technischen Hochschule Aachen, Pauwelsstrasse 30, 52074 Aachen, Germany
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