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Zhong J, Xu Z, Ding N, Wang Y, Chen W. The biological function of demethylase ALKBH1 and its role in human diseases. Heliyon 2024; 10:e33489. [PMID: 39040364 PMCID: PMC11260981 DOI: 10.1016/j.heliyon.2024.e33489] [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] [Received: 02/14/2024] [Revised: 06/21/2024] [Accepted: 06/21/2024] [Indexed: 07/24/2024] Open
Abstract
AlkB homolog 1 (ALKBH1) is a member of the AlkB family of dioxygenases that are dependent on Fe(II) and α-ketoglutarate. Mounting evidence demonstrates that ALKBH1 exhibits enzymatic activity against various substrates, including N6-methyladenosine (m6A), N1-methyladenosine (m1A), N3-methylcytidine (m3C), 5-methylcytosine (m5C), N6-methyladenine (N6-mA, 6mA), and H2A, indicating its dual roles in different biological processes and involvement in human diseases. Up to the present, there is ongoing debate regarding ALKBH1's enzymatic activity. In this review, we present a comprehensive summary of recent research on ALKBH1, including its substrate diversity and pathological roles in a wide range of human disorders, the underlying mechanisms of its functions, and its dysregulation. We also explored the potential of ALKBH1 as a prognostic target.
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Affiliation(s)
- Jing Zhong
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310009, China
| | - Zhengyang Xu
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310009, China
| | - Ning Ding
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310009, China
| | - Yanting Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310009, China
| | - Wenwen Chen
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
- Institute of Gastroenterology, Zhejiang University, Hangzhou 310009, China
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2
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Pan B, Ye F, Li T, Wei F, Warren A, Wang Y, Gao S. Potential role of N 6-adenine DNA methylation in alternative splicing and endosymbiosis in Paramecium bursaria. iScience 2023; 26:106676. [PMID: 37182097 PMCID: PMC10173741 DOI: 10.1016/j.isci.2023.106676] [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: 05/21/2022] [Revised: 12/02/2022] [Accepted: 04/11/2023] [Indexed: 05/16/2023] Open
Abstract
N6-adenine DNA methylation (6mA), a rediscovered epigenetic mark in eukaryotic organisms, diversifies in abundance, distribution, and function across species, necessitating its study in more taxa. Paramecium bursaria is a typical model organism with endosymbiotic algae of the species Chlorella variabilis. This consortium therefore serves as a valuable system to investigate the functional role of 6mA in endosymbiosis, as well as the evolutionary importance of 6mA among eukaryotes. In this study, we report the first genome-wide, base pair-resolution map of 6mA in P. bursaria and identify its methyltransferase PbAMT1. Functionally, 6mA exhibits a bimodal distribution at the 5' end of RNA polymerase II-transcribed genes and possibly participates in transcription by facilitating alternative splicing. Evolutionarily, 6mA co-evolves with gene age and likely serves as a reverse mark of endosymbiosis-related genes. Our results offer new insights for the functional diversification of 6mA in eukaryotes as an important epigenetic mark.
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Affiliation(s)
- Bo Pan
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Fei Ye
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
| | - Tao Li
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
| | - Fan Wei
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Yuanyuan Wang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
- Corresponding author
| | - Shan Gao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao 266003, China
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3
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Liu B, Wang H. Detection of N 6-Methyladenine in Eukaryotes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1280:83-95. [PMID: 33791976 DOI: 10.1007/978-3-030-51652-9_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
DNA N6-methyladenine (6mA) is a chemical modification at the N6-positon of adenine. In the last decades, 6mA had been found in genome from numerous prokaryotic species, but only existed in a few lower eukaryotes. In prokaryotes, 6mA plays an important role in restriction-modification, DNA replication, and DNA mismatch repair. Because of the too low abundance of 6mA, it was long-stalled whether 6mA existed in multicellular eukaryotes and playing any functions, particularly in mammals. In recent years, partially benefitting from the advances in analytical methods, 6mA was found in the genomes from Drosophila melanogaster, Chlamydomonas algae, Caenorhabditis elegans, zebrafish, Xenopus laevis and mouse embryonic stem cells and even in the human genome. The 6mA was dynamic changed in early embryonic development of fly and zebrafish and much more enriched in gene body of transposons in fly, repetitive regions in zebrafish, around the transcription start sites in Chlamydomonas, and widespread distribution in C. elegans, indicating 6mA probably playing different functions in different species. Meanwhile, 6mA methylases and demethylases were found in fly, worm, and Chlamydomonas. In this chapter, we will briefly review the distribution, regulation, and function of 6mA in eukaryotes and focus on the advances of 6mA analysis methods, especially LC-MS/MS, immunoprecipitation, next-generation sequencing, and single-molecule real-time sequencing technology.
