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Feng X, Cui X, Zhang LS, Ye C, Wang P, Zhong Y, Wu T, Zheng Z, He C. Sequencing of N 6-methyl-deoxyadenosine at single-base resolution across the mammalian genome. Mol Cell 2024; 84:596-610.e6. [PMID: 38215754 PMCID: PMC10872247 DOI: 10.1016/j.molcel.2023.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 07/25/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Although DNA N6-methyl-deoxyadenosine (6mA) is abundant in bacteria and protists, its presence and function in mammalian genomes have been less clear. We present Direct-Read 6mA sequencing (DR-6mA-seq), an antibody-independent method, to measure 6mA at base resolution. DR-6mA-seq employs a unique mutation-based strategy to reveal 6mA sites as misincorporation signatures without any chemical or enzymatic modulation of 6mA. We validated DR-6mA-seq through the successful mapping of the well-characterized G(6mA)TC motif in the E. coli DNA. As expected, when applying DR-6mA-seq to mammalian systems, we found that genomic DNA (gDNA) 6mA abundance is generally low in most mammalian tissues and cells; however, we did observe distinct gDNA 6mA sites in mouse testis and glioblastoma cells. DR-6mA-seq provides an enabling tool to detect 6mA at single-base resolution for a comprehensive understanding of DNA 6mA in eukaryotes.
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Affiliation(s)
- Xinran Feng
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Xiaolong Cui
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Li-Sheng Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA; Department of Chemistry, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Chang Ye
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Pingluan Wang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Yuhao Zhong
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Tong Wu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Zhong Zheng
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
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2
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Boulet M, Gilbert G, Renaud Y, Schmidt-Dengler M, Plantié E, Bertrand R, Nan X, Jurkowski T, Helm M, Vandel L, Waltzer L. Adenine methylation is very scarce in the Drosophila genome and not erased by the ten-eleven translocation dioxygenase. eLife 2023; 12:RP91655. [PMID: 38126351 PMCID: PMC10735219 DOI: 10.7554/elife.91655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
N6-methyladenine (6mA) DNA modification has recently been described in metazoans, including in Drosophila, for which the erasure of this epigenetic mark has been ascribed to the ten-eleven translocation (TET) enzyme. Here, we re-evaluated 6mA presence and TET impact on the Drosophila genome. Using axenic or conventional breeding conditions, we found traces of 6mA by LC-MS/MS and no significant increase in 6mA levels in the absence of TET, suggesting that this modification is present at very low levels in the Drosophila genome but not regulated by TET. Consistent with this latter hypothesis, further molecular and genetic analyses showed that TET does not demethylate 6mA but acts essentially in an enzymatic-independent manner. Our results call for further caution concerning the role and regulation of 6mA DNA modification in metazoans and underline the importance of TET non-enzymatic activity for fly development.
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Affiliation(s)
- Manon Boulet
- Université Clermont Auvergne, CNRS, INSERM, iGReDClermont-FerrandFrance
| | - Guerric Gilbert
- Université Clermont Auvergne, CNRS, INSERM, iGReDClermont-FerrandFrance
| | - Yoan Renaud
- Université Clermont Auvergne, CNRS, INSERM, iGReDClermont-FerrandFrance
| | - Martina Schmidt-Dengler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-UniversitätMainzGermany
| | - Emilie Plantié
- Université Clermont Auvergne, CNRS, INSERM, iGReDClermont-FerrandFrance
| | - Romane Bertrand
- Université Clermont Auvergne, CNRS, INSERM, iGReDClermont-FerrandFrance
| | - Xinsheng Nan
- School of Biosciences, Cardiff UniversityCardiffUnited Kingdom
| | | | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-UniversitätMainzGermany
| | - Laurence Vandel
- Université Clermont Auvergne, CNRS, INSERM, iGReDClermont-FerrandFrance
| | - Lucas Waltzer
- Université Clermont Auvergne, CNRS, INSERM, iGReDClermont-FerrandFrance
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3
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Ma CJ, Li G, Shao WX, Min YH, Wang P, Ding JH, Xie NB, Wang M, Tang F, Feng YQ, Ci W, Wang Y, Yuan BF. Single-Nucleotide Resolution Mapping of N6-Methyladenine in Genomic DNA. ACS CENTRAL SCIENCE 2023; 9:1799-1809. [PMID: 37780356 PMCID: PMC10540296 DOI: 10.1021/acscentsci.3c00481] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Indexed: 10/03/2023]
Abstract
N6-Methyladenine (6mA) is a naturally occurring DNA modification in both prokaryotes and eukaryotes. Herein, we developed a deaminase-mediated sequencing (DM-seq) method for genome-wide mapping of 6mA at single-nucleotide resolution. The method capitalizes on the selective deamination of adenine, but not 6mA, in DNA mediated by an evolved adenine deaminase, ABE8e. By employing this method, we achieved genome-wide mapping of 6mA in Escherichia coli and in mammalian mitochondrial DNA (mtDNA) at single-nucleotide resolution. We found that the 6mA sites are mainly located in the GATC motif in the E. coli genome. We also identified 17 6mA sites in mtDNA of HepG2 cells, where all of the 6mA sites are distributed in the heavy strand of mtDNA. We envision that DM-seq will be a valuable tool for uncovering new functions of 6mA in DNA and for exploring its potential roles in mitochondria-related human diseases.
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Affiliation(s)
- Cheng-Jie Ma
- School
of Public Health, Department of Radiation and Medical Oncology, Zhongnan
Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Sauvage
Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
- Department
of Chemistry, University of California,
Riverside, Riverside, California 92521-0403, United States
| | - Gaojie Li
- Key
Laboratory of Genomics and Precision Medicine, and China National
Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen-Xuan Shao
- School
of Public Health, Department of Radiation and Medical Oncology, Zhongnan
Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Sauvage
Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Yi-Hao Min
- School
of Public Health, Department of Radiation and Medical Oncology, Zhongnan
Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Sauvage
Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Ping Wang
- Key
Laboratory of Genomics and Precision Medicine, and China National
Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiang-Hui Ding
- School
of Public Health, Department of Radiation and Medical Oncology, Zhongnan
Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Sauvage
Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Neng-Bin Xie
- School
of Public Health, Department of Radiation and Medical Oncology, Zhongnan
Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Sauvage
Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Min Wang
- School
of Public Health, Department of Radiation and Medical Oncology, Zhongnan
Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Sauvage
Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Feng Tang
- Department
of Chemistry, University of California,
Riverside, Riverside, California 92521-0403, United States
| | - Yu-Qi Feng
- School
of Public Health, Department of Radiation and Medical Oncology, Zhongnan
Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Sauvage
Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Weimin Ci
- Key
Laboratory of Genomics and Precision Medicine, and China National
Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Yinsheng Wang
- Department
of Chemistry, University of California,
Riverside, Riverside, California 92521-0403, United States
| | - Bi-Feng Yuan
- School
of Public Health, Department of Radiation and Medical Oncology, Zhongnan
Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Sauvage
Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
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4
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Febrimarsa, Gornik SG, Barreira SN, Salinas‐Saavedra M, Schnitzler CE, Baxevanis AD, Frank U. Randomly incorporated genomic N6-methyldeoxyadenosine delays zygotic transcription initiation in a cnidarian. EMBO J 2023; 42:e112934. [PMID: 37708295 PMCID: PMC10390872 DOI: 10.15252/embj.2022112934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 09/16/2023] Open
Abstract
N6-methyldeoxyadenosine (6mA) is a chemical alteration of DNA, observed across all realms of life. Although the functions of 6mA are well understood in bacteria and protists, its roles in animal genomes have been controversial. We show that 6mA randomly accumulates in early embryos of the cnidarian Hydractinia symbiolongicarpus, with a peak at the 16-cell stage followed by clearance to background levels two cell cycles later, at the 64-cell stage-the embryonic stage at which zygotic genome activation occurs in this animal. Knocking down Alkbh1, a putative initiator of animal 6mA clearance, resulted in higher levels of 6mA at the 64-cell stage and a delay in the initiation of zygotic transcription. Our data are consistent with 6mA originating from recycled nucleotides of degraded m6A-marked maternal RNA postfertilization. Therefore, while 6mA does not function as an epigenetic mark in Hydractinia, its random incorporation into the early embryonic genome inhibits transcription. In turn, Alkbh1 functions as a genomic 6mA "cleaner," facilitating timely zygotic genome activation. Given the random nature of genomic 6mA accumulation and its ability to interfere with gene expression, defects in 6mA clearance may represent a hitherto unknown cause of various pathologies.
