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De Plano LM, Saitta A, Oddo S, Caccamo A. Epigenetic Changes in Alzheimer's Disease: DNA Methylation and Histone Modification. Cells 2024; 13:719. [PMID: 38667333 PMCID: PMC11049073 DOI: 10.3390/cells13080719] [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: 03/08/2024] [Revised: 04/10/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Alzheimer's disease (AD) is a devastating neurodegenerative disorder characterized by progressive cognitive decline and memory loss, imposing a significant burden on affected individuals and their families. Despite the recent promising progress in therapeutic approaches, more needs to be done to understand the intricate molecular mechanisms underlying the development and progression of AD. Growing evidence points to epigenetic changes as playing a pivotal role in the pathogenesis of the disease. The dynamic interplay between genetic and environmental factors influences the epigenetic landscape in AD, altering gene expression patterns associated with key pathological events associated with disease pathogenesis. To this end, epigenetic alterations not only impact the expression of genes implicated in AD pathogenesis but also contribute to the dysregulation of crucial cellular processes, including synaptic plasticity, neuroinflammation, and oxidative stress. Understanding the complex epigenetic mechanisms in AD provides new avenues for therapeutic interventions. This review comprehensively examines the role of DNA methylation and histone modifications in the context of AD. It aims to contribute to a deeper understanding of AD pathogenesis and facilitate the development of targeted therapeutic strategies.
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Affiliation(s)
- Laura Maria De Plano
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.S.); (S.O.)
| | | | | | - Antonella Caccamo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.S.); (S.O.)
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2
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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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3
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Mortishire-Smith B, Becker SM, Simeone A, Melidis L, Balasubramanian S. A Photoredox Reaction for the Selective Modification of 5-Carboxycytosine in DNA. J Am Chem Soc 2023; 145:10505-10511. [PMID: 37141595 PMCID: PMC10197125 DOI: 10.1021/jacs.2c12558] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Indexed: 05/06/2023]
Abstract
Covalent epigenetic modifications contribute to the regulation of important cellular processes during development and differentiation, and changes in their genomic distribution and frequency are linked to the emergence of genetic disease states. Chemical and enzymatic methods that selectively target the orthogonal chemical functionality of epigenetic markers are central to the study of their distribution and function, and considerable research effort has been focused on the development of nondestructive sequencing approaches which preserve valuable DNA samples. Photoredox catalysis enables transformations with tunable chemoselectivity under mild, biocompatible reaction conditions. We report the reductive decarboxylation of 5-carboxycytosine via a novel iridium-based treatment, which represents the first application of visible-light photochemistry to epigenetic sequencing via direct base conversion. We propose that the reaction involves an oxidative quenching cycle beginning with single-electron reduction of the nucleobase by the photocatalyst, followed by hydrogen atom transfer from a thiol. The saturation of the C5-C6 backbone permits decarboxylation of the nonaromatic intermediate, and hydrolysis of the N4-amine constitutes a conversion from a cytosine derivative to a T-like base. This conversion demonstrates selectivity for 5-carboxycytosine over other canonical or modified nucleoside monomers, and is thereby applied to the sequencing of 5-carboxycytosine within modified oligonucleotides. The photochemistry explored in this study can also be used in conjunction with enzymatic oxidation by TET to profile 5-methylcytosine at single-base resolution. Compared to other base-conversion treatments, the rapid photochemical reaction takes place within minutes, which could provide advantages for high-throughput detection and diagnostic applications.
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Affiliation(s)
| | - Sidney M. Becker
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge, CB2 1EW, U.K.
| | - Angela Simeone
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge, CB2 1EW, U.K.
- Cancer
Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, U.K.
| | - Larry Melidis
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge, CB2 1EW, U.K.
- Cancer
Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, U.K.
| | - Shankar Balasubramanian
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge, CB2 1EW, U.K.
- Cancer
Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, U.K.
- School
of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SP, United Kingdom
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4
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Ji TT, Xie NB, Ding JH, Wang M, Guo X, Chen YY, Yu SY, Feng YQ, Yuan BF. Enzymatic Cleavage-Mediated Extension Stalling Enables Accurate Recognition and Quantification of Locus-Specific Uracil Modification in DNA. Anal Chem 2023; 95:8384-8392. [PMID: 37192336 DOI: 10.1021/acs.analchem.3c01410] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Chemical modifications in DNA have profound influences on the structures and functions of DNA. Uracil, a naturally occurring DNA modification, can originate from the deamination of cytosine or arise from misincorporation of dUTP into DNA during DNA replication. Uracil in DNA will imperil genomic stability due to their potential in producing detrimental mutations. An in-depth understanding of the functions of uracil modification requires the accurate determination of its site as well as content in genomes. Herein, we characterized that a new member of the uracil-DNA glycosylase (UDG) family enzyme (UdgX-H109S) could selectively cleave both uracil-containing single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). Based on this unique property of UdgX-H109S, we developed an enzymatic cleavage-mediated extension stalling (ECES) method for the locus-specific detection and quantification of uracil in genomic DNA. In the ECES method, UdgX-H109S specifically recognizes and cleaves the N-glycosidic bond of uracil from dsDNA and generates an apurinic/apyrimidinic (AP) site, which could be broken by APE1 to form a one-nucleotide gap. The specific cleavage by UdgX-H109S is then evaluated and quantified by qPCR. With the developed ECES approach, we demonstrated that the level of uracil at position Chr4:50566961 in genomic DNA of breast cancer tissues was significantly decreased. Collectively, the ECES method has been proved to be accurate and reproducible in the locus-specific quantification of uracil in genomic DNA from biological and clinical samples.
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Affiliation(s)
- Tong-Tong Ji
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Neng-Bin Xie
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
- School of Public Health, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430060, China
| | - Jiang-Hui Ding
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Min Wang
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Xia Guo
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Ying-Ying Chen
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
| | - Si-Yu Yu
- School of Public Health, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430060, China
| | - Yu-Qi Feng
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
- School of Public Health, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430060, China
| | - Bi-Feng Yuan
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430071, China
- School of Public Health, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430060, China
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Wuhan Research Center for Infectious Diseases and Cancer, Zhongnan Hospital of Wuhan University, Chinese Academy of Medical Sciences, Wuhan, Hubei 430071, China
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5
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Huang H, Wu Y, Qian M, Yang X, Qi H. Iridium(III) solvent complex-based electrogenerated chemiluminescence and photoluminescence sensor array for the discrimination of bases in oligonucleotides. Bioelectrochemistry 2023; 150:108368. [PMID: 36634465 DOI: 10.1016/j.bioelechem.2023.108368] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/24/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023]
Abstract
Development of rapid and sensitive method for the discrimination of bases in oligonucleotides is of great importance in clinical diagnosis. Here, we demonstrate the first case of single iridium(III) solvent complex-based electrogenerated chemiluminescence (ECL) and photoluminescence (PL) sensor array for the discrimination of bases in oligonucleotides. One iridium (III) solvent complex ([Ir(ppy)2(DMSO)Cl], ppy = 2-phenylpyridine, probe 1) was designed as both ECL and PL probe while five bases (guanine, adenine, cytosine, thymine and uracil) were chosen as analytes. Two-element sensor array was built for the discrimination of five bases based on the fingerprint response of probe 1 to bases via coordination interactions. The combination of unique ECL and PL variations with principal component analysis was applied for the quantitative analysis of five bases in a linear range of 1.0 μM-10 μM and for the effective discrimination of individual base, the mixture of bases and oligonucleotides. Moreover, the sensor array was successfully applied to discriminate different mismatched ss-DNAs from HIV gene (a fully-matched ss-DNA), even at single-base difference. This work demonstrates that the sensor array using single iridium (III) solvent complex is a promising approach for the discrimination of bases with good sensitivity and simpleness in clinical diagnosis.