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Affiliation(s)
- Baodong Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
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4
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Woodcock CB, Horton JR, Zhang X, Blumenthal RM, Cheng X. Beta class amino methyltransferases from bacteria to humans: evolution and structural consequences. Nucleic Acids Res 2020; 48:10034-10044. [PMID: 32453412 PMCID: PMC7544214 DOI: 10.1093/nar/gkaa446] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 01/09/2023] Open
Abstract
S-adenosyl-l-methionine dependent methyltransferases catalyze methyl transfers onto a wide variety of target molecules, including DNA and RNA. We discuss a family of methyltransferases, those that act on the amino groups of adenine or cytosine in DNA, have conserved motifs in a particular order in their amino acid sequence, and are referred to as class beta MTases. Members of this class include M.EcoGII and M.EcoP15I from Escherichia coli, Caulobacter crescentus cell cycle-regulated DNA methyltransferase (CcrM), the MTA1-MTA9 complex from the ciliate Oxytricha, and the mammalian MettL3-MettL14 complex. These methyltransferases all generate N6-methyladenine in DNA, with some members having activity on single-stranded DNA as well as RNA. The beta class of methyltransferases has a unique multimeric feature, forming either homo- or hetero-dimers, allowing the enzyme to use division of labor between two subunits in terms of substrate recognition and methylation. We suggest that M.EcoGII may represent an ancestral form of these enzymes, as its activity is independent of the nucleic acid type (RNA or DNA), its strandedness (single or double), and its sequence (aside from the target adenine).
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Affiliation(s)
- Clayton B Woodcock
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Beh LY, Debelouchina GT, Clay DM, Thompson RE, Lindblad KA, Hutton ER, Bracht JR, Sebra RP, Muir TW, Landweber LF. Identification of a DNA N6-Adenine Methyltransferase Complex and Its Impact on Chromatin Organization. Cell 2019; 177:1781-1796.e25. [PMID: 31104845 DOI: 10.1016/j.cell.2019.04.028] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/31/2019] [Accepted: 04/12/2019] [Indexed: 11/27/2022]
Abstract
DNA N6-adenine methylation (6mA) has recently been described in diverse eukaryotes, spanning unicellular organisms to metazoa. Here, we report a DNA 6mA methyltransferase complex in ciliates, termed MTA1c. It consists of two MT-A70 proteins and two homeobox-like DNA-binding proteins and specifically methylates dsDNA. Disruption of the catalytic subunit, MTA1, in the ciliate Oxytricha leads to genome-wide loss of 6mA and abolishment of the consensus ApT dimethylated motif. Mutants fail to complete the sexual cycle, which normally coincides with peak MTA1 expression. We investigate the impact of 6mA on nucleosome occupancy in vitro by reconstructing complete, full-length Oxytricha chromosomes harboring 6mA in native or ectopic positions. We show that 6mA directly disfavors nucleosomes in vitro in a local, quantitative manner, independent of DNA sequence. Furthermore, the chromatin remodeler ACF can overcome this effect. Our study identifies a diverged DNA N6-adenine methyltransferase and defines the role of 6mA in chromatin organization.