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Affiliation(s)
- Febrimarsa
- Centre for Chromosome Biology, School of Biological and Chemical SciencesUniversity of GalwayGalwayRepublic of Ireland
| | - Sebastian G Gornik
- Centre for Chromosome Biology, School of Biological and Chemical SciencesUniversity of GalwayGalwayRepublic of Ireland
- Present address:
Centre for Organismal StudiesHeidelberg UniversityHeidelbergGermany
| | - Sofia N Barreira
- Computational and Statistical Genomics Branch, Division of Intramural ResearchNational Human Genome Research Institute, National Institutes of HealthBethesdaMDUSA
| | - Miguel Salinas‐Saavedra
- Centre for Chromosome Biology, School of Biological and Chemical SciencesUniversity of GalwayGalwayRepublic of Ireland
| | - Christine E Schnitzler
- Whitney Laboratory for Marine BioscienceUniversity of FloridaSt. AugustineFLUSA
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
| | - Andreas D Baxevanis
- Computational and Statistical Genomics Branch, Division of Intramural ResearchNational Human Genome Research Institute, National Institutes of HealthBethesdaMDUSA
| | - Uri Frank
- Centre for Chromosome Biology, School of Biological and Chemical SciencesUniversity of GalwayGalwayRepublic of Ireland
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5
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Wang M, Zhu J, Ye Y, Li P, Sun W, Zhang M. N6AMT1 is a novel potential diagnostic, prognostic and immunotherapy response biomarker in pan-cancer. Aging (Albany NY) 2023; 15:6526-6544. [PMID: 37437243 PMCID: PMC10373955 DOI: 10.18632/aging.204868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/15/2023] [Indexed: 07/14/2023]
Abstract
BACKGROUND The N-6-adenine-specific DNA methyltransferase 1 (N6AMT1) is the only writer responsible for DNA 6mA modifications. At present, its role in cancer is still unclear, and further systematic pan-cancer analysis is needed to explore its value in diagnosis, prognosis and immunological function. METHODS The subcellular localization of N6AMT1 was explored by UniProt and HPA database. The expression data and prognosis data of N6AMT1 were downloaded from the UCSC (cohort: TCGA pan-cancer), and the diagnostic and prognostic value of N6AMT1 in pan-cancer was explored. The value of N6AMT1-guided immunotherapy was explored through three cohorts (GSE168204, GSE67501 and IMvigor210 cohort). The correlation between N6AMT1 expression and tumor immune microenvironment was explored using CIBERSORT and ESTIMATE calculation methods, combined with TISIDB database. The biological role of N6AMT1 in specific tumors was explored by GSEA method. Finally, we explored chemicals affecting N6AMT1 expression through the CTD. RESULTS N6AMT1 is mainly localized in the nucleus and differentially expressed in 9 cancer types. In addition, N6AMT1 showed early diagnostic value in 7 cancers and showed potential prognostic value in multiple cancer types. We also demonstrated that N6AMT1 expression was significantly associated with immunomodulator-related molecules, infiltration of lymphocyte subsets, and biomarkers of immunotherapy response. Furthermore, we show that N6AMT1 is differentially expressed in the immunotherapy cohort. Finally, we explored 43 chemicals that can affect N6AMT1 expression. CONCLUSIONS N6AMT1 has shown excellent diagnostic and prognostic capabilities in a variety of cancers, and it may reshape the tumor microenvironment and contribute to the ability to predict response to immunotherapy.
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Affiliation(s)
- Mingqi Wang
- Department of Chinese Integrative Medicine Oncology, The First Affiliated Hospital of Anhui Medical University, Shushan, Hefei 230022, Anhui, China
- Department of Integrated Traditional Chinese and Western Medicine, Anhui Medical University, Shushan, Hefei 230022, Anhui, China
| | - Jiajie Zhu
- Department of Gastroenterology, Tongde Hospital of Zhejiang Province, Xihu, Hangzhou 310012, Zhejiang, China
| | - Yingquan Ye
- Department of Chinese Integrative Medicine Oncology, The First Affiliated Hospital of Anhui Medical University, Shushan, Hefei 230022, Anhui, China
- Department of Integrated Traditional Chinese and Western Medicine, Anhui Medical University, Shushan, Hefei 230022, Anhui, China
| | - Ping Li
- Department of Chinese Integrative Medicine Oncology, The First Affiliated Hospital of Anhui Medical University, Shushan, Hefei 230022, Anhui, China
- Department of Integrated Traditional Chinese and Western Medicine, Anhui Medical University, Shushan, Hefei 230022, Anhui, China
| | - Weijie Sun
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Shushan, Hefei 230022, Anhui, China
| | - Mei Zhang
- Department of Chinese Integrative Medicine Oncology, The First Affiliated Hospital of Anhui Medical University, Shushan, Hefei 230022, Anhui, China
- Department of Integrated Traditional Chinese and Western Medicine, Anhui Medical University, Shushan, Hefei 230022, Anhui, China
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6
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Arkhipova IR, Yushenova IA, Rodriguez F. Shaping eukaryotic epigenetic systems by horizontal gene transfer. Bioessays 2023; 45:e2200232. [PMID: 37339822 PMCID: PMC10287040 DOI: 10.1002/bies.202200232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 05/07/2023] [Accepted: 05/08/2023] [Indexed: 06/22/2023]
Abstract
DNA methylation constitutes one of the pillars of epigenetics, relying on covalent bonds for addition and/or removal of chemically distinct marks within the major groove of the double helix. DNA methyltransferases, enzymes which introduce methyl marks, initially evolved in prokaryotes as components of restriction-modification systems protecting host genomes from bacteriophages and other invading foreign DNA. In early eukaryotic evolution, DNA methyltransferases were horizontally transferred from bacteria into eukaryotes several times and independently co-opted into epigenetic regulatory systems, primarily via establishing connections with the chromatin environment. While C5-methylcytosine is the cornerstone of plant and animal epigenetics and has been investigated in much detail, the epigenetic role of other methylated bases is less clear. The recent addition of N4-methylcytosine of bacterial origin as a metazoan DNA modification highlights the prerequisites for foreign gene co-option into the host regulatory networks, and challenges the existing paradigms concerning the origin and evolution of eukaryotic regulatory systems.
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Affiliation(s)
- Irina R Arkhipova
- Marine Biological Laboratory, Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, Massachusetts, USA
| | - Irina A Yushenova
- Marine Biological Laboratory, Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, Massachusetts, USA
| | - Fernando Rodriguez
- Marine Biological Laboratory, Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, Massachusetts, USA
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7
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Kong Y, Mead EA, Fang G. Navigating the pitfalls of mapping DNA and RNA modifications. Nat Rev Genet 2023; 24:363-381. [PMID: 36653550 PMCID: PMC10722219 DOI: 10.1038/s41576-022-00559-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2022] [Indexed: 01/19/2023]
Abstract
Chemical modifications to nucleic acids occur across the kingdoms of life and carry important regulatory information. Reliable high-resolution mapping of these modifications is the foundation of functional and mechanistic studies, and recent methodological advances based on next-generation sequencing and long-read sequencing platforms are critical to achieving this aim. However, mapping technologies may have limitations that sometimes lead to inconsistent results. Some of these limitations are technical in nature and specific to certain types of technology. Here, however, we focus on common (yet not always widely recognized) pitfalls that are shared among frequently used mapping technologies and discuss strategies to help technology developers and users mitigate their effects. Although the emphasis is primarily on DNA modifications, RNA modifications are also discussed.
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Affiliation(s)
- Yimeng Kong
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edward A Mead
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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8
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Lyu C, Wang HD, Lai W, Wang H. Identification and quantification of DNA N 6-methyladenine modification in mammals: A challenge to modern analytical technologies. Curr Opin Chem Biol 2023; 73:102259. [PMID: 36652775 DOI: 10.1016/j.cbpa.2022.102259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 01/18/2023]
Abstract
DNA N6-methyladenine modification (6mA) is a predominant epigenetic mark in prokaryotes but rarely present in multicellular metazoa. The analytical technologies have been developed for sensitive detection of 6mA, including ultra-high performance liquid chromatography coupled with mass spectrometry (UHPLC-MS/MS) and single molecule real-time sequencing (SMRTseq). However, it remains challenging to detect 6mA at global level and/or in the context of sequence in multicellular metazoa (including mammals). This mini-review brings insights into current dilemma and potential solutions for the identification and quantifications of 6mA in mammals.
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Affiliation(s)
- Cong Lyu
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hui-Dong Wang
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Weiyi Lai
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hailin Wang
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China; University of Chinese Academy of Sciences, Beijing, China.
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9
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Bai S, Han X, Feng D. Shoot-root signal circuit: Phytoremediation of heavy metal contaminated soil. FRONTIERS IN PLANT SCIENCE 2023; 14:1139744. [PMID: 36890896 PMCID: PMC9987563 DOI: 10.3389/fpls.2023.1139744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
High concentrations of heavy metals in the environment will cause serious harm to ecosystems and human health. It is urgent to develop effective methods to control soil heavy metal pollution. Phytoremediation has advantages and potential for soil heavy metal pollution control. However, the current hyperaccumulators have the disadvantages of poor environmental adaptability, single enrichment species and small biomass. Based on the concept of modularity, synthetic biology makes it possible to design a wide range of organisms. In this paper, a comprehensive strategy of "microbial biosensor detection - phytoremediation - heavy metal recovery" for soil heavy metal pollution control was proposed, and the required steps were modified by using synthetic biology methods. This paper summarizes the new experimental methods that promote the discovery of synthetic biological elements and the construction of circuits, and combs the methods of producing transgenic plants to facilitate the transformation of constructed synthetic biological vectors. Finally, the problems that should be paid more attention to in the remediation of soil heavy metal pollution based on synthetic biology were discussed.