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Affiliation(s)
- Hong Huang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, PR China
| | - Yang Wu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, PR China
| | - Manping Qian
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, PR China
| | - Xiaolin Yang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, PR China.
| | - Honglan Qi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, PR China.
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6
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Nielsen TK, Forero-Junco LM, Kot W, Moineau S, Hansen LH, Riber L. Detection of nucleotide modifications in bacteria and bacteriophages: Strengths and limitations of current technologies and software. Mol Ecol 2023; 32:1236-1247. [PMID: 36052951 DOI: 10.1111/mec.16679] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 11/27/2022]
Abstract
RNA and DNA modifications occur in eukaryotes and prokaryotes, as well as in their viruses, and serve a wide range of functions, from gene regulation to nucleic acid protection. Although the first nucleotide modification was discovered almost 100 years ago, new and unusual modifications are still being described. Nucleotide modifications have also received more attention lately because of their increased significance, but also because new sequencing approaches have eased their detection. Chiefly, third generation sequencing platforms PacBio and Nanopore offer direct detection of modified bases by measuring deviations of the signals. These unusual modifications are especially prevalent in bacteriophage genomes, the viruses of bacteria, where they mostly appear to protect DNA against degradation from host nucleases. In this Opinion article, we highlight and discuss current approaches to detect nucleotide modifications, including hardwares and softwares, and look onward to future applications, especially for studying unusual, rare, or complex genome modifications in bacteriophages. The ability to distinguish between several types of nucleotide modifications may even shed new light on metagenomic studies.
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Affiliation(s)
- Tue Kjaergaard Nielsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Quebec, Canada
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Leise Riber
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
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7
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Ahmed LR, Chuang CH, Lüder J, Yang HW, EL-Mahdy AFM. Direct Metal-Free Synthesis of Uracil- and Pentaazaphenalene-Functionalized Porous Organic Polymers via Quadruple Mannich Cyclization and Their Nucleobase Recognition Activities. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c01627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lamiaa Reda Ahmed
- Department of Materials and Optoelectronic Science, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
- Institute of Medical Science and Technology, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
| | - Cheng-Hsin Chuang
- Institute of Medical Science and Technology, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
| | - Johann Lüder
- Department of Materials and Optoelectronic Science, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
- Center for Theoretical and computational Physics, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
| | - Hung-Wei Yang
- Institute of Medical Science and Technology, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
| | - Ahmed F. M. EL-Mahdy
- Department of Materials and Optoelectronic Science, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
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8
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Xiong J, Chen KK, Xie NB, Ji TT, Yu SY, Tang F, Xie C, Feng YQ, Yuan BF. Bisulfite-Free and Single-Base Resolution Detection of Epigenetic DNA Modification of 5-Methylcytosine by Methyltransferase-Directed Labeling with APOBEC3A Deamination Sequencing. Anal Chem 2022; 94:15489-15498. [DOI: 10.1021/acs.analchem.2c03808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jun Xiong
- 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, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Ke-Ke Chen
- Sauvage Center for Molecular Sciences, College of Chemistry and Molecular Sciences, 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, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Tong-Tong Ji
- Sauvage Center for Molecular Sciences, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Si-Yu Yu
- School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Feng Tang
- Sauvage Center for Molecular Sciences, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Conghua Xie
- School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - 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, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - 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, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
- Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430071, China
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9
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Guo S, Li L, Yu K, Tan Y, Wang Y. LC-MS/MS for Assessing the Incorporation and Repair of N2-Alkyl-2'-deoxyguanosine in Genomic DNA. Chem Res Toxicol 2022; 35:1814-1820. [PMID: 35584366 PMCID: PMC9588702 DOI: 10.1021/acs.chemrestox.2c00101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Understanding the occurrence, repair, and biological consequences of DNA damage is important in environmental toxicology and risk assessment. The most common way to assess DNA damage elicited by exogenous sources in a laboratory setting is to expose cells or experimental animals with chemicals that modify DNA. Owing to the lack of reaction specificities of DNA damaging agents, the approach frequently does not allow for induction of a specific DNA lesion. Herein, we employed metabolic labeling to selectively incorporate N2-methyl-dG (N2-MedG) and N2-n-butyl-dG (N2-nBudG) into genomic DNA of cultured mammalian cells, and investigated how the levels of the two lesions in cellular DNA are modulated by different DNA repair factors. Our results revealed that nucleotide excision repair (NER) exert moderate effects on the removal of N2-MedG and N2-nBudG from genomic DNA. We also observed that DNA polymerases κ and η contribute to the incorporation of N2-MedG into genomic DNA and modulate its repair in human cells. In addition, loss of ALKBH3 resulted in higher frequencies of N2-MedG and N2-nBuG incorporation into genomic DNA, suggesting a role of oxidative dealkylation in the reversal of these lesions. Together, our study provided new insights into the repair of minor-groove N2-alkyl-dG lesions in mammalian cells.
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Affiliation(s)
- Su Guo
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
| | - Lin Li
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Kailin Yu
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Ying Tan
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
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10
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Chen J, Hickey BL, Gao Z, Raz AAP, Hooley RJ, Zhong W. Sensing Base Modifications in Non-Canonically Folded DNA with an Optimized Host:Guest Sensing Array. ACS Sens 2022; 7:2164-2169. [PMID: 35917160 DOI: 10.1021/acssensors.2c00839] [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: 12/14/2022]
Abstract
An arrayed host:guest fluorescence sensor system can discriminate DNA G-quadruplex structures that differ only in the presence of single oxidation or methylation modification in the guanine base. These small modifications make subtle changes to G4 folding that are often not detectable by CD but induce differential fluorescence responses in the array. The sensing is functional in diluted serum and is capable of distinguishing individual modifications in DNA mixtures, providing a powerful method of detecting folding changes caused by DNA damage.