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Affiliation(s)
- Leslie Y Beh
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY 10032, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA; Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | | | - Derek M Clay
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY 10032, USA
| | - Robert E Thompson
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Kelsi A Lindblad
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY 10032, USA
| | - Elizabeth R Hutton
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - John R Bracht
- Department of Biology, American University, Washington, DC 20016, USA
| | - Robert P Sebra
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.
| | - Laura F Landweber
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY 10032, USA.
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6
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Wang Y, Chen X, Sheng Y, Liu Y, Gao S. N6-adenine DNA methylation is associated with the linker DNA of H2A.Z-containing well-positioned nucleosomes in Pol II-transcribed genes in Tetrahymena. Nucleic Acids Res 2017; 45:11594-11606. [PMID: 29036602 PMCID: PMC5714169 DOI: 10.1093/nar/gkx883] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 09/12/2017] [Accepted: 09/23/2017] [Indexed: 01/01/2023] Open
Abstract
DNA N6-methyladenine (6mA) is newly rediscovered as a potential epigenetic mark across a more diverse range of eukaryotes than previously realized. As a unicellular model organism, Tetrahymena thermophila is among the first eukaryotes reported to contain 6mA modification. However, lack of comprehensive information about 6mA distribution hinders further investigations into its function and regulatory mechanism. In this study, we provide the first genome-wide, base pair-resolution map of 6mA in Tetrahymena by applying single-molecule real-time (SMRT) sequencing. We provide evidence that 6mA occurs mostly in the AT motif of the linker DNA regions. More strikingly, these linker DNA regions with 6mA are usually flanked by well-positioned nucleosomes and/or H2A.Z-containing nucleosomes. We also find that 6mA is exclusively associated with RNA polymerase II (Pol II)-transcribed genes, but is not an unambiguous mark for active transcription. These results support that 6mA is an integral part of the chromatin landscape shaped by adenosine triphosphate (ATP)-dependent chromatin remodeling and transcription.
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Affiliation(s)
- Yuanyuan Wang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Xiao Chen
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yalan Sheng
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yifan Liu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shan Gao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
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7
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DNA N 6-methyladenine in metazoans: functional epigenetic mark or bystander? Nat Struct Mol Biol 2017; 24:503-506. [PMID: 28586322 DOI: 10.1038/nsmb.3412] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 04/18/2017] [Indexed: 02/06/2023]
Abstract
The DNA-adenine modification N6-methyladenine (6mA), initially thought to be mainly restricted to prokaryotes and certain unicellular eukaryotes, has recently been found in metazoans. Proposed functions vary from gene activation to transposon suppression. However, since most metazoan genomes possess 5-methylcytosine (5mC) as a dominant epigenetic mark, it raises the question of why 6mA is required. This Perspective summarizes the latest discoveries and suggests potential functional roles for 6mA in metazoan genomes.
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8
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Liu B, Liu X, Lai W, Wang H. Metabolically Generated Stable Isotope-Labeled Deoxynucleoside Code for Tracing DNA N 6-Methyladenine in Human Cells. Anal Chem 2017; 89:6202-6209. [PMID: 28471639 DOI: 10.1021/acs.analchem.7b01152] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DNA N6-methyl-2'-deoxyadenosine (6mdA) is an epigenetic modification in both eukaryotes and bacteria. Here we exploited stable isotope-labeled deoxynucleoside [15N5]-2'-deoxyadenosine ([15N5]-dA) as an initiation tracer and for the first time developed a metabolically differential tracing code for monitoring DNA 6mdA in human cells. We demonstrate that the initiation tracer [15N5]-dA undergoes a specific and efficient adenine deamination reaction leading to the loss the exocyclic amine 15N, and further utilizes the purine salvage pathway to generate mainly both [15N4]-dA and [15N4]-2'-deoxyguanosine ([15N4]-dG) in mammalian genomes. However, [15N5]-dA is largely retained in the genomes of mycoplasmas, which are often found in cultured cells and experimental animals. Consequently, the methylation of dA generates 6mdA with a consistent coding pattern, with a predominance of [15N4]-6mdA. Therefore, mammalian DNA 6mdA can be potentially discriminated from that generated by infecting mycoplasmas. Collectively, we show a promising approach for identification of authentic DNA 6mdA in human cells and determine if the human cells are contaminated with mycoplasmas.