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Affiliation(s)
- Shiyan Bai
- College of Biological Science and Engineering, Fuzhou University, Fujian, China
| | - Xiao Han
- College of Biological Science and Engineering, Fuzhou University, Fujian, China
| | - Dan Feng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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10
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Yang M, Li X, Tian Z, Ma L, Ma J, Liu Y, Shang G, Liang A, Wu W, Chen Z. Structures of MPND Reveal the Molecular Recognition of Nucleosomes. Int J Mol Sci 2023; 24:ijms24043368. [PMID: 36834777 PMCID: PMC9963953 DOI: 10.3390/ijms24043368] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Adenine N6 methylation in DNA (6mA) is a well-known epigenetic modification in bacteria, phages, and eukaryotes. Recent research has identified the Mpr1/Pad1 N-terminal (MPN) domain-containing protein (MPND) as a sensor protein that may recognize DNA 6mA modification in eukaryotes. However, the structural details of MPND and the molecular mechanism of their interaction remain unknown. Herein, we report the first crystal structures of the apo-MPND and MPND-DNA complex at resolutions of 2.06 Å and 2.47 Å, respectively. In solution, the assemblies of both apo-MPND and MPND-DNA are dynamic. In addition, MPND was found to possess the ability to bind directly to histones, no matter the N-terminal restriction enzyme-adenine methylase-associated domain or the C-terminal MPN domain. Moreover, the DNA and the two acidic regions of MPND synergistically enhance the interaction between MPND and histones. Therefore, our findings provide the first structural information regarding the MPND-DNA complex and also provide evidence of MPND-nucleosome interactions, thereby laying the foundation for further studies on gene control and transcriptional regulation.
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11
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Feng X, He C. Mammalian DNA N 6-methyladenosine: Challenges and new insights. Mol Cell 2023; 83:343-351. [PMID: 36736309 PMCID: PMC10182828 DOI: 10.1016/j.molcel.2023.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 02/05/2023]
Abstract
DNA N6-methyldeoxyadenosine (6mA) modification was first discovered in Bacterium coli in the 1950s. Over the next several decades, 6mA was recognized as a critical DNA modification in the genomes of prokaryotes and protists. While important in prokaryotes, less is known about the presence and functional roles of DNA 6mA in eukaryotes, particularly in mammals. Taking advantage of recent technology advances that made 6mA detection and sequencing possible, studies over the past several years have brought new insights into 6mA biology in mammals. In this perspective, we present recent progress, discuss challenges, and pose four questions for future research regarding mammalian DNA 6mA.
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Affiliation(s)
- Xinran Feng
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
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12
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Han K, Wang J, Wang Y, Zhang L, Yu M, Xie F, Zheng D, Xu Y, Ding Y, Wan J. A review of methods for predicting DNA N6-methyladenine sites. Brief Bioinform 2023; 24:6887111. [PMID: 36502371 DOI: 10.1093/bib/bbac514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/07/2022] [Accepted: 10/27/2022] [Indexed: 12/14/2022] Open
Abstract
Deoxyribonucleic acid(DNA) N6-methyladenine plays a vital role in various biological processes, and the accurate identification of its site can provide a more comprehensive understanding of its biological effects. There are several methods for 6mA site prediction. With the continuous development of technology, traditional techniques with the high costs and low efficiencies are gradually being replaced by computer methods. Computer methods that are widely used can be divided into two categories: traditional machine learning and deep learning methods. We first list some existing experimental methods for predicting the 6mA site, then analyze the general process from sequence input to results in computer methods and review existing model architectures. Finally, the results were summarized and compared to facilitate subsequent researchers in choosing the most suitable method for their work.
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Affiliation(s)
- Ke Han
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China.,College of Pharmacy, Harbin University of Commerce, Harbin, 150076, China
| | - Jianchun Wang
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China
| | - Yu Wang
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China
| | - Lei Zhang
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China
| | - Mengyao Yu
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China
| | - Fang Xie
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China
| | - Dequan Zheng
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China
| | - Yaoqun Xu
- School of Computer and Information Engineering, Heilongjiang Provincial Key Laboratory of Electronic Commerce and Information Processing, Harbin University of Commerce, Harbin, 150028, China
| | - Yijie Ding
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, 324000, China
| | - Jie Wan
- Laboratory for Space Environment and Physical Sciences, Harbin Institute of Technology, Harbin, 150001, China
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13
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DNA Modification Patterns Filtering and Analysis Using DNAModAnnot. Methods Mol Biol 2023; 2624:87-114. [PMID: 36723811 DOI: 10.1007/978-1-0716-2962-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mapping DNA modifications at the base resolution is now possible at the genome level thanks to advances in sequencing technologies. Long-read sequencing data can be used to identify modified base patterns. However, the downstream analysis of Pacific Biosciences (PacBio) or Oxford Nanopore Technologies (ONT) data requires the integration of genomic annotation and comprehensive filtering to prevent the accumulation of artifact signals. We present in this chapter, a linear workflow to fully analyze modified base patterns using the DNA Modification Annotation (DNAModAnnot) package. This workflow includes a thorough filtering based on sequencing quality and false discovery rate estimation and provides tools for a global analysis of DNA modifications. Here, we provide an application example of this workflow with PacBio data and guide the user by explaining expected outputs via a fully integrated Rmarkdown script. This protocol is presented with tips showing how to adapt the provided code for annotating epigenomes of any organism according to the user needs.
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14
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Chen LQ, Zhang Z, Chen HX, Xi JF, Liu XH, Ma DZ, Zhong YH, Ng WH, Chen T, Mak DW, Chen Q, Chen YQ, Luo GZ. High-precision mapping reveals rare N 6-deoxyadenosine methylation in the mammalian genome. Cell Discov 2022; 8:138. [PMID: 36575183 PMCID: PMC9794812 DOI: 10.1038/s41421-022-00484-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 10/16/2022] [Indexed: 12/28/2022] Open
Abstract
N6-deoxyadenosine methylation (6mA) is the most widespread type of DNA modification in prokaryotes and is also abundantly distributed in some unicellular eukaryotes. However, 6mA levels are remarkably low in mammals. The lack of a precise and comprehensive mapping method has hindered more advanced investigations of 6mA. Here, we report a new method MM-seq (modification-induced mismatch sequencing) for genome-wide 6mA mapping based on a novel detection principle. We found that modified DNA bases are prone to form a local open region that allows capture by antibody, for example, via a DNA breathing or base-flipping mechanism. Specified endonuclease or exonuclease can recognize the antibody-stabilized mismatch-like structure and mark the exact modified sites for sequencing readout. Using this method, we examined the genomic positions of 6mA in bacteria (E. coli), green algae (C. reinhardtii), and mammalian cells (HEK239T, Huh7, and HeLa cells). In contrast to bacteria and green algae, human cells possess a very limited number of 6mA sites which are sporadically distributed across the genome of different cell types. After knocking out the RNA m6A methyltransferase METTL3 in mouse ES cells, 6mA becomes mostly diminished. Our results imply that rare 6mA in the mammalian genome is introduced by RNA m6A machinery via a non-targeted mechanism.
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Affiliation(s)
- Li-Qian Chen
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China ,grid.410643.4Guangdong Cardiovascular Institute, Medical Research Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong China
| | - Zhang Zhang
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Hong-Xuan Chen
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Jian-Fei Xi
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Xue-Hong Liu
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Dong-Zhao Ma
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Yu-Hao Zhong
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Wen Hui Ng
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Tao Chen
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
| | - Daniel W. Mak
- grid.194645.b0000000121742757School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Qi Chen
- grid.12981.330000 0001 2360 039XSchool of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong China
| | - Yao-Qing Chen
- grid.12981.330000 0001 2360 039XSchool of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong China
| | - Guan-Zheng Luo
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong China
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15
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Yang L, Zhang P, Wang Y, Hu G, Guo W, Gu X, Pu L. Plant synthetic epigenomic engineering for crop improvement. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2191-2204. [PMID: 35851940 DOI: 10.1007/s11427-021-2131-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Efforts have been directed to redesign crops with increased yield, stress adaptability, and nutritional value through synthetic biology-the application of engineering principles to biology. A recent expansion in our understanding of how epigenetic mechanisms regulate plant development and stress responses has unveiled a new set of resources that can be harnessed to develop improved crops, thus heralding the promise of "synthetic epigenetics." In this review, we summarize the latest advances in epigenetic regulation and highlight how innovative sequencing techniques, epigenetic editing, and deep learning-driven predictive tools can rapidly extend these insights. We also proposed the future directions of synthetic epigenetics for the development of engineered smart crops that can actively monitor and respond to internal and external cues throughout their life cycles.
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Affiliation(s)
- Liwen Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Pingxian Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yifan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guihua Hu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weijun Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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16
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Seong HJ, Roux S, Hwang CY, Sul WJ. Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics. MICROBIOME 2022; 10:157. [PMID: 36167684 PMCID: PMC9516812 DOI: 10.1186/s40168-022-01340-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 07/28/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in culturable microorganisms, resulting in a limited understanding of DNA methylation from a microbial ecology perspective. Here, we analyze the distribution patterns of several microbial epigenetics marks in the ocean microbiome through genome-centric metagenomics across all domains of life. RESULTS We reconstructed 15,056 viral, 252 prokaryotic, 56 giant viral, and 6 eukaryotic metagenome-assembled genomes from northwest Pacific Ocean seawater samples using short- and long-read sequencing approaches. These metagenome-derived genomes mostly represented novel taxa, and recruited a majority of reads. Thanks to single-molecule real-time (SMRT) sequencing technology, base modification could also be detected for these genomes. This showed that DNA methylation can readily be detected across dominant oceanic bacterial, archaeal, and viral populations, and microbial epigenetic changes correlate with population differentiation. Furthermore, our genome-wide epigenetic analysis of Pelagibacter suggests that GANTC, a DNA methyltransferase target motif, is related to the cell cycle and is affected by environmental conditions. Yet, the presence of this motif also partitions the phylogeny of the Pelagibacter phages, possibly hinting at a competitive co-evolutionary history and multiple effects of a single methylation mark. CONCLUSIONS Overall, this study elucidates that DNA methylation patterns are associated with ecological changes and virus-host dynamics in the ocean microbiome. Video Abstract.