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11
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Chen F, Xue J, Bai M, Fan C, Zhao Y. Lighting Up Nucleic Acid Modifications in Single Cells with DNA-Encoded Amplification. Acc Chem Res 2022; 55:2248-2259. [PMID: 35904502 DOI: 10.1021/acs.accounts.2c00269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Nucleic acids are naturally decorated with various chemical modifications at nucleobases. Most nucleic acid modifications (NAMs) do not alter Watson-Crick base pairing but can regulate gene expression known as "epigenetics". Their abundances present a very wide range, approximately 10-2 to 10-6 of total bases. Different NAMs may coexist in spatial proximity (e.g., <20 nm) in the crowded intracellular environment. Considering the highly dynamic chromatin accessibility (physical access to DNA), the NAMs in inaccessible DNA probably plays different roles. These multilayered features of NAMs vary from cell to cell. Our understanding of the function and mechanism of NAMs in biological processes and disease states has largely been driven by the expanding array of sequencing-based methodologies. However, an underexplored aspect is the measurement of the subcellular distribution, spatial proximity, and inaccessibility of NAMs in single cells. In recent years, we have developed new approaches that light up single-cell NAMs with single-site sensitivity. These methods are mainly based on the integration of chemical or chemoenzymatic tools, DNA amplification and nanotechnology, and/or microfluidics. An overview of these methods together with conventional methods such as immunofluorescence (IF) and fluorescence in situ hybridization (FISH) is provided in this Account.Our laboratory has proposed DNA-encoded amplification (DEA) as the main strategy for developing a set of single-cell NAM imaging methods. In brief, DEA transforms the different features of NAMs into unique DNA primers for rolling circle amplification (RCA) followed by FISH imaging. The first method is base-encoded amplifying FISH (BEA-FISH), in which we convert individual NAMs into RCA primers via chemoselective labeling and click bioconjugation. It enables the in situ visualization of low-abundance NAMs (e.g., 5hmU), which is impracticable by conventional methods. We subsequently developed pairwise proximity-differentiated amplifying FISH (PPDA-FISH), which integrates BEA-FISH with DNA nanotechnology. PPDA-FISH utilizes proximity ligation and toehold strand displacement to label the adjacent site of two different NAMs (one-to-one proximity) and their respective residual sites with three unique RCA probes. It achieves simultaneous counting of the above-mentioned three types of modified sites in the same cells. The third method is cellular macromolecule-tethered DNA walking indexing (Cell-TALKING) to probe more than two NAMs within the same nanoenvironments. Cell-TALKING uses dynamic DNA proximity cleavage to continuously activate different preblocked RCA primers (for each NAM) near one walking probe (for one target molecule). We have explored three NAMs around one histone (one-to-many proximity) in different cancer cell lines and clinical specimens. Then, we describe a single-cell hydrogel encoding amplification (scHEA) method by integrating droplet microfluidics with BEA-FISH. This method generates hydrogel beads that encapsulate single cells and their genomic DNA after cell lysis. It realizes the analysis of global (accessible and inaccessible) DNA from the same cells. We find that the global levels of both 5hmC and 5hmU in single cells can distinguish different breast cancer cells. Finally, the current limitations of these strategies and the future development directions are also discussed. We hope that this Account can spark new ideas and invite new efforts from different disciplines for single-cell NAM analysis.
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Affiliation(s)
- Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Jing Xue
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Min Bai
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
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12
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Chen J, Li S, Chen Y, Yang J, Dong J. Highly selective detection of adenine and guanine by NH 2-MIL-53(Fe)/CS/MXene nanocomposites with excellent electrochemical performance. Mikrochim Acta 2022; 189:328. [PMID: 35962293 DOI: 10.1007/s00604-022-05376-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/17/2022] [Indexed: 11/28/2022]
Abstract
Adenine (A) and guanine (G) are mainly found in deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) and play a crucial role in genetic information transfer and protein synthesis. In this study, NH2-MIL-53(Fe)/CS/MXene nanocomposites were prepared for detecting guanine and adenine. With high specific surface area, excellent water dispersion, and numerous active sites, MXene (transition metal carbides, nitrides, and carbonitrides) provides a good platform for loading primitive metal-organic frameworks (MOFs). At the same time, the problem of poor conductivity and dispersion of MOFs is solved. The electrochemical catalytic oxidation of adenine and guanine of NH2-MIL-53 (Fe)/CS/MXene nanocomposites was carried out by differential pulse voltammetry (DPV). Operating voltage of DPV: 0.7-0.9 V (vs. Ag/AgCl) for G, 1.0-1.2 V (vs. Ag/AgCl) for A, 0.8 V (vs. Ag/AgCl), and 1.1 V (vs. Ag/AgCl) for G and A. The concentration ranges for detecting A and G were 3-118 μM and 2-120 μM with detection limits of 0.57 μM and 0.17 μM (S/N = 3), respectively. The nanocomposite was used for detecting G and A in herring sperm DNA, and the content of G and A was found to be about 9 and 11 μM; the RSD values were 3.4 and 1.3%, respectively.
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Affiliation(s)
- Jing Chen
- Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, 730070, People's Republic of China.
| | - Shuying Li
- Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, 730070, People's Republic of China
| | | | - Jiao Yang
- Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, 730070, People's Republic of China
| | - Jianbin Dong
- Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, 730070, People's Republic of China
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13
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Li W, Wang Y, Xiao Y, Li M, Liu Q, Liang L, Xie W, Wang D, Guan X, Wang L. Simultaneous Dual-Site Identification of 5 mC/8 oG in DNA Triplex Using a Nanopore Sensor. ACS APPLIED MATERIALS & INTERFACES 2022; 14:32948-32959. [PMID: 35816657 DOI: 10.1021/acsami.2c08478] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
DNA triplex participates in delivering site-specific epigenetic modifications critical for the regulation of gene expression. Among these marks, 5mC with 8oG functions comprehensively on gene expression. Recently, few research studies have emphasized the necessity of incorporation detection of 5mC with 8oG using one DNA triplex at the same time. Herein, DNA triplex structure was designed and tailored for the site-specific identification of 5mC with 8oG by means of nanopore electroanalysis. The identification was associated with the distinguishable current modulation types caused by DNA unzipping through the nanopore in an electrical field. Results demonstrated that the epigenetic modification proximity to the latch zone or constriction area of the nanopore enables differentiation of modification series at single nucleotide resolution in one DNA triplex, at both physiological and mildly acidic environment. In addition, our nanopore method enables the kinetic and thermodynamic studies to calculate the free energy of modified DNA triplex with applied potentials. Gibbs' energy provided the direct evidence that the DNA triplex with these epigenetic modifications is more stable in acidic environment. Considering modified DNA functions significantly in gene expression, the presented method may provide future opportunities to understand incorporating epigenetic mechanisms of many dysregulated biological processes on the basis of accurate detection.
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Affiliation(s)
- Wei Li
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, University of Chinese Academy of Sciences, Chongqing 401147, China
| | - Yunjiao Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Yicen Xiao
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, University of Chinese Academy of Sciences, Chongqing 401147, China
| | - Minghan Li
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, University of Chinese Academy of Sciences, Chongqing 401147, China
| | - Qianshan Liu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, University of Chinese Academy of Sciences, Chongqing 401147, China
| | - Liyuan Liang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Wanyi Xie
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, University of Chinese Academy of Sciences, Chongqing 401147, China
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14
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Chen JJ, You XJ, Li L, Xie NB, Ding JH, Yuan BF, Feng YQ. Single-Base Resolution Detection of Adenosine-to-Inosine RNA Editing by Endonuclease-Mediated Sequencing. Anal Chem 2022; 94:8740-8747. [PMID: 35678728 DOI: 10.1021/acs.analchem.2c01226] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RNA molecules contain diverse modifications that play crucial roles in a wide variety of biological processes. Adenosine-to-inosine (A-to-Ino) RNA editing is one of the most prevalent modifications among all types of RNA. Abnormal A-to-InoRNA editing has been demonstrated to be associated with many human diseases. Identification of A-to-Ino editing sites is indispensable to deciphering their biological roles. Herein, by employing the unique property of human endonuclease V (hEndoV), we proposed a hEndoV-mediated sequencing (hEndoV-seq) method for the single-base resolution detection of A-to-InoRNA editing sites. In this approach, the terminal 3'OH of RNA is first blocked by 3'-deoxyadenosine (3'-deoxy-A). Specific cleavage of Ino sites by hEndoV protein produces new terminal 3'OH, which can be identified by sequencing analysis, and therefore offers the site-specific detection of Ino in RNA. The principle of hEndoV-seq is straightforward and the analytical procedure is simple. No chemical reaction is involved in the sequencing library preparation. The whole procedure in hEndoV-seq is carried out under mild conditions and RNA is not prone to degradation. Taken together, the proposed hEndoV-seq method is capable of site-specific identification of A-to-Ino editing in RNA, which provides a valuable tool for elucidating the functions of A-to-Ino editing in RNA.