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Affiliation(s)
- Baodong Liu
- 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
| | - Xiaoling Liu
- 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
| | - Weiyi Lai
- 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
| | - Hailin 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
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Wang Y, Sheng Y, Liu Y, Pan B, Huang J, Warren A, Gao S. N 6 -methyladenine DNA modification in the unicellular eukaryotic organism Tetrahymena thermophila. Eur J Protistol 2017; 58:94-102. [DOI: 10.1016/j.ejop.2016.12.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 12/08/2016] [Accepted: 12/12/2016] [Indexed: 01/30/2023]
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Abstract
DNA N(6)-adenine methylation (N(6)-methyladenine; 6mA) in prokaryotes functions primarily in the host defence system. The prevalence and significance of this modification in eukaryotes had been unclear until recently. Here, we discuss recent publications documenting the presence of 6mA in Chlamydomonas reinhardtii, Drosophila melanogaster and Caenorhabditis elegans; consider possible roles for this DNA modification in regulating transcription, the activity of transposable elements and transgenerational epigenetic inheritance; and propose 6mA as a new epigenetic mark in eukaryotes.
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Sun Q, Huang S, Wang X, Zhu Y, Chen Z, Chen D. N6-methyladenine functions as a potential epigenetic mark in eukaryotes. Bioessays 2015; 37:1155-62. [PMID: 26293475 DOI: 10.1002/bies.201500076] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
N(6)-methyladenine (6mA) is one of the most abundant types of DNA methylation, and plays an important role in bacteria; however, its roles in higher eukaryotes, such as plants, insects, and mammals, have been considered less important. Recent studies highlight that 6mA does indeed occur, and that it plays an important role in eukaryotes, such as worm, fly, and green algae, and thus the regulation of 6mA has emerged as a novel epigenetic mechanism in higher eukaryotes. Despite this intriguing development, a number of important issues regarding its biological roles are yet to be addressed. In this review, we focus on the 5mC and 6mA modifications in terms of their production, distribution, and the erasure of 6mA in higher eukaryotes including mammals. We perform an analysis of the potential functions of 6mA, hence widening understanding of this new epigenetic mark in higher eukaryotes, and suggesting future studies in this field.
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Affiliation(s)
- Qinmiao Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shoujun Huang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Center for Developmental Biology, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiaona Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yuanxiang Zhu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhenping Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Dahua Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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12
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Abstract
Nuclear dualism is a characteristic feature of the ciliated protozoa. Tetrahymena have two different nuclei in each cell. The larger, polyploid, somatic macronucleus (MAC) is the site of transcriptional activity in the vegetatively growing cell. The smaller, diploid micronucleus (MIC) is transcriptionally inactive in vegetative cells, but is transcriptionally active in mating cells and responsible for the genetic continuity during sexual reproduction. Although the MICs and MACs develop from mitotic products of a common progenitor and reside in a common cytoplasm, they are different from one another in almost every respect.
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Affiliation(s)
- Kathleen M Karrer
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA
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Pardo CE, Darst RP, Nabilsi NH, Delmas AL, Kladde MP. Simultaneous single-molecule mapping of protein-DNA interactions and DNA methylation by MAPit. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2011; Chapter 21:Unit 21.22. [PMID: 21732317 PMCID: PMC3214598 DOI: 10.1002/0471142727.mb2122s95] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Sites of protein binding to DNA are inferred from footprints or spans of protection against a probing reagent. In most protocols, sites of accessibility to a probe are detected by mapping breaks in DNA strands. As discussed in this unit, such methods obscure molecular heterogeneity by averaging cuts at a given site over all DNA strands in a sample population. The DNA methyltransferase accessibility protocol for individual templates (MAPit), an alternative method described in this unit, localizes protein-DNA interactions by probing with cytosine-modifying DNA methyltransferases followed by bisulfite sequencing. Sequencing individual DNA products after amplification of bisulfite-converted sequences permits assignment of the methylation status of every enzyme target site along a single DNA strand. Use of the GC-methylating enzyme M.CviPI allows simultaneous mapping of chromatin accessibility and endogenous CpG methylation. MAPit is therefore the only footprinting method that can detect subpopulations of molecules with distinct patterns of protein binding or chromatin architecture and correlate them directly with the occurrence of endogenous methylation. Additional advantages of MAPit methylation footprinting as well as considerations for experimental design and potential sources of error are discussed.