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Affiliation(s)
- Hoon Je Seong
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Chung Yeon Hwang
- School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul, Republic of Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
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17
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Di Stefano L. All Quiet on the TE Front? The Role of Chromatin in Transposable Element Silencing. Cells 2022; 11:cells11162501. [PMID: 36010577 PMCID: PMC9406493 DOI: 10.3390/cells11162501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/27/2022] [Accepted: 08/03/2022] [Indexed: 01/09/2023] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that constitute a sizeable portion of many eukaryotic genomes. Through their mobility, they represent a major source of genetic variation, and their activation can cause genetic instability and has been linked to aging, cancer and neurodegenerative diseases. Accordingly, tight regulation of TE transcription is necessary for normal development. Chromatin is at the heart of TE regulation; however, we still lack a comprehensive understanding of the precise role of chromatin marks in TE silencing and how chromatin marks are established and maintained at TE loci. In this review, I discuss evidence documenting the contribution of chromatin-associated proteins and histone marks in TE regulation across different species with an emphasis on Drosophila and mammalian systems.
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Affiliation(s)
- Luisa Di Stefano
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
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18
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Li H, Zhang N, Wang Y, Xia S, Zhu Y, Xing C, Tian X, Du Y. DNA N6-Methyladenine Modification in Eukaryotic Genome. Front Genet 2022; 13:914404. [PMID: 35812743 PMCID: PMC9263368 DOI: 10.3389/fgene.2022.914404] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/08/2022] [Indexed: 11/18/2022] Open
Abstract
DNA methylation is treated as an important epigenetic mark in various biological activities. In the past, a large number of articles focused on 5 mC while lacking attention to N6-methyladenine (6 mA). The presence of 6 mA modification was previously discovered only in prokaryotes. Recently, with the development of detection technologies, 6 mA has been found in several eukaryotes, including protozoans, metazoans, plants, and fungi. The importance of 6 mA in prokaryotes and single-celled eukaryotes has been widely accepted. However, due to the incredibly low density of 6 mA and restrictions on detection technologies, the prevalence of 6 mA and its role in biological processes in eukaryotic organisms are highly debated. In this review, we first summarize the advantages and disadvantages of 6 mA detection methods. Then, we conclude existing reports on the prevalence of 6 mA in eukaryotic organisms. Next, we highlight possible methyltransferases, demethylases, and the recognition proteins of 6 mA. In addition, we summarize the functions of 6 mA in eukaryotes. Last but not least, we summarize our point of view and put forward the problems that need further research.
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Affiliation(s)
- Hao Li
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- First School of Clinical Medicine, Anhui Medical University, Hefei, China
- First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Ning Zhang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- First School of Clinical Medicine, Anhui Medical University, Hefei, China
- First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yuechen Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Second School of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Siyuan Xia
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Second School of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Yating Zhu
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Chen Xing
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Xuefeng Tian
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- First School of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Yinan Du
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- *Correspondence: Yinan Du,
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19
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Hesami M, Alizadeh M, Jones AMP, Torkamaneh D. Machine learning: its challenges and opportunities in plant system biology. Appl Microbiol Biotechnol 2022; 106:3507-3530. [PMID: 35575915 DOI: 10.1007/s00253-022-11963-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 03/14/2022] [Accepted: 05/07/2022] [Indexed: 12/25/2022]
Abstract
Sequencing technologies are evolving at a rapid pace, enabling the generation of massive amounts of data in multiple dimensions (e.g., genomics, epigenomics, transcriptomic, metabolomics, proteomics, and single-cell omics) in plants. To provide comprehensive insights into the complexity of plant biological systems, it is important to integrate different omics datasets. Although recent advances in computational analytical pipelines have enabled efficient and high-quality exploration and exploitation of single omics data, the integration of multidimensional, heterogenous, and large datasets (i.e., multi-omics) remains a challenge. In this regard, machine learning (ML) offers promising approaches to integrate large datasets and to recognize fine-grained patterns and relationships. Nevertheless, they require rigorous optimizations to process multi-omics-derived datasets. In this review, we discuss the main concepts of machine learning as well as the key challenges and solutions related to the big data derived from plant system biology. We also provide in-depth insight into the principles of data integration using ML, as well as challenges and opportunities in different contexts including multi-omics, single-cell omics, protein function, and protein-protein interaction. KEY POINTS: • The key challenges and solutions related to the big data derived from plant system biology have been highlighted. • Different methods of data integration have been discussed. • Challenges and opportunities of the application of machine learning in plant system biology have been highlighted and discussed.
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Affiliation(s)
- Mohsen Hesami
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Milad Alizadeh
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | | | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec City, QC, G1V 0A6, Canada. .,Institut de Biologie Intégrative Et Des Systèmes (IBIS), Université Laval, Québec City, QC, G1V 0A6, Canada.
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20
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Takahashi Y, Shoura M, Fire A, Morishita S. Context-dependent DNA polymerization effects can masquerade as DNA modification signals. BMC Genomics 2022; 23:249. [PMID: 35361121 PMCID: PMC8973881 DOI: 10.1186/s12864-022-08471-2] [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: 05/13/2021] [Accepted: 03/15/2022] [Indexed: 11/23/2022] Open
Abstract
Background Single molecule measurements of DNA polymerization kinetics provide a sensitive means to detect both secondary structures in DNA and deviations from primary chemical structure as a result of modified bases. In one approach to such analysis, deviations can be inferred by monitoring the behavior of DNA polymerase using single-molecule, real-time sequencing with zero-mode waveguide. This approach uses a Single Molecule Real Time (SMRT)-sequencing measurement of time between fluorescence pulse signals from consecutive nucleosides incorporated during DNA replication, called the interpulse duration (IPD). Results In this paper we present an analysis of loci with high IPDs in two genomes, a bacterial genome (E. coli) and a eukaryotic genome (C. elegans). To distinguish the potential effects of DNA modification on DNA polymerization speed, we paired an analysis of native genomic DNA with whole-genome amplified (WGA) material in which DNA modifications were effectively removed. Adenine modification sites for E. coli are known and we observed the expected IPD shifts at these sites in the native but not WGA samples. For C. elegans, such differences were not observed. Instead, we found a number of novel sequence contexts where IPDs were raised relative to the average IPDs for each of the four nucleotides, but for which the raised IPD was present in both native and WGA samples. Conclusion The latter results argue strongly against DNA modification as the underlying driver for high IPD segments for C. elegans, and provide a framework for separating effects of DNA modification from context-dependent DNA polymerase kinetic patterns inherent in underlying DNA sequence for a complex eukaryotic genome. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08471-2.
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Affiliation(s)
- Yusuke Takahashi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Massa Shoura
- Departments of Pathology and Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Andrew Fire
- Departments of Pathology and Genetics, School of Medicine, Stanford University, Stanford, CA, USA.
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.
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21
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Liu M, Sun ZL, Zeng Z, Lam KM. MGF6mARice: prediction of DNA N6-methyladenine sites in rice by exploiting molecular graph feature and residual block. Brief Bioinform 2022; 23:6553606. [PMID: 35325050 DOI: 10.1093/bib/bbac082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 11/12/2022] Open
Abstract
DNA N6-methyladenine (6mA) is produced by the N6 position of the adenine being methylated, which occurs at the molecular level, and is involved in numerous vital biological processes in the rice genome. Given the shortcomings of biological experiments, researchers have developed many computational methods to predict 6mA sites and achieved good performance. However, the existing methods do not consider the occurrence mechanism of 6mA to extract features from the molecular structure. In this paper, a novel deep learning method is proposed by devising DNA molecular graph feature and residual block structure for 6mA sites prediction in rice, named MGF6mARice. Firstly, the DNA sequence is changed into a simplified molecular input line entry system (SMILES) format, which reflects chemical molecular structure. Secondly, for the molecular structure data, we construct the DNA molecular graph feature based on the principle of graph convolutional network. Then, the residual block is designed to extract higher level, distinguishable features from molecular graph features. Finally, the prediction module is used to obtain the result of whether it is a 6mA site. By means of 10-fold cross-validation, MGF6mARice outperforms the state-of-the-art approaches. Multiple experiments have shown that the molecular graph feature and residual block can promote the performance of MGF6mARice in 6mA prediction. To the best of our knowledge, it is the first time to derive a feature of DNA sequence by considering the chemical molecular structure. We hope that MGF6mARice will be helpful for researchers to analyze 6mA sites in rice.