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Affiliation(s)
- Juan-Juan Chen
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Xue-Jiao You
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China.,School of Public Health, Wuhan University, Wuhan 430071, China
| | - Lin Li
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Neng-Bin Xie
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Jiang-Hui Ding
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Bi-Feng Yuan
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China.,School of Public Health, Wuhan University, Wuhan 430071, China.,Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430071, China
| | - Yu-Qi Feng
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China.,School of Public Health, Wuhan University, Wuhan 430071, China.,Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430071, China
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15
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Chakrapani A, Ruiz‐Larrabeiti O, Pohl R, Svoboda M, Krásný L, Hocek M. Glucosylated 5‐Hydroxymethylpyrimidines as Epigenetic DNA Bases Regulating Transcription and Restriction Cleavage. Chemistry 2022; 28:e202200911. [DOI: 10.1002/chem.202200911] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Indexed: 12/13/2022]
Affiliation(s)
- Aswathi Chakrapani
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry, Faculty of Science Charles University Hlavova 8 CZ-12843 Prague 2 Czech Republic
| | - Olatz Ruiz‐Larrabeiti
- Dept. of Microbial Genetics and Gene Expression Institute of Microbiology Czech Academy of Sciences 14220 Prague 4 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Martin Svoboda
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Libor Krásný
- Dept. of Microbial Genetics and Gene Expression Institute of Microbiology Czech Academy of Sciences 14220 Prague 4 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry, Faculty of Science Charles University Hlavova 8 CZ-12843 Prague 2 Czech Republic
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16
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Schmidl D, Jonasson NSW, Menke A, Schneider S, Daumann L. Spectroscopic and in vitro investigations of Fe2+/α-Ketoglutarate-dependent enzymes involved in nucleic acid repair and modification. Chembiochem 2022; 23:e202100605. [PMID: 35040547 PMCID: PMC9401043 DOI: 10.1002/cbic.202100605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/14/2022] [Indexed: 11/08/2022]
Abstract
The activation of molecular oxygen for the highly selective functionalization and repair of DNA and RNA nucleobases is achieved by α-ketoglutarate (α-KG)/iron-dependent dioxygenases. Enzymes of special interest are the human homologs AlkBH of Escherichia coli EcAlkB and ten-eleven translocation (TET) enzymes. These enzymes are involved in demethylation or dealkylation of DNA and RNA, although additional physiological functions are continuously being revealed. Given their importance, studying enzyme-substrate interactions, turnover and kinetic parameters is pivotal for the understanding of the mode of action of these enzymes. Diverse analytical methods, including X-ray crystallography, UV/Vis absorption, electron paramagnetic resonance (EPR), circular dichroism (CD) and NMR spectroscopy have been employed to study the changes in the active site and the overall enzyme structure upon substrate, cofactor and inhibitor addition. Several methods are now available to assess activity of these enzymes. By discussing limitations and possibilities of these techniques for EcAlkB, AlkBH and TET we aim to give a comprehensive synopsis from a bioinorganic point of view, addressing researchers from different disciplines working in the highly interdisciplinary and rapidly evolving field of epigenetic processes and DNA/RNA repair and modification.
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Affiliation(s)
- David Schmidl
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Niko S W Jonasson
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Annika Menke
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Sabine Schneider
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Lena Daumann
- Ludwig-Maximilians-Universität München, Department of Chemistry, Butenandtstr. 5-13, 81377, München, GERMANY
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17
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Xiong J, Wang P, Shao WX, Li G, Ding JH, Xie NB, Wang M, Cheng QY, Xie C, Feng YQ, Ci W, Yuan BF. Genome-wide mapping of N4-methylcytosine at single-base resolution by APOBEC3A-mediated deamination sequencing. Chem Sci 2022; 13:9960-9972. [PMID: 36128236 PMCID: PMC9430668 DOI: 10.1039/d2sc02446b] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/04/2022] [Indexed: 12/15/2022] Open
Abstract
N4-methylcytosine (4mC) is a natural DNA modification occurring in thermophiles and plays important roles in restriction-modification (R-M) systems in bacterial genomes. However, the precise location and sequence context of 4mC in the whole genome are limited. In this study, we developed an APOBEC3A-mediated deamination sequencing (4mC-AMD-seq) method for genome-wide mapping of 4mC at single-base resolution. In the 4mC-AMD-seq method, cytosine and 5-methylcytosine (5mC) are deaminated by APOBEC3A (A3A) protein to generate uracil and thymine, both of which are read as thymine in sequencing, while 4mC is resistant to deamination and therefore read as cytosine. Thus, the readouts of cytosines from sequencing could manifest the original 4mC sites in genomes. With the 4mC-AMD-seq method, we achieved the genome-wide mapping of 4mC in Deinococcus radiodurans (D. radiodurans). In addition, we confirmed that 4mC, but not 5mC, was the major modification in the D. radiodurans genome. We identified 1586 4mC sites in the genome of D. radiodurans, among which 564 sites were located in the CCGCGG motif. The average methylation levels in the CCGCGG motif and non-CCGCGG sequence were 70.0% and 22.8%, respectively. We envision that the 4mC-AMD-seq method will facilitate the investigation of 4mC functions, including the 4mC-involved R-M systems, in uncharacterized but potentially useful strains. Genome-wide mapping of N4-methylcytosine (4mC) at single-base resolution with APOBEC3A-mediated deamination sequencing (4mC-AMD-seq).![]()
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Affiliation(s)
- Jun Xiong
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ping Wang
- Key Laboratory of Genomics and Precision Medicine, 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
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Gaojie Li
- Key Laboratory of Genomics and Precision Medicine, 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
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Neng-Bin Xie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Min Wang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Qing-Yun Cheng
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China
| | - Conghua Xie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yu-Qi Feng
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, School of Public Health, 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, 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
| | - Bi-Feng Yuan
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, China
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18
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Du Y, Lai Y, Liu JY, Diao J. Epigenetic Quantification of DNA 5-Hydroxymethylcytosine Using DNA Hybridization-Based Single-Molecule Immunofluorescent Imaging. SMALL METHODS 2021; 5:e2100061. [PMID: 34928080 DOI: 10.1002/smtd.202100061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/15/2021] [Indexed: 02/05/2023]
Abstract
5-Hydroxymethylcytosine (5hmC) is a deoxyribonucleic acid (DNA) epigenetic modification that has an important function in embryonic development and human diseases. However, the numerous methods that have been developed to detect and quantify 5hmC, require large amounts of DNA sample to be modified via chemical reactions, which considerably limits their application with cell-free DNA (cfDNA). Meanwhile, other antibody-based methods of detecting 5hmC do not offer information about the DNA sequence. Here, in this article DNA hybridization-based single-molecule immunofluorescent imaging is presented, an ultrasensitive method of detecting 5hmC modification in DNA. Via using the probe DNA to capture the DNA fragment of interest and the 5hmC antibody to detect the 5hmC modification in DNA, the fluorescent response signal of the 5hmC modification from the secondary antibody at the single-molecule level is successfully detected. Using the method, one could determine the quantity of 5hmC in the gene of interest within 6 h. In addition, it requires only 3 pg of the DNA sample and minimal experience and training for operation and analysis.