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Affiliation(s)
- Carolina E. Pardo
- Department of Biochemistry and Molecular Biology and UF Shands Cancer Center Program in Cancer Genetics, Epigenetics and Tumor Virology, University of Florida College of Medicine, 2033 Mowry Road, Box 103633, Gainesville, Florida 32610-3633, USA, Telephone: (352) 273-8541, Fax: (352) 273-8299
| | - Russell P. Darst
- Department of Biochemistry and Molecular Biology and UF Shands Cancer Center Program in Cancer Genetics, Epigenetics and Tumor Virology, University of Florida College of Medicine, 2033 Mowry Road, Box 103633, Gainesville, Florida 32610-3633, USA, Telephone: (352) 273-8541, Fax: (352) 273-8299
| | - Nancy H. Nabilsi
- Department of Biochemistry and Molecular Biology and UF Shands Cancer Center Program in Cancer Genetics, Epigenetics and Tumor Virology, University of Florida College of Medicine, 2033 Mowry Road, Box 103633, Gainesville, Florida 32610-3633, USA, Telephone: (352) 273-8541, Fax: (352) 273-8299
| | - Amber L. Delmas
- Department of Biochemistry and Molecular Biology and UF Shands Cancer Center Program in Cancer Genetics, Epigenetics and Tumor Virology, University of Florida College of Medicine, 2033 Mowry Road, Box 103633, Gainesville, Florida 32610-3633, USA, Telephone: (352) 273-8541, Fax: (352) 273-8299
| | - Michael P. Kladde
- Department of Biochemistry and Molecular Biology and UF Shands Cancer Center Program in Cancer Genetics, Epigenetics and Tumor Virology, University of Florida College of Medicine, 2033 Mowry Road, Box 103633, Gainesville, Florida 32610-3633, USA, Telephone: (352) 273-8541, Fax: (352) 273-8299
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14
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NG STEPHENF. Cytidine Analogues and Stomatogenic Recovery in AmicronucleateParamecium tetraureliaandParamecium jenningsi. ACTA ACUST UNITED AC 2007. [DOI: 10.1111/j.1550-7408.1989.tb02710.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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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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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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Vanyushin BF. Enzymatic DNA methylation is an epigenetic control for genetic functions of the cell. BIOCHEMISTRY (MOSCOW) 2005; 70:488-99. [PMID: 15948703 DOI: 10.1007/s10541-005-0143-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In eukaryotic cells nuclear DNA is subjected to enzymatic methylation resulting in formation of 5-methylcytosine residues mainly in CG and CNG sequences. In plants and animals, this DNA methylation is species-, tissue-, and organelle-specific. It changes (diminishes) with age and is regulated by hormones. On the other hand, genome methylation can control hormonal signal. There are replicative and post-replicative DNA methylations. They are served by multiple DNA-methyltransferases with different site specificity. Replication is accompanied by appearance of hemi-methylated sites in DNA; pronounced asymmetry of DNA chain methylation disappears at the end of the cell cycle; a model of regulation of replication by DNA methylation is suggested. DNA methylation controls all genetic processes in the cell (replication, transcription, DNA repair, recombination, gene transposition) and it is a mechanism of cell differentiation, gene discrimination, and silencing. Prohibition of DNA methylation stops development (embryogenesis), switches on apoptosis, and is usually lethal. Distortions in DNA methylations result in cancerous cell transformation, and the DNA methylation pattern is one of the safe cancer diagnostics at early stages of carcinogenesis. The malignant cell has a different DNA methylation pattern and a set of DNA-methyltransferase activities expressed as compared with normal cells. Inhibition of DNA methylation in plants is accompanied by induction of genes of seed storage proteins and flowering. In eukaryotes one and the same gene can be methylated both on cytosine and adenine residues; thus, there are, at least, two different and probably interdependent systems of DNA methylation in the cell. First higher eukaryotic adenine DNA-methyltransferase was isolated from plants; this enzyme methylates DNA with formation of N6-methyladenine residues in the sequence TGATCA --> TGm6ATCA. Plants have AdoMet-dependent endonucleases sensitive to DNA methylation status; therefore, like microorganisms, plants seem to have a restriction-modification (R-S) system. Revelation of an essential role of DNA methylation in the regulation of genetic processes has laid a foundation for and materialized epigenetics and epigenomics.