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Affiliation(s)
- Mengya Liu
- School of Computer Science and Technology, Anhui University, Hefei, 230601, China
| | - Zhan-Li Sun
- School of Artificial Intelligence, Anhui University, Hefei, 230601, China
| | - Zhigang Zeng
- School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Kin-Man Lam
- Department of Electronic and Information Engineering, The Hong Kong Polytechnic University, Hong Kong, China
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22
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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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23
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Bacterial N4-methylcytosine as an epigenetic mark in eukaryotic DNA. Nat Commun 2022; 13:1072. [PMID: 35228526 PMCID: PMC8885841 DOI: 10.1038/s41467-022-28471-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 01/21/2022] [Indexed: 01/04/2023] Open
Abstract
DNA modifications are used to regulate gene expression and defend against invading genetic elements. In eukaryotes, modifications predominantly involve C5-methylcytosine (5mC) and occasionally N6-methyladenine (6mA), while bacteria frequently use N4-methylcytosine (4mC) in addition to 5mC and 6mA. Here we report that 4mC can serve as an epigenetic mark in eukaryotes. Bdelloid rotifers, tiny freshwater invertebrates with transposon-poor genomes rich in foreign genes, lack canonical eukaryotic C5-methyltransferases for 5mC addition, but encode an amino-methyltransferase, N4CMT, captured from bacteria >60 Mya. N4CMT deposits 4mC at active transposons and certain tandem repeats, and fusion to a chromodomain shapes its “histone-read-DNA-write” architecture recognizing silent chromatin marks. Furthermore, amplification of SETDB1 H3K9me3 histone methyltransferases yields variants preferentially binding 4mC-DNA, suggesting “DNA-read-histone-write” partnership to maintain chromatin-based silencing. Our results show how non-native DNA methyl groups can reshape epigenetic systems to silence transposons and demonstrate the potential of horizontal gene transfer to drive regulatory innovation in eukaryotes. Eukaryotic DNA can be methylated as 5-methylcytosine and N6-methyladenine, but whether other forms of DNA methylation occur has been controversial. Here the authors show that a bacterial DNA methyltransferase was acquired >60 Mya in bdelloid rotifers that catalyzes N4-methylcytosine addition and is involved in suppression of transposon proliferation.
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24
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Kong Y, Cao L, Deikus G, Fan Y, Mead EA, Lai W, Zhang Y, Yong R, Sebra R, Wang H, Zhang XS, Fang G. Critical assessment of DNA adenine methylation in eukaryotes using quantitative deconvolution. Science 2022; 375:515-522. [PMID: 35113693 PMCID: PMC9382770 DOI: 10.1126/science.abe7489] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The discovery of N6-methyldeoxyadenine (6mA) across eukaryotes led to a search for additional epigenetic mechanisms. However, some studies have highlighted confounding factors that challenge the prevalence of 6mA in eukaryotes. We developed a metagenomic method to quantitatively deconvolve 6mA events from a genomic DNA sample into species of interest, genomic regions, and sources of contamination. Applying this method, we observed high-resolution 6mA deposition in two protozoa. We found that commensal or soil bacteria explained the vast majority of 6mA in insect and plant samples. We found no evidence of high abundance of 6mA in Drosophila, Arabidopsis, or humans. Plasmids used for genetic manipulation, even those from Dam methyltransferase mutant Escherichia coli, could carry abundant 6mA, confounding the evaluation of candidate 6mA methyltransferases and demethylases. On the basis of this work, we advocate for a reassessment of 6mA in eukaryotes.
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Affiliation(s)
- Yimeng Kong
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
| | - Lei Cao
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
| | - Yu Fan
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
| | - Edward A. Mead
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
| | - Weiyi Lai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences; Beijing 100085, China
| | - Yizhou Zhang
- Department of Neurosurgery and Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York; NY 10029, USA
| | - Raymund Yong
- Department of Neurosurgery and Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York; NY 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
- Sema4, a Mount Sinai venture; Stamford, CT, 06902, USA
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences; Beijing 100085, China
| | - Xue-Song Zhang
- Center for Advanced Biotechnology and Medicine, Rutgers University; New Brunswick, NJ, 08854, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
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25
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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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26
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Bonet J, Chen M, Dabad M, Heath S, Gonzalez-Perez A, Lopez-Bigas N, Lagergren J. DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data. Bioinformatics 2021; 38:1235-1243. [PMID: 34718417 PMCID: PMC8826383 DOI: 10.1093/bioinformatics/btab745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/20/2021] [Accepted: 10/25/2021] [Indexed: 01/05/2023] Open
Abstract
MOTIVATION DNA methylation plays a key role in a variety of biological processes. Recently, Nanopore long-read sequencing has enabled direct detection of these modifications. As a consequence, a range of computational methods have been developed to exploit Nanopore data for methylation detection. However, current approaches rely on a human-defined threshold to detect the methylation status of a genomic position and are not optimized to detect sites methylated at low frequency. Furthermore, most methods use either the Nanopore signals or the basecalling errors as the model input and do not take advantage of their combination. RESULTS Here, we present DeepMP, a convolutional neural network-based model that takes information from Nanopore signals and basecalling errors to detect whether a given motif in a read is methylated or not. Besides, DeepMP introduces a threshold-free position modification calling model sensitive to sites methylated at low frequency across cells. We comprehensively benchmarked DeepMP against state-of-the-art methods on Escherichia coli, human and pUC19 datasets. DeepMP outperforms current approaches at read-based and position-based methylation detection across sites methylated at different frequencies in the three datasets. AVAILABILITY AND IMPLEMENTATION DeepMP is implemented and freely available under MIT license at https://github.com/pepebonet/DeepMP. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jose Bonet
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain,Research Program on Biomedical Informatics, Universitat Pompeu Fabra, 08002 Barcelona, Catalonia, Spain,To whom correspondence should be addressed. or
| | - Mandi Chen
- Department of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, 114 28 Stockholm, Sweden,Science for Life Laboratory, 171 65 Solna Stockholm, Sweden,To whom correspondence should be addressed. or
| | - Marc Dabad
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain,Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Simon Heath
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain,Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Abel Gonzalez-Perez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain,Research Program on Biomedical Informatics, Universitat Pompeu Fabra, 08002 Barcelona, Catalonia, Spain
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain,Research Program on Biomedical Informatics, Universitat Pompeu Fabra, 08002 Barcelona, Catalonia, Spain,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Jens Lagergren
- Department of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, 114 28 Stockholm, Sweden,Science for Life Laboratory, 171 65 Solna Stockholm, Sweden
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Sugita E, Hayashi K, Hishikawa A, Itoh H. Epigenetic Alterations in Podocytes in Diabetic Nephropathy. Front Pharmacol 2021; 12:759299. [PMID: 34630127 PMCID: PMC8497789 DOI: 10.3389/fphar.2021.759299] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 09/13/2021] [Indexed: 01/19/2023] Open
Abstract
Recently, epigenetic alterations have been shown to be involved in the pathogenesis of diabetes and its complications. Kidney podocytes, which are glomerular epithelial cells, are important cells that form a slit membrane—a barrier for proteinuria. Podocytes are terminally differentiated cells without cell division or replenishment abilities. Therefore, podocyte damage is suggested to be one of the key factors determining renal prognosis. Recent studies, including ours, suggest that epigenetic changes in podocytes are associated with chronic kidney disease, including diabetic nephropathy. Furthermore, the association between DNA damage repair and epigenetic changes in diabetic podocytes has been demonstrated. Detection of podocyte DNA damage and epigenetic changes using human samples, such as kidney biopsy and urine-derived cells, may be a promising strategy for estimating kidney damage and renal prognoses in patients with diabetes. Targeting epigenetic podocyte changes and associated DNA damage may become a novel therapeutic strategy for preventing progression to end-stage renal disease (ESRD) and provide a possible prognostic marker in diabetic nephropathy. This review summarizes recent advances regarding epigenetic changes, especially DNA methylation, in podocytes in diabetic nephropathy and addresses detection of these alterations in human samples. Additionally, we focused on DNA damage, which is increased under high-glucose conditions and associated with the generation of epigenetic changes in podocytes. Furthermore, epigenetic memory in diabetes is discussed. Understanding the role of epigenetic changes in podocytes in diabetic nephropathy may be of great importance considering the increasing diabetic nephropathy patient population in an aging society.
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Affiliation(s)
- Erina Sugita
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Kaori Hayashi
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Akihito Hishikawa
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Hiroshi Itoh
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
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28
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Liang Z, Kidwell RL, Deng H, Xie Q. Epigenetic N6-methyladenosine modification of RNA and DNA regulates cancer. Cancer Biol Med 2021; 17:9-19. [PMID: 32296573 PMCID: PMC7142843 DOI: 10.20892/j.issn.2095-3941.2019.0347] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 01/02/2020] [Indexed: 12/29/2022] Open
Abstract
The biological roles of N6 methylation of nucleic acids have been extensively studied. Adenine methylation of RNA is the most prevalent RNA modification and has widespread effects on RNA splicing, translation, localization, and stability. Aberrant dynamic regulation of RNA N6-methyladenosine (m6A) has been reported in numerous human diseases, including several cancers. In recent years, eukaryotic DNA N6-methyladenosine (6mA) has also been reported and implicated in cancer progression and tumorigenesis. In this review, we summarize the contributions of N6-methyladenosine modification to cancer biology and pathogenesis in the context of both RNA and DNA. We also highlight the clinical relevance of targeting these modifications as a therapeutic strategy for cancer.