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Affiliation(s)
- Yang Du
- Department of Biotherapy, Cancer Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Ying Lai
- State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, The Center of Gerontology and Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Ji-Yan Liu
- Department of Biotherapy, Cancer Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
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19
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Wang Q, Yin H, Zhou Y, Cao L, Yu Z, Xu Y, Ai S. Photoelectrochemical Biosensor for
5‐Formylcytosine
Based on
WS
2
/Bi/
Bi
2
O
2
CO
3
Nanocomposite and Rolling Circle Amplification. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Qian Wang
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University Taian Shandong 271018 China
| | - Huanshun Yin
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University Taian Shandong 271018 China
| | - Yunlei Zhou
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University Taian Shandong 271018 China
| | - Lulu Cao
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University Taian Shandong 271018 China
| | - Zhengkun Yu
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University Taian Shandong 271018 China
| | - Yamin Xu
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University Taian Shandong 271018 China
| | - Shiyun Ai
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University Taian Shandong 271018 China
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20
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Jonasson NSW, Janßen R, Menke A, Zott FL, Zipse H, Daumann LJ. TET-Like Oxidation in 5-Methylcytosine and Derivatives: A Computational and Experimental Study. Chembiochem 2021; 22:3333-3340. [PMID: 34498783 PMCID: PMC9293240 DOI: 10.1002/cbic.202100420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/08/2021] [Indexed: 01/05/2023]
Abstract
The epigenetic marker 5-methylcytosine (5mC) is an important factor in DNA modification and epigenetics. It can be modified through a three-step oxidation performed by ten-eleven-translocation (TET) enzymes and we have previously reported that the iron(IV)-oxo complex [Fe(O)(Py5 Me2 H)]2+ (1) can oxidize 5mC. Here, we report the reactivity of this iron(IV)-oxo complex towards a wider scope of methylated cytosine and uracil derivatives relevant for synthetic DNA applications, such as 1-methylcytosine (1mC), 5-methyl-iso-cytosine (5miC) and thymine (T/5mU). The observed kinetic parameters are corroborated by calculation of the C-H bond energies at the reactive sites which was found to be an efficient tool for reaction rate prediction of 1 towards methylated DNA bases. We identified oxidation products of methylated cytosine derivatives using HPLC-MS and GC-MS. Thereby, we shed light on the impact of the methyl group position and resulting C-H bond dissociation energies on reactivity towards TET-like oxidation.
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Affiliation(s)
- Niko S. W. Jonasson
- Department of ChemistryLudwig-Maximilians-University MunichButenandtstr. 5–1381377MünchenGermany
| | - Rachel Janßen
- Department of ChemistryLudwig-Maximilians-University MunichButenandtstr. 5–1381377MünchenGermany
| | - Annika Menke
- Department of ChemistryLudwig-Maximilians-University MunichButenandtstr. 5–1381377MünchenGermany
| | - Fabian L. Zott
- Department of ChemistryLudwig-Maximilians-University MunichButenandtstr. 5–1381377MünchenGermany
| | - Hendrik Zipse
- Department of ChemistryLudwig-Maximilians-University MunichButenandtstr. 5–1381377MünchenGermany
| | - Lena J. Daumann
- Department of ChemistryLudwig-Maximilians-University MunichButenandtstr. 5–1381377MünchenGermany
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21
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Ma CJ, Li L, Shao WX, Ding JH, Cai XL, Lun ZR, Yuan BF, Feng YQ. An enzyme-mediated bioorthogonal labeling method for genome-wide mapping of 5-hydroxymethyluracil. Chem Sci 2021; 12:14126-14132. [PMID: 34760197 PMCID: PMC8565368 DOI: 10.1039/d1sc03812e] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/03/2021] [Indexed: 12/29/2022] Open
Abstract
DNA 5-hydroxymethyluracil (5hmU) is a thymine modification existing in the genomes of various organisms. The post-replicative formation of 5hmU occurs via hydroxylation of thymine by ten-eleven translocation (TET) dioxygenases in mammals and J-binding proteins (JBPs) in protozoans, respectively. In addition, 5hmU can also be generated through oxidation of thymine by reactive oxygen species or deamination of 5hmC by cytidine deaminase. While the biological roles of 5hmU have not yet been fully explored, determining its genomic location will highly assist in elucidating its functions. Herein, we report a novel enzyme-mediated bioorthogonal labeling method for selective enrichment of 5hmU in genomes. 5hmU DNA kinase (5hmUDK) was utilized to selectively install an azide (N3) group or alkynyl group into the hydroxyl moiety of 5hmU followed by incorporation of the biotin linker through click chemistry, which enabled the capture of 5hmU-containing DNA fragments via streptavidin pull-down. The enriched fragments were applied to deep sequencing to determine the genomic distribution of 5hmU. With this established enzyme-mediated bioorthogonal labeling strategy, we achieved the genome-wide mapping of 5hmU in Trypanosoma brucei. The method described here will allow for a better understanding of the functional roles and dynamics of 5hmU in genomes.
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Affiliation(s)
- Cheng-Jie Ma
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 China
| | - Lin Li
- School of Pharmacy, Shanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Wen-Xuan Shao
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 China
| | - Jiang-Hui Ding
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 China
| | - Xiao-Li Cai
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Zhao-Rong Lun
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Bi-Feng Yuan
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 China .,School of Public Health, Wuhan University Wuhan 430071 China
| | - Yu-Qi Feng
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 China .,School of Public Health, Wuhan University Wuhan 430071 China
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22
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5-Formyluracil targeted biochemical reactions with proteins inhibit DNA replication, induce mutations and interference gene expression in living cells. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.02.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Feng Y, Huang W, Paul C, Liu X, Sadayappan S, Wang Y, Pauklin S. Mitochondrial nucleoid in cardiac homeostasis: bidirectional signaling of mitochondria and nucleus in cardiac diseases. Basic Res Cardiol 2021; 116:49. [PMID: 34392401 PMCID: PMC8364536 DOI: 10.1007/s00395-021-00889-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/20/2021] [Indexed: 01/11/2023]
Abstract
Metabolic function and energy production in eukaryotic cells are regulated by mitochondria, which have been recognized as the intracellular 'powerhouses' of eukaryotic cells for their regulation of cellular homeostasis. Mitochondrial function is important not only in normal developmental and physiological processes, but also in a variety of human pathologies, including cardiac diseases. An emerging topic in the field of cardiovascular medicine is the implication of mitochondrial nucleoid for metabolic reprogramming. This review describes the linear/3D architecture of the mitochondrial nucleoid (e.g., highly organized protein-DNA structure of nucleoid) and how it is regulated by a variety of factors, such as noncoding RNA and its associated R-loop, for metabolic reprogramming in cardiac diseases. In addition, we highlight many of the presently unsolved questions regarding cardiac metabolism in terms of bidirectional signaling of mitochondrial nucleoid and 3D chromatin structure in the nucleus. In particular, we explore novel techniques to dissect the 3D structure of mitochondrial nucleoid and propose new insights into the mitochondrial retrograde signaling, and how it regulates the nuclear (3D) chromatin structures in mitochondrial diseases.
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Affiliation(s)
- Yuliang Feng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Oxford, OX3 7LD, UK
| | - Wei Huang
- Department of Pathology and Laboratory Medicine, Regenerative Medicine Research, University of Cincinnati College of Medicine, 231 Albert Sabin Way, CincinnatiCincinnati, OH, 45267-0529, USA
| | - Christian Paul
- Department of Pathology and Laboratory Medicine, Regenerative Medicine Research, University of Cincinnati College of Medicine, 231 Albert Sabin Way, CincinnatiCincinnati, OH, 45267-0529, USA
| | - Xingguo Liu
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Guangzhou, 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Sakthivel Sadayappan
- Heart, Lung and Vascular Institute, Division of Cardiovascular Health and Disease, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Yigang Wang
- Department of Pathology and Laboratory Medicine, Regenerative Medicine Research, University of Cincinnati College of Medicine, 231 Albert Sabin Way, CincinnatiCincinnati, OH, 45267-0529, USA.