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Affiliation(s)
- B F Vanyushin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia.
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20
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Abstract
DNA methylation in lower eukaryotes, in contrast to vertebrates, can involve modification of adenine to N6-methyladenine (m6A). While DNA-[cytosine] methylation in higher eukaryotes has been implicated in many important cellular processes, the function(s) of DNA-[adenine] methylation in lower eukaryotes remains unknown. I have chosen to study the ciliate Tetrahymena thermophila as a model system, since this organism is known to contain m6A, but not m5C, in its macronuclear DNA. A BLAST analysis revealed an open reading frame (ORF) that appears to encode for the Tetrahymena DNA-[adenine] methyltransferase (MTase), based on the presence of motifs characteristic of the enzymes in prokaryotes. Possible biological roles for DNA-[adenine] methylation in Tetrahymena are discussed. Experiments to test these hypotheses have begun with the cloning of the gene. Orthologous ORFs are also present in three species of the malarial parasite Plasmodium. They are compared to one another and to the putative Tetrahymena DNA-[adenine] MTase. The gene from the human parasite P. falciparum has been cloned.
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Affiliation(s)
- S Hattman
- Department of Biology, University of Rochester, Rochester, NY 14627-0211, USA.
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21
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Affiliation(s)
- K M Karrer
- Department of Biology, Marquette University, Milwaukee, Wisconsin 53201, USA
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Affiliation(s)
- M P Kladde
- Department of Biochemistry and Molecular Biology, Pennsylvania State University 16802-4500, USA
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23
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Abstract
A groundswell of interest in chromatin structure and its role in regulating the function of DNA in transcription, replication, recombination and repair has developed in the past decade. Fueled by genetic observations of effects of histone mutations on transcription and identification of genes whose products must alter chromatin structure as they affect gene activity, this subject leapt to the forefront in the past two years with the correlation of certain transcription factors with enzymes that post-translationally modify histones and are presumed to alter chromatin structure thereby. Surprisingly few experimental reports have actually addressed chromatin structure. In part, this may be related to the technical difficulties of traditional approaches to structure inference. Methods have become available recently for assessment of various aspects of chromatin structure in vivo. Study in intact cells may limit potential problems resulting from loss of components or rearrangement of structures and simplify analysis by eliminating the need for isolation of organelles.
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Affiliation(s)
- R T Simpson
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 308 Althouse, University Park, Pennsylvania 16802, USA.
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Karrer KM, VanNuland TA. Position effect takes precedence over target sequence in determination of adenine methylation patterns in the nuclear genome of a eukaryote, Tetrahymena thermophila. Nucleic Acids Res 1998; 26:4566-73. [PMID: 9753722 PMCID: PMC147886 DOI: 10.1093/nar/26.20.4566] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Approximately 0.8% of the adenine residues in the macronuclear DNA of the ciliated protozoan Tetrahymena thermophila are modified to N 6-methyladenine. DNA methylation is site specific and the pattern of methylation is constant between clonal cell lines. In vivo, modification of adenine residues appears to occur exclusively in the sequence 5'-NAT-3', but no consensus sequence for modified sites has been found. In this study, DNA fragments containing a site that is uniformly methylated on the 50 copies of the macronuclear chromosome were cloned into the extrachromosomal rDNA. In the novel location on the rDNA minichromosome, the site was unmethylated. The result was the same whether the sequences were introduced in a methylated or unmethylated state and regardless of the orientation of the sequence with respect to the origin of DNA replication. The data show that sequence is insufficient to account for site-specific methylation in Tetrahymena and argue that other factors determine the pattern of DNA methylation.