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Affiliation(s)
- Zhixian Liang
- School of Life Sciences, Westlake University, Hangzhou 310024, China.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Reilly L Kidwell
- Division of Regenerative Medicine, Department of Medicine, University of California San Diego, San Diego, CA 92037, USA.,University of California San Diego, School of Medicine, La Jolla, CA 92037, USA
| | - Haijing Deng
- School of Life Sciences, Westlake University, Hangzhou 310024, China.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Qi Xie
- School of Life Sciences, Westlake University, Hangzhou 310024, China.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, China
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29
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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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30
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Ouyang L, Su X, Li W, Tang L, Zhang M, Zhu Y, Xie C, Zhang P, Chen J, Huang H. ALKBH1-demethylated DNA N6-methyladenine modification triggers vascular calcification via osteogenic reprogramming in chronic kidney disease. J Clin Invest 2021; 131:146985. [PMID: 34003800 PMCID: PMC8279589 DOI: 10.1172/jci146985] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/11/2021] [Indexed: 02/05/2023] Open
Abstract
Vascular calcification (VC) predicts cardiovascular morbidity and mortality in chronic kidney disease (CKD). To date, the underlying mechanisms remain unclear. We detected leukocyte DNA N6-methyladenine (6mA) levels in patients with CKD with or without aortic arch calcification. We used arteries from CKD mice infected with vascular smooth muscle cell-targeted (VSMC-targeted) adeno-associated virus encoding alkB homolog 1 (Alkbh1) gene or Alkbh1 shRNA to evaluate features of calcification. We identified that leukocyte 6mA levels were significantly reduced as the severity of VC increased in patients with CKD. Decreased 6mA demethylation resulted from the upregulation of ALKBH1. Here, ALKBH1 overexpression aggravated whereas its depletion blunted VC progression and osteogenic reprogramming in vivo and in vitro. Mechanistically, ALKBH1-demethylated DNA 6mA modification could facilitate the binding of octamer-binding transcription factor 4 (Oct4) to bone morphogenetic protein 2 (BMP2) promoter and activate BMP2 transcription. This resulted in osteogenic reprogramming of VSMCs and subsequent VC progression. Either BMP2 or Oct4 depletion alleviated the procalcifying effects of ALKBH1. This suggests that targeting ALKBH1 might be a therapeutic method to reduce the burden of VC in CKD.
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Affiliation(s)
- Liu Ouyang
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Cardiology, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Xiaoyan Su
- Department of Nephropathy, Tungwah Hospital, Sun Yat-sen University, Dongguan, China
| | - Wenxin Li
- Department of Cardiology, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Liangqiu Tang
- Department of Cardiology, Yuebei People’s Hospital, Shantou University Medical College, Shaoguan, China
| | - Mengbi Zhang
- Department of Nephropathy, Tungwah Hospital, Sun Yat-sen University, Dongguan, China
| | - Yongjun Zhu
- Department of Cardiology, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Changming Xie
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Cardiology, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Puhua Zhang
- Department of Nephrology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jie Chen
- Department of Radiation Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hui Huang
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Cardiology, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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31
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Chachar S, Liu J, Zhang P, Riaz A, Guan C, Liu S. Harnessing Current Knowledge of DNA N6-Methyladenosine From Model Plants for Non-model Crops. Front Genet 2021; 12:668317. [PMID: 33995495 PMCID: PMC8118384 DOI: 10.3389/fgene.2021.668317] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetic modifications alter the gene activity and function by causing change in the chromosomal architecture through DNA methylation/demethylation, or histone modifications without causing any change in DNA sequence. In plants, DNA cytosine methylation (5mC) is vital for various pathways such as, gene regulation, transposon suppression, DNA repair, replication, transcription, and recombination. Thanks to recent advances in high throughput sequencing (HTS) technologies for epigenomic “Big Data” generation, accumulated studies have revealed the occurrence of another novel DNA methylation mark, N6-methyladenosine (6mA), which is highly present on gene bodies mainly activates gene expression in model plants such as eudicot Arabidopsis (Arabidopsis thaliana) and monocot rice (Oryza sativa). However, in non-model crops, the occurrence and importance of 6mA remains largely less known, with only limited reports in few species, such as Rosaceae (wild strawberry), and soybean (Glycine max). Given the aforementioned vital roles of 6mA in plants, hereinafter, we summarize the latest advances of DNA 6mA modification, and investigate the historical, known and vital functions of 6mA in plants. We also consider advanced artificial-intelligence biotechnologies that improve extraction and prediction of 6mA concepts. In this Review, we discuss the potential challenges that may hinder exploitation of 6mA, and give future goals of 6mA from model plants to non-model crops.
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Affiliation(s)
- Sadaruddin Chachar
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China.,Department of Biotechnology, Faculty of Crop Production, Sindh Agriculture University, Tandojam, Pakistan
| | - Jingrong Liu
- College of Mathematics and Statistics, Northwest Normal University, Lanzhou, China
| | - Pingxian Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Adeel Riaz
- Deaprtment of Biochemistry, Faculty of Life Sciences, University of Okara, Okara, Pakistan
| | - Changfei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
| | - Shuyuan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
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32
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Cheng M, Shu X, Cao J, Gao M, Xiang S, Wang F, Wang Y, Liu J. A Mutation-Based Method for Pinpointing a DNA N 6 -Methyladenine Methyltransferase Modification Site at Single Base Resolution. Chembiochem 2021; 22:1936-1939. [PMID: 33779011 DOI: 10.1002/cbic.202100088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/26/2021] [Indexed: 01/01/2023]
Abstract
DNA N6 -methyladenine (6mA) has recently received notable attention due to an increased finding of its functional roles in higher eukaryotes. Here we report an enzyme-assisted chemical labeling method to pinpoint the DNA 6mA methyltransferase (MTase) substrate modification site at single base resolution. A designed allyl-substituted MTase cofactor was applied in the catalytic transfer reaction, and the allyl group was installed to the N6 -position of adenine within a specific DNA sequence to form N6 -allyladenine (6aA). The iodination of 6aA allyl group induced the formation of 1, N6 -cyclized adenine which caused mutations during DNA replication by a polymerase. Thus the modification site could be precisely detected by a mutation signal. We synthesized 6aA deoxynucleoside and deoxynucleotide model compounds and a 6aA-containing DNA probe, and screened nine DNA polymerases to define an optimal system capable of detecting the substrate modification site of a DNA 6mA MTase at single-base resolution.
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Affiliation(s)
- Mohan Cheng
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou, 310027, China
| | - Xiao Shu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou, 310027, China
| | - Jie Cao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou, 310027, China
| | - Minsong Gao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou, 310027, China
| | - Siying Xiang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou, 310027, China
| | - Fengqin Wang
- College of Animal Sciences, Key Laboratory of Animal Nutrition and Feed Sciences, Ministry of Agriculture, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, China
| | - Yizhen Wang
- College of Animal Sciences, Key Laboratory of Animal Nutrition and Feed Sciences, Ministry of Agriculture, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, China
| | - Jianzhao Liu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou, 310027, China
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Abstract
Use of methylation-specific antibodies with methylated-DNA-immunoprecipitation sequencing allows for the mapping of methylated DNA, such as N6-methyldeoxyadenosine (6mA). However, such mapping methods only detect methylated DNA at low resolution. Here, we describe 6mA Cross-linking Exonuclease sequencing (6mACE-seq), which utilizes 6mA-specific antibodies cross-linked to 6mA sites to protect 6mA-DNA fragments from subsequent exonuclease treatment. This allowed 6mACE-seq to map human-genome-wide 6mA at single-nucleotide resolution.
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34
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Prokaryotic DNA methylation and its functional roles. J Microbiol 2021; 59:242-248. [DOI: 10.1007/s12275-021-0674-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/31/2022]
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35
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Hardy A, Matelot M, Touzeau A, Klopp C, Lopez-Roques C, Duharcourt S, Defrance M. DNAModAnnot: a R toolbox for DNA modification filtering and annotation. Bioinformatics 2021; 37:2738-2740. [PMID: 33471071 PMCID: PMC8428616 DOI: 10.1093/bioinformatics/btab032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/17/2020] [Accepted: 01/13/2021] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Long-read sequencing technologies can be employed to detect and map DNA modifications at the nucleotide resolution on a genome-wide scale. However, published software packages neglect the integration of genomic annotation and comprehensive filtering when analyzing patterns of modified bases detected using Pacific Biosciences (PacBio) or Oxford Nanopore Technologies (ONT) data. Here, we present DNAModAnnot, a R package designed for the global analysis of DNA modification patterns using adapted filtering and visualization tools. RESULTS We tested our package using PacBio sequencing data to analyze patterns of the 6-methyladenine (6 mA) in the ciliate Paramecium tetraurelia, in which high 6 mA amounts were previously reported. We found Paramecium tetraurelia 6 mA genome-wide distribution to be similar to other ciliates. We also performed 5-methylcytosine (5mC) analysis in human lymphoblastoid cells using ONT data and confirmed previously known patterns of 5mC. DNAModAnnot provides a toolbox for the genome-wide analysis of different DNA modifications using PacBio and ONT long-read sequencing data. AVAILABILITY DNAModAnnot is distributed as a R package available via GitHub (https://github.com/AlexisHardy/DNAModAnnot). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Alexis Hardy
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France
| | - Mélody Matelot
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France
| | - Amandine Touzeau
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France
| | - Christophe Klopp
- Plateforme bioinformatique Genotoul, UR875 Mathématique et Informatique Appliquée de Toulouse, INRA, 31326, Castanet-Tolosan, France
| | | | - Sandra Duharcourt
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France
| | - Matthieu Defrance
- Université Libre de Bruxelles, Interuniversity Institute of Bioinformatics in Brussels (IB2), Brussels, 1050, Belgium
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36
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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: 1.3] [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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Abstract
A complete understanding of the dynamics and function of cytosine modifications in mammalian biology is lacking. Central to achieving this understanding is the availability of techniques that permit sensitive and specific genome-wide mapping of DNA modifications in mammalian DNA. The last decade has seen the development of a vast arsenal of novel profiling approaches enabling epigeneticists to tackle research questions that were previously out of reach. Here, we review the techniques currently available for profiling DNA modifications in mammals, discuss their strengths and weaknesses, and speculate on the future direction of DNA modification profiling technologies.