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Oxford, OX3 7LD, UK.
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Wang T, Loo CE, Kohli RM. Enzymatic approaches for profiling cytosine methylation and hydroxymethylation. Mol Metab 2021; 57:101314. [PMID: 34375743 PMCID: PMC8829811 DOI: 10.1016/j.molmet.2021.101314] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/26/2021] [Accepted: 08/03/2021] [Indexed: 12/20/2022] Open
Abstract
Background In mammals, modifications to cytosine bases, particularly in cytosine-guanine (CpG) dinucleotide contexts, play a major role in shaping the epigenome. The canonical epigenetic mark is 5-methylcytosine (5mC), but oxidized versions of 5mC, including 5-hydroxymethylcytosine (5hmC), are now known to be important players in epigenomic dynamics. Understanding the functional role of these modifications in gene regulation, normal development, and pathological conditions requires the ability to localize these modifications in genomic DNA. The classical approach for sequencing cytosine modifications has involved differential deamination via the chemical sodium bisulfite; however, bisulfite is destructive, limiting its utility in important biological or clinical settings where detection of low frequency populations is critical. Additionally, bisulfite fails to resolve 5mC from 5hmC. Scope of review To summarize how enzymatic rather than chemical approaches can be leveraged to localize and resolve different cytosine modifications in a non-destructive manner. Major conclusions Nature offers a suite of enzymes with biological roles in cytosine modification in organisms spanning from bacteriophages to mammals. These enzymatic activities include methylation by DNA methyltransferases, oxidation of 5mC by TET family enzymes, hypermodification of 5hmC by glucosyltransferases, and the generation of transition mutations from cytosine to uracil by DNA deaminases. Here, we describe how insights into the natural reactivities of these DNA-modifying enzymes can be leveraged to convert them into powerful biotechnological tools. Application of these enzymes in sequencing can be accomplished by relying on their natural activity, exploiting their ability to discriminate between cytosine modification states, reacting them with functionalized substrate analogs to introduce chemical handles, or engineering the DNA-modifying enzymes to take on new reactivities. We describe how these enzymatic reactions have been combined and permuted to localize DNA modifications with high specificity and without the destructive limitations posed by chemical methods for epigenetic sequencing. Chemical sequencing methods damage DNA and can confound cytosine modifications. DNA modifying enzymes offer non-destructive and selective biotechnological tools. DNA deaminases, methyltransferases, oxygenases and glucosyltransferases can be used. Permuting enzymes with various activities can reveal distinct cytosine states. Engineered enzymes utilizing unnatural co-substrates expand sequencing scope.
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Affiliation(s)
- Tong Wang
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christian E Loo
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rahul M Kohli
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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25
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Dai Y, Yuan BF, Feng YQ. Quantification and mapping of DNA modifications. RSC Chem Biol 2021; 2:1096-1114. [PMID: 34458826 PMCID: PMC8341653 DOI: 10.1039/d1cb00022e] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022] Open
Abstract
Apart from the four canonical nucleobases, DNA molecules carry a number of natural modifications. Substantial evidence shows that DNA modifications can regulate diverse biological processes. Dynamic and reversible modifications of DNA are critical for cell differentiation and development. Dysregulation of DNA modifications is closely related to many human diseases. The research of DNA modifications is a rapidly expanding area and has been significantly stimulated by the innovations of analytical methods. With the recent advances in methods and techniques, a series of new DNA modifications have been discovered in the genomes of prokaryotes and eukaryotes. Deciphering the biological roles of DNA modifications depends on the sensitive detection, accurate quantification, and genome-wide mapping of modifications in genomic DNA. This review provides an overview of the recent advances in analytical methods and techniques for both the quantification and genome-wide mapping of natural DNA modifications. We discuss the principles, advantages, and limitations of these developed methods. It is anticipated that new methods and techniques will resolve the current challenges in this burgeoning research field and expedite the elucidation of the functions of DNA modifications.
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Affiliation(s)
- Yi Dai
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 P. R. China +86-27-68755595 +86-27-68755595
| | - Bi-Feng Yuan
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 P. R. China +86-27-68755595 +86-27-68755595
- School of Health Sciences, Wuhan University Wuhan 430071 China
| | - Yu-Qi Feng
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 P. R. China +86-27-68755595 +86-27-68755595
- School of Health Sciences, Wuhan University Wuhan 430071 China
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26
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Mao B, Qian L, Govindhan M, Liu Z, Chen A. Simultaneous electrochemical detection of guanine and adenine using reduced graphene oxide decorated with AuPt nanoclusters. Mikrochim Acta 2021; 188:276. [PMID: 34319444 DOI: 10.1007/s00604-021-04926-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 07/04/2021] [Indexed: 01/14/2023]
Abstract
A rapid and sensitive electrochemical sensing platform is reported based on bimetallic gold-platinum nanoclusters (AuPtNCs) dispersed on reduced graphene oxide (rGO) for the simultaneous detection of guanine and adenine using square wave voltammetry (SWV). The synthesis of AuPtNCs-rGO nanocomposite was achieved by a simultaneous reduction of graphene oxide (GO) and metal ions (Au3+ and Pt4+) in an aqueous solution. The developed AuPtNCs-rGO electrochemical sensor with the optimized 50:50 bimetallic (Au:Pt) nanoclusters exhibited an outstanding electrocatalytic performance towards the simultaneous oxidation of guanine and adenine without the aid of any enzymes or mediators in physiological pH. The electrochemical sensor platform showed low detection limits of 60 nM and 100 nM (S/N = 3) for guanine and adenine, respectively, with high sensitivity and an extensive linear range from 1.0 μM to 0.2 mM for both guanine and adenine. The interference from the most common electrochemically active interferents, including ascorbic acid, uric acid, and dopamine, was almost negligible. The simultaneous sensing of guanine and adenine in denatured Salmon Sperm DNA sample was successfully achieved using the proposed platform, showing that the AuPtNCs-rGO nanocomposite could provide auspicious clinical diagnosis and biomedical applications.