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Affiliation(s)
- K M Karrer
- Department of Biology, Marquette University, Milwaukee, WI 53201-1881, USA.
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25
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Au KY, Yao CM, Cowan R, Ng SF. Programming of the macronucleus of Paramecium during asexual and sexual reproduction: A further study with cytidine analogues, dimethylsulfoxide, L-ethionine and N-butyric acid. Eur J Protistol 1990. [DOI: 10.1016/s0932-4739(11)80386-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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26
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Abstract
DNA isolated from the protozoan Trypanosoma cruzi has been found to contain 5-methylcytosine. Analysis of T. cruzi DNA by both HpaII and MspI restriction endonucleases suggests that the sequence -CCGG- is not methylated. Probably T. cruzi DNA also contains N6-methyladenine. This report constitutes the first clear demonstration of the presence of methylated bases in the nuclear DNA from trypanosomes.
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Affiliation(s)
- M V Rojas
- Department of Cell Biology and Genetics, School of Medicine, University of Chile, Santiago
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27
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Affiliation(s)
- K M Karrer
- Department of Biology, Brandeis University, Waltham, MA 02254
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28
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Abstract
Core-protected DNA can drive only 60% of the Tetrahymena thermophila macronuclear genome into duplexes in hybridization experiments. This core-protected DNA therefore contains only a subset of the genome complexity. We interpret this to mean that a large fraction, if not all, of the genome is phased with respect to nucleosome placement. Among the sequences present in total DNA and absent from core-protected DNA are most of the sequences containing N6-methyladenine (MeAde) residues, consistent with our previous demonstration that most of these residues lie in linker DNA. We show that these results are not due to artifacts resulting from the small size of the DNA driver, nor are they due to any sequence preferences exhibited by staphylococcal (staph) nuclease. This is the first evidence that nucleosome phasing may be a bulk genome characteristic.
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PRATT KAREN, HATTMAN STANLEY. Nucleosome Phasing in Tetrahymena Macronuclei. J Eukaryot Microbiol 1983. [DOI: 10.1111/j.1550-7408.1983.tb05483.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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30
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Abstract
Active genes are packaged into an altered nucleosome structure forming a chromosomal domain defined by increased sensitivity to nucleases. This structure, reflecting a potential for transcription, contains sites hypersensitive to nuclease digestion adjacent to the coding regions and may also be distinguished by specific non-histone proteins, variant or modified histones or modified DNA. Its formation, by unfolding of a tightly packed chromatin fibre by factors which might affect DNA supercoiling, may be the first step in gene activation.
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Bromberg S, Pratt K, Hattman S. Sequence specificity of DNA adenine methylase in the protozoan Tetrahymena thermophila. J Bacteriol 1982; 150:993-6. [PMID: 6950932 PMCID: PMC216459 DOI: 10.1128/jb.150.2.993-996.1982] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The sequence specificity of the Tetrahymena DNA-adenine methylase was determined by nearest-neighbor analyses of in vivo and in vitro methylated DNA. In vivo all four common bases were found to the 5' side of N6-methyladenine, but only thymidine was 3'. Homologous DNA already methylated in vivo and heterologous Micrococcus luteus DNA were methylated in vitro by a partially purified DNA-adenine methylase activity isolated from Tetrahymena macronuclei. The in vitro-methylated sequence differed from the in vivo sequence in that both thymidine and cytosine were 3' nearest neighbors of N6-methyladenine.
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