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Affiliation(s)
- Antonio Lentini
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Colm E Nestor
- Department of Biomedical and Clinical Sciences (BKV), Crown Princess Victoria Children's Hospital, Linköping University, Linköping, Sweden.
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38
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Bochtler M, Fernandes H. DNA adenine methylation in eukaryotes: Enzymatic mark or a form of DNA damage? Bioessays 2020; 43:e2000243. [PMID: 33244833 DOI: 10.1002/bies.202000243] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 12/16/2022]
Abstract
6-methyladenine (6mA) is fairly abundant in nuclear DNA of basal fungi, ciliates and green algae. In these organisms, 6mA is maintained near transcription start sites in ApT context by a parental-strand instruction dependent maintenance methyltransferase and is positively associated with transcription. In animals and plants, 6mA levels are high only in organellar DNA. The 6mA levels in nuclear DNA are very low. They are attributable to nucleotide salvage and the activity of otherwise mitochondrial METTL4, and may be considered as a price that cells pay for adenine methylation in RNA and/or organellar DNA. Cells minimize this price by sanitizing dNTP pools to limit 6mA incorporation, and by converting 6mA that has been incorporated into DNA back to adenine. Hence, 6mA in nuclear DNA should be described as an epigenetic mark only in basal fungi, ciliates and green algae, but not in animals and plants.
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Affiliation(s)
- Matthias Bochtler
- International Institute of Molecular and Cell Biology, Warsaw, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Humberto Fernandes
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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39
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Brunet M, Vargas C, Larrieu D, Torrisani J, Dufresne M. E3 Ubiquitin Ligase TRIP12: Regulation, Structure, and Physiopathological Functions. Int J Mol Sci 2020; 21:ijms21228515. [PMID: 33198194 PMCID: PMC7697007 DOI: 10.3390/ijms21228515] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023] Open
Abstract
The Thyroid hormone Receptor Interacting Protein 12 (TRIP12) protein belongs to the 28-member Homologous to the E6-AP C-Terminus (HECT) E3 ubiquitin ligase family. First described as an interactor of the thyroid hormone receptor, TRIP12’s biological importance was revealed by the embryonic lethality of a murine model bearing an inactivating mutation in the TRIP12 gene. Further studies showed the participation of TRIP12 in the regulation of major biological processes such as cell cycle progression, DNA damage repair, chromatin remodeling, and cell differentiation by an ubiquitination-mediated degradation of key protein substrates. Moreover, alterations of TRIP12 expression have been reported in cancers that can serve as predictive markers of therapeutic response. The TRIP12 gene is also referenced as a causative gene associated to intellectual disorders such as Clark–Baraitser syndrome and is clearly implicated in Autism Spectrum Disorder. The aim of the review is to provide an exhaustive and integrated overview of the different aspects of TRIP12 ranging from its regulation, molecular functions and physio-pathological implications.
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Affiliation(s)
- Manon Brunet
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
| | - Claire Vargas
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
| | - Dorian Larrieu
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
| | - Jérôme Torrisani
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
- Correspondence: (J.T.); (M.D.); Tel.: +33-582-741-644 (J.T.); +33-582-741-643 (M.D.)
| | - Marlène Dufresne
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
- Correspondence: (J.T.); (M.D.); Tel.: +33-582-741-644 (J.T.); +33-582-741-643 (M.D.)
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40
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Mahdavi-Amiri Y, Chung Kim Chung K, Hili R. Single-nucleotide resolution of N 6-adenine methylation sites in DNA and RNA by nitrite sequencing. Chem Sci 2020; 12:606-612. [PMID: 34163791 PMCID: PMC8179008 DOI: 10.1039/d0sc03509b] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A single-nucleotide resolution sequencing method of N6-adenine methylation sites in DNA and RNA is described. Using sodium nitrite under acidic conditions, chemoselective deamination of unmethylated adenines readily occurs, without competing deamination of N6-adenine sites. The deamination of adenines results in the formation of hypoxanthine bases, which are read by polymerases and reverse transcriptases as guanine; the methylated adenine sites resist deamination and are read as adenine. The approach, when coupled with high-throughput DNA sequencing and mutational analysis, enables the identification of N6-adenine sites in RNA and DNA within various sequence contexts. Chemoselective deamination of adenine in the presence of N6-methyladenine using nitrite enables single-nucleotide resolution sequencing of N6-adenine methylation sites in DNA and RNA.![]()
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Affiliation(s)
- Yasaman Mahdavi-Amiri
- Department of Chemistry, Centre for Research on Biomolecular Interactions, York University 4700 Keele Street Toronto ON M3J 1P3 Canada www.yorku.ca/rhili
| | - Kimberley Chung Kim Chung
- Department of Chemistry, Centre for Research on Biomolecular Interactions, York University 4700 Keele Street Toronto ON M3J 1P3 Canada www.yorku.ca/rhili
| | - Ryan Hili
- Department of Chemistry, Centre for Research on Biomolecular Interactions, York University 4700 Keele Street Toronto ON M3J 1P3 Canada www.yorku.ca/rhili
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41
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Ouyang J, Zhan X, Guo S, Cai S, Lei J, Zeng S, Yu L. Progress and trends on the analysis of nucleic acid and its modification. J Pharm Biomed Anal 2020; 191:113589. [DOI: 10.1016/j.jpba.2020.113589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/18/2020] [Accepted: 08/20/2020] [Indexed: 12/17/2022]
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42
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Li Y, Ge YZ, Xu L, Xu Z, Dou Q, Jia R. The Potential Roles of RNA N6-Methyladenosine in Urological Tumors. Front Cell Dev Biol 2020; 8:579919. [PMID: 33015074 PMCID: PMC7510505 DOI: 10.3389/fcell.2020.579919] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/24/2020] [Indexed: 12/11/2022] Open
Abstract
N6-methyladenosine (m6A) is regarded as the most abundant, prevalent and conserved internal mRNA modification in mammalian cells. M6A can be catalyzed by m6A methyltransferases METTL3, METTL14 and WTAP (writers), reverted by demethylases ALKBH5 and FTO (erasers), and recognized by m6A -binding proteins such as YTHDF1/2/3, IGF2BP1/2/3 and HNRNPA2B1 (readers). Emerging evidence suggests that m6A modification is significant for regulating many biological and cellular processes and participates in the pathological development of various diseases, including tumors. This article reviews recent studies on the biological function of m6A modification and the methylation modification of m6A in urological tumors.
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Affiliation(s)
- Yang Li
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yu-Zheng Ge
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Luwei Xu
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Zheng Xu
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Quanliang Dou
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Ruipeng Jia
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
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43
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Saak CC, Dinh CB, Dutton RJ. Experimental approaches to tracking mobile genetic elements in microbial communities. FEMS Microbiol Rev 2020; 44:606-630. [PMID: 32672812 PMCID: PMC7476777 DOI: 10.1093/femsre/fuaa025] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022] Open
Abstract
Horizontal gene transfer is an important mechanism of microbial evolution and is often driven by the movement of mobile genetic elements between cells. Due to the fact that microbes live within communities, various mechanisms of horizontal gene transfer and types of mobile elements can co-occur. However, the ways in which horizontal gene transfer impacts and is impacted by communities containing diverse mobile elements has been challenging to address. Thus, the field would benefit from incorporating community-level information and novel approaches alongside existing methods. Emerging technologies for tracking mobile elements and assigning them to host organisms provide promise for understanding the web of potential DNA transfers in diverse microbial communities more comprehensively. Compared to existing experimental approaches, chromosome conformation capture and methylome analyses have the potential to simultaneously study various types of mobile elements and their associated hosts. We also briefly discuss how fermented food microbiomes, given their experimental tractability and moderate species complexity, make ideal models to which to apply the techniques discussed herein and how they can be used to address outstanding questions in the field of horizontal gene transfer in microbial communities.
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Affiliation(s)
- Christina C Saak
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Cong B Dinh
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Rachel J Dutton
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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44
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Li Z, Zhao S, Nelakanti RV, Lin K, Wu TP, Alderman MH, Guo C, Wang P, Zhang M, Min W, Jiang Z, Wang Y, Li H, Xiao AZ. N 6-methyladenine in DNA antagonizes SATB1 in early development. Nature 2020; 583:625-630. [PMID: 32669713 PMCID: PMC8596487 DOI: 10.1038/s41586-020-2500-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 05/04/2020] [Indexed: 02/08/2023]
Abstract
The recent discovery of N6-mA in mammalian genomes suggests that it may serve as an epigenetic regulatory mechanism1. However, the biological role of N6-mA and molecular pathways exerting its function remain elusive. Herein, we demonstrate that N6-mA plays a critical role in changing the epigenetic landscape during cell fate transitions in early development. We found that N6-mA is upregulated during trophoblast stem cell development, specifically at Stress Induced DNA Double Helix Destabilization (SIDD) regions2-4. It is well-known that SIDD regions are conducive to topological stress-induced double helix unpairing and play critical roles in organizing large-scale chromatin structures3,5,6. We demonstrated that the presence of N6-mA abolishes (>500-fold) the in vitro interactions between SIDD and SATB1, a critical chromatin organizer interacting with SIDD regions; N6-mA deposition also effectively antagonizes SATB1 function in vivo by preventing its binding to chromatin. Concordantly, N6-mA functions at the boundaries between eu-/hetero- chromatin to restrict the spreading of euchromatin. N6-mA mediated repression is critical for gene regulation during trophoblast development in cell culture models and in vivo. Overall, our study discovers an unexpected molecular mechanism for N6-mA function via SATB1, and reveals surprising connections between DNA modification, DNA secondary structures and large chromatin domains in early embryonic development.