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Affiliation(s)
- Brennan Mao
- Department of Chemistry, Lakehead University, 955 Oliver Road, Thunder Bay, ON, P7B 5E1, Canada
| | - Lanting Qian
- Electrochemical Technology Centre, Department of Chemistry, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Maduraiveeran Govindhan
- Department of Chemistry, Lakehead University, 955 Oliver Road, Thunder Bay, ON, P7B 5E1, Canada.,Department of Chemistry, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Chennai, Tamil Nadu, 603 203, India
| | - Zhonggang Liu
- Electrochemical Technology Centre, Department of Chemistry, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.,Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, Anhui, People's Republic of China
| | - Aicheng Chen
- Department of Chemistry, Lakehead University, 955 Oliver Road, Thunder Bay, ON, P7B 5E1, Canada. .,Electrochemical Technology Centre, Department of Chemistry, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
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27
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Bai M, Cao X, Chen F, Xue J, Zhao Y, Zhao Y. Bioorthogonal Chemical Signature Enabling Amplified Visualization of Cellular Oxidative Thymines. Anal Chem 2021; 93:10495-10501. [PMID: 34293865 DOI: 10.1021/acs.analchem.1c01285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Cellular oxidative thymines, 5-hydroxymethyluracil (5hmU) and 5-formyluracil (5fU), are found in the genomes of a diverse range of organisms, the distribution of which profoundly influence biological processes and living systems. However, the distribution of cellular oxidative thymines has not been explored because of lacking both specific bioorthogonal labeling and sensitivity methods for single-cell analysis. Herein, we report a bioorthogonal chemical signature enabling amplified visualization of cellular oxidative thymines in single cells. The synthesized ATP-γ-alkyne, an ATP analogue with bioorthogonal tag modified on γ-phosphate can be specifically linked to cellular 5hmU by chemoenzymatic labeling. DNA with 5-alkynephosphomethyluracil were then clicked with azide (N3)-modified 5hmU-primer. Identification of 5fU is based on selective reduction from 5fU to 5hmU, subsequent chemoenzymatic labeling of the newly generated 5hmU, and cross-linking with N3-modified 5fU-primer via click chemistry. Then, all of the 5hmU and 5fU sites are encoded with respective circularized barcodes. These barcodes are simultaneously amplified for multiplexed single-molecule imaging. The above two kinds of barcodes can be simultaneously amplified for differentiated visualization of 5hmU and 5fU in single cells. We find these two kinds of cellular oxidative thymines are spatially organized in a cell-type-dependent style with cell-to-cell heterogeneity. We also investigate their multilevel subcellular information and explore their dynamic changes during cell cycles. Further, using DNA sequencing instead of fluorescence imaging, our proposed bioorthogonal chemical signature holds great potential to offer the sequence information of these oxidative thymines in cells and may provide a reliable chemical biology approach for studying the whole-genome oxidative thymines profiles and insights into their functional role and dynamics in biology.
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Affiliation(s)
- Min Bai
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, Shaanxi, P. R. China
| | - Xiaowen Cao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, Shaanxi, P. R. China
| | - Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, Shaanxi, P. R. China
| | - Jing Xue
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, Shaanxi, P. R. China
| | - Yue Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, Shaanxi, P. R. China
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, Shaanxi, P. R. China
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28
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Callet T, Li H, Coste P, Glise S, Heraud C, Maunas P, Mercier Y, Turonnet N, Zunzunegui C, Panserat S, Bolliet V, Marandel L. Modulation of Energy Metabolism and Epigenetic Landscape in Rainbow Trout Fry by a Parental Low Protein/High Carbohydrate Diet. BIOLOGY 2021; 10:biology10070585. [PMID: 34202225 PMCID: PMC8301017 DOI: 10.3390/biology10070585] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/17/2021] [Accepted: 06/20/2021] [Indexed: 12/13/2022]
Abstract
Simple Summary While the effects of parental diets on their progeny have been highly described in mammals, such studies are lacking in fish. To explore such a question in a high trophic level teleost fish, two-year old male and female rainbow trout were fed either a control diet (0% carbohydrate and 63.89% protein) or a high-carbohydrate diet (35% carbohydrate and 42.96% protein), for a complete reproductive cycle for females and for a period of 5 months for males. Neither the maternal nor the paternal high-carbohydrate diet alone had induced significant effects on their progeny. Nevertheless, when both parents were fed the high-carbohydrate diet, the energy metabolism and mitochondrial dynamics of their progeny were altered. Moreover, the epigenetic landscape was also highly affected. Even though, offspring growth was only slightly affected at the early stage of life; the effect of parental high-carbohydrate diet should be explored over the long term. Abstract It is now recognized that parental diets could highly affect offspring metabolism and growth. Studies in fish are, however, lacking. In particular, the effect of a parental diet high in carbohydrate (HC) and low in protein (LP) on progeny has never been examined in higher trophic level teleost fish. Thus, two-year old male and female rainbow trout (Oncorhynchus mykiss) were fed either a control diet (0% carbohydrate and 63.89% protein) or a diet containing 35% carbohydrate and 42.96% protein (HC/LP) for a complete reproductive cycle for females and over a 5-month period for males. Cross-fertilizations were then carried out. To evaluate the effect of the parental diet on their offspring, different phenotypic and metabolic traits were recorded for offspring before their first feeding and again three weeks later. When considering the paternal and maternal HC/LP nutrition independently, fry phenotypes and transcriptomes were only slightly affected. The combination of the maternal and paternal HC/LP diets altered the energy metabolism and mitochondrial dynamics of their progeny, demonstrating the existence of a synergistic effect. The global DNA methylation of whole fry was also highly affected by the HC/LP parental diet, indicating that it could be one of the fundamental mechanisms responsible for the effects of nutritional programming.
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Affiliation(s)
- Thérèse Callet
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, NUMEA, 64310 Saint-Pée-sur-Nivelle, France; (T.C.); (H.L.); (C.H.); (P.M.); (Y.M.); (N.T.); (C.Z.); (S.P.)
| | - Hongyan Li
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, NUMEA, 64310 Saint-Pée-sur-Nivelle, France; (T.C.); (H.L.); (C.H.); (P.M.); (Y.M.); (N.T.); (C.Z.); (S.P.)
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Pascale Coste
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, ECOBIOP, 64310 Saint-Pée-sur-Nivelle, France; (P.C.); (S.G.); (V.B.)
| | - Stéphane Glise
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, ECOBIOP, 64310 Saint-Pée-sur-Nivelle, France; (P.C.); (S.G.); (V.B.)
| | - Cécile Heraud
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, NUMEA, 64310 Saint-Pée-sur-Nivelle, France; (T.C.); (H.L.); (C.H.); (P.M.); (Y.M.); (N.T.); (C.Z.); (S.P.)
| | - Patrick Maunas
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, NUMEA, 64310 Saint-Pée-sur-Nivelle, France; (T.C.); (H.L.); (C.H.); (P.M.); (Y.M.); (N.T.); (C.Z.); (S.P.)
| | - Yvan Mercier
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, NUMEA, 64310 Saint-Pée-sur-Nivelle, France; (T.C.); (H.L.); (C.H.); (P.M.); (Y.M.); (N.T.); (C.Z.); (S.P.)
| | - Nicolas Turonnet
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, NUMEA, 64310 Saint-Pée-sur-Nivelle, France; (T.C.); (H.L.); (C.H.); (P.M.); (Y.M.); (N.T.); (C.Z.); (S.P.)
| | - Chloé Zunzunegui
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, NUMEA, 64310 Saint-Pée-sur-Nivelle, France; (T.C.); (H.L.); (C.H.); (P.M.); (Y.M.); (N.T.); (C.Z.); (S.P.)
| | - Stéphane Panserat
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, NUMEA, 64310 Saint-Pée-sur-Nivelle, France; (T.C.); (H.L.); (C.H.); (P.M.); (Y.M.); (N.T.); (C.Z.); (S.P.)
| | - Valérie Bolliet
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, ECOBIOP, 64310 Saint-Pée-sur-Nivelle, France; (P.C.); (S.G.); (V.B.)
| | - Lucie Marandel
- INRAE, Université de Pau et des Pays de L’Adour, E2S UPPA, NUMEA, 64310 Saint-Pée-sur-Nivelle, France; (T.C.); (H.L.); (C.H.); (P.M.); (Y.M.); (N.T.); (C.Z.); (S.P.)