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Affiliation(s)
- Zheng Li
- Department of Genetics and Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
| | - Shuai Zhao
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Raman V Nelakanti
- Department of Genetics and Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
| | - Kaixuan Lin
- Department of Genetics and Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
| | - Tao P Wu
- Department of Genetics and Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Myles H Alderman
- Department of Genetics and Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
| | - Cheng Guo
- Department of Chemistry, University of California, Riverside, CA, USA.,Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Pengcheng Wang
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Min Zhang
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Wang Min
- Interdepartmental Program in Vascular Biology and Therapeutics, Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Zongliang Jiang
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.
| | - Andrew Z Xiao
- Department of Genetics and Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA.
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45
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DNA methylation dynamics at transposable elements in mammals. Essays Biochem 2020; 63:677-689. [PMID: 31654072 DOI: 10.1042/ebc20190039] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/29/2019] [Accepted: 09/30/2019] [Indexed: 12/18/2022]
Abstract
Transposable elements dominate the mammalian genome, but their contribution to genetic and epigenetic regulation has been largely overlooked. This was in part due to technical limitations, which made the study of repetitive sequences at single copy resolution difficult. The advancement of next-generation sequencing assays in the last decade has greatly enhanced our understanding of transposable element function. In some instances, specific transposable elements are thought to have been co-opted into regulatory roles during both mouse and human development, while in disease such regulatory potential can contribute to malignancy. DNA methylation is arguably the best characterised regulator of transposable element activity. DNA methylation is associated with transposable element repression, and acts to limit their genotoxic potential. In specific developmental contexts, erasure of DNA methylation is associated with a burst of transposable element expression. Developmental regulation of DNA methylation enables transposon activation, ensuring their survival and propagation throughout the host genome, and also allows the host access to regulatory sequences encoded within the elements. Here I discuss DNA methylation at transposable elements, describing its function and dynamic regulation throughout murine and human development.
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46
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Yang S, Wang Y, Chen Y, Dai Q. MASQC: Next Generation Sequencing Assists Third Generation Sequencing for Quality Control in N6-Methyladenine DNA Identification. Front Genet 2020; 11:269. [PMID: 32269589 PMCID: PMC7109398 DOI: 10.3389/fgene.2020.00269] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 03/05/2020] [Indexed: 11/13/2022] Open
Abstract
DNA N6-methyladenine (6mA) modification has been discovered as the most prevalent DNA modification in prokaryotes and eukaryotes, involving gene expression, DNA replication and repair, and host-pathogen interactions. Single-molecule real-time sequencing (SMRT-seq) can detect 6mA events in prokaryotic and eukaryotic genomes at the single-nucleotide level. However, there are no strict and economical quality control methods for high false-positive 6mA events in eukaryotic genomes. Therefore, by analyzing the distribution of 6mA in eukaryotic and prokaryotes, we proposed a method named MASQC (MeDIP-seq assists SMRT-seq for quality control in 6mA identification), which can identify 6mA events without doing the whole genome amplification (WGA) sequencing. The proposed MASQC method was assessed on two eukaryotic genomes and six bacterial genomes, our results demonstrate that MASQC performs well in quality control of false positive 6mA identification for both eukaryotic and prokaryotic genomes.
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Affiliation(s)
- Siqian Yang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yaoxin Wang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Ying Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qi Dai
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
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47
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Mammalian ALKBH1 serves as an N 6-mA demethylase of unpairing DNA. Cell Res 2020; 30:197-210. [PMID: 32051560 PMCID: PMC7054317 DOI: 10.1038/s41422-019-0237-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/30/2019] [Indexed: 01/07/2023] Open
Abstract
N6-methyladenine (N6-mA) of DNA is an emerging epigenetic mark in mammalian genome. Levels of N6-mA undergo drastic fluctuation during early embryogenesis, indicative of active regulation. Here we show that the 2-oxoglutarate-dependent oxygenase ALKBH1 functions as a nuclear eraser of N6-mA in unpairing regions (e.g., SIDD, Stress-Induced DNA Double Helix Destabilization regions) of mammalian genomes. Enzymatic profiling studies revealed that ALKBH1 prefers bubbled or bulged DNAs as substrate, instead of single-stranded (ss-) or double-stranded (ds-) DNAs. Structural studies of ALKBH1 revealed an unexpected "stretch-out" conformation of its "Flip1" motif, a conserved element that usually bends over catalytic center to facilitate substrate base flipping in other DNA demethylases. Thus, lack of a bending "Flip1" explains the observed preference of ALKBH1 for unpairing substrates, in which the flipped N6-mA is primed for catalysis. Co-crystal structural studies of ALKBH1 bound to a 21-mer bulged DNA explained the need of both flanking duplexes and a flipped base for recognition and catalysis. Key elements (e.g., an ALKBH1-specific α1 helix) as well as residues contributing to structural integrity and catalytic activity were validated by structure-based mutagenesis studies. Furthermore, ssDNA-seq and DIP-seq analyses revealed significant co-occurrence of base unpairing regions with N6-mA in mouse genome. Collectively, our biochemical, structural and genomic studies suggest that ALKBH1 is an important DNA demethylase that regulates genome N6-mA turnover of unpairing regions associated with dynamic chromosome regulation.
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48
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Douvlataniotis K, Bensberg M, Lentini A, Gylemo B, Nestor CE. No evidence for DNA N 6-methyladenine in mammals. SCIENCE ADVANCES 2020; 6:eaay3335. [PMID: 32206710 PMCID: PMC7080441 DOI: 10.1126/sciadv.aay3335] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 12/18/2019] [Indexed: 05/28/2023]
Abstract
N 6-methyladenine (6mdA) is a widespread DNA modification in bacteria. More recently, 6mdA has also been characterized in mammalian DNA. However, measurements of 6mdA abundance and profiles are often very dissimilar between studies, even when performed on DNA from identical mammalian cell types. Using comprehensive bioinformatics analyses of published data and novel experimental approaches, we reveal that efforts to assay 6mdA in mammals have been severely compromised by bacterial contamination, RNA contamination, technological limitations, and antibody nonspecificity. These complications render 6mdA an exceptionally problematic DNA modification to study and have resulted in erroneous detection of 6mdA in several mammalian systems. Together, our results strongly imply that the evidence published to date is not sufficient to support the presence of 6mdA in mammals.
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49
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Liang Z, Riaz A, Chachar S, Ding Y, Du H, Gu X. Epigenetic Modifications of mRNA and DNA in Plants. MOLECULAR PLANT 2020; 13:14-30. [PMID: 31863849 DOI: 10.1016/j.molp.2019.12.007] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/22/2019] [Accepted: 12/05/2019] [Indexed: 05/21/2023]
Abstract
Advances in the detection and mapping of messenger RNA (mRNA) N6-methyladenosine (m6A) and 5-methylcytosine (m5C), and DNA N6-methyldeoxyadenosine (6mA) redefined our understanding of these modifications as additional tiers of epigenetic regulation. In plants, the most prevalent internal mRNA modifications, m6A and m5C, play crucial and dynamic roles in many processes, including embryo development, stem cell fate determination, trichome branching, leaf morphogenesis, floral transition, stress responses, fruit ripening, and root development. The newly identified and widespread epigenetic marker 6mA DNA methylation is associated with gene expression, plant development, and stress responses. Here, we review the latest research progress on mRNA and DNA epigenetic modifications, including the detection, dynamics, distribution, functions, regulatory proteins, and evolution, with a focus on m6A, m5C, and 6mA. We also provide some perspectives on future research of the newly identified and unknown epigenetic modifications of mRNA and DNA in plants.
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Affiliation(s)
- Zhe Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Centre for Organismal Studies, Heidelberg University, Heidelberg 69120, Germany
| | - Adeel Riaz
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sadaruddin Chachar
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yike Ding
- Department of Entomology, University of California Riverside, Riverside, CA 92521, USA
| | - Hai Du
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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50
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Abstract
DNA modifications are a major form of epigenetic regulation that eukaryotic cells utilize in concert with histone modifications. While much work has been done elucidating the role of 5-methylcytosine over the past several decades, only recently has it been recognized that N(6)-methyladenine (N6-mA) is present in quantifiable and biologically active levels in the DNA of eukaryotic cells. Unlike prokaryotes which utilize N6-mA to recognize "self" from "foreign" DNA, eukaryotes have been found to use N6-mA in varying ways, from regulating transposable elements to gene regulation in response to hypoxia and stress. In this review, we examine the current state of the N6-mA in research field, and the current understanding of the biochemical mechanisms which deposit and remove N6-mA from the eukaryotic genome.
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Affiliation(s)
- Myles H Alderman
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Andrew Z Xiao
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, 06520, USA.
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