- Correspondence:
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29
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Wang Y, Zhang X, Han S, Yang W, Chen Z, Wu F, Liu J, Weng X, Zhou X. Base-Resolution Analysis of Deoxyuridine at the Genome Scale Based on the Artificial Incorporation Modified Nucleobase. ACS CENTRAL SCIENCE 2021; 7:973-979. [PMID: 34235258 PMCID: PMC8227591 DOI: 10.1021/acscentsci.0c01504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Indexed: 05/11/2023]
Abstract
Deamination of cytosine and dUMP misincorporation have been found to be capable of producing uracil in the genome. This study presents the AI-seq (artificial incorporation modified nucleobase for sequencing), a "base substitution", which not only is capable of profiling uracil at single-nucleotide resolution and showing its centromeric enrichment but could also reveal that the identified uracil sites are derived from cytosine deamination. All the results indicate the potential biological significance of uracil as the epigenetic modification.
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Affiliation(s)
- Yafen Wang
- College
of Chemistry and Molecular Sciences, Key Laboratory of Biomedical
Polymers of Ministry of Education, Wuhan
University, Wuhan, 430072 Hubei, China
| | - Xiong Zhang
- College
of Chemistry and Molecular Sciences, Key Laboratory of Biomedical
Polymers of Ministry of Education, Wuhan
University, Wuhan, 430072 Hubei, China
| | - Shaoqing Han
- College
of Chemistry and Molecular Sciences, Key Laboratory of Biomedical
Polymers of Ministry of Education, Wuhan
University, Wuhan, 430072 Hubei, China
| | - Wei Yang
- College
of Chemistry and Molecular Sciences, Key Laboratory of Biomedical
Polymers of Ministry of Education, Wuhan
University, Wuhan, 430072 Hubei, China
| | - Zonggui Chen
- State
Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for
Seed Design, Chinese Academy of Sciences, Wuhan 430072, China
| | - Fan Wu
- College
of Chemistry and Molecular Sciences, Key Laboratory of Biomedical
Polymers of Ministry of Education, Wuhan
University, Wuhan, 430072 Hubei, China
| | - Jizhou Liu
- College
of Chemistry and Molecular Sciences, Key Laboratory of Biomedical
Polymers of Ministry of Education, Wuhan
University, Wuhan, 430072 Hubei, China
| | - Xiaocheng Weng
- College
of Chemistry and Molecular Sciences, Key Laboratory of Biomedical
Polymers of Ministry of Education, Wuhan
University, Wuhan, 430072 Hubei, China
- E-mail:
| | - Xiang Zhou
- College
of Chemistry and Molecular Sciences, Key Laboratory of Biomedical
Polymers of Ministry of Education, Wuhan
University, Wuhan, 430072 Hubei, China
- E-mail:
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30
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Genome-wide detection of cytosine methylation by single molecule real-time sequencing. Proc Natl Acad Sci U S A 2021; 118:2019768118. [PMID: 33495335 PMCID: PMC7865158 DOI: 10.1073/pnas.2019768118] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Single molecule real-time (SMRT) sequencing theoretically offers the opportunity to directly assess certain base modifications of native DNA molecules without any prior chemical/enzymatic conversions and PCR amplification, using kinetic signals of a DNA polymerase. However, the kinetic signal changes caused by 5mC modification are extremely subtle. Hence, the robust genome-wide measurement of 5mC modification has not been achieved. We enhanced 5mC detection using SMRT sequencing by holistically analyzing kinetic signals of a DNA polymerase and sequence context for every base within a measurement window. We employed a convolutional neural network to train a methylation classification model, leading to genome-wide 5mC detection. The sensitivity and specificity reached 90% and 94%, with a 99% correlation of overall methylation level with bisulfite sequencing. 5-Methylcytosine (5mC) is an important type of epigenetic modification. Bisulfite sequencing (BS-seq) has limitations, such as severe DNA degradation. Using single molecule real-time sequencing, we developed a methodology to directly examine 5mC. This approach holistically examined kinetic signals of a DNA polymerase (including interpulse duration and pulse width) and sequence context for every nucleotide within a measurement window, termed the holistic kinetic (HK) model. The measurement window of each analyzed double-stranded DNA molecule comprised 21 nucleotides with a cytosine in a CpG site in the center. We used amplified DNA (unmethylated) and M.SssI-treated DNA (methylated) (M.SssI being a CpG methyltransferase) to train a convolutional neural network. The area under the curve for differentiating methylation states using such samples was up to 0.97. The sensitivity and specificity for genome-wide 5mC detection at single-base resolution reached 90% and 94%, respectively. The HK model was then tested on human–mouse hybrid fragments in which each member of the hybrid had a different methylation status. The model was also tested on human genomic DNA molecules extracted from various biological samples, such as buffy coat, placental, and tumoral tissues. The overall methylation levels deduced by the HK model were well correlated with those by BS-seq (r = 0.99; P < 0.0001) and allowed the measurement of allele-specific methylation patterns in imprinted genes. Taken together, this methodology has provided a system for simultaneous genome-wide genetic and epigenetic analyses.
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31
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Chen C, He R, Zhang Z, Chen Y. Dual-recognition-based determination of ctDNA via the clamping function of peptide nucleic acid and terminal protection of small-molecule-linked DNA. Analyst 2021; 145:7603-7608. [PMID: 32990694 DOI: 10.1039/d0an01305f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A new dual-recognition fluorescent biosensor for circulating tumor DNA (ctDNA) detection has been developed, which combines the clamping function of peptide nucleic acid (PNA) and terminal protection of small-molecule-linked DNA (TPSMLD). Taking the tumor-specific E542K mutation and methylation of the PIK3CA gene as the target ctDNA, a low detection limit of 0.3161 pM ctDNA is achieved with good selectivity. This study not only offers a sensitive, selective and accurate ctDNA detection method, but can also be used to detect the target in complex biological samples.
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Affiliation(s)
- Chaohui Chen
- Institute for Interdisciplinary Research, Jianghan University, Wuhan 430056, P. R. China.
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32
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Programmable tools for targeted analysis of epigenetic DNA modifications. Curr Opin Chem Biol 2021; 63:1-10. [PMID: 33588304 DOI: 10.1016/j.cbpa.2021.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/04/2021] [Accepted: 01/04/2021] [Indexed: 11/21/2022]
Abstract
Modifications of the cytosine 5-position are dynamic epigenetic marks of mammalian DNA with important regulatory roles in development and disease. Unraveling biological functions of such modified nucleobases is tightly connected with the potential of available methods for their analysis. Whereas genome-wide nucleobase quantification and mapping are first-line analyses, targeted analyses move into focus the more genomic sites with high biological significance are identified. We here review recent developments in an emerging field that addresses such targeted analyses via probes that combine a programmable, sequence-specific DNA-binding domain with the ability to directly recognize or cross-link an epigenetically modified nucleobase of interest. We highlight how such probes offer simple, high-resolution nucleobase analyses in vitro and enable in situ correlations between a nucleobase and other chromatin regulatory elements at user-defined loci on the single-cell level by imaging.
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33
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Li CC, Chen HY, Dong YH, Luo X, Hu J, Zhang CY. Advances in Detection of Epigenetic Modification—5-Hydroxymethylcytosine. ACTA CHIMICA SINICA 2021. [DOI: 10.6023/a20120564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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34
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Sun Y, Lu Z, Ma W, Wang R, Zhang C, Liu J. A porous organic polymer nanosphere-based fluorescent biosensing platform for simultaneous detection of multiplexed DNA via electrostatic attraction and π–π stacking interactions. RSC Adv 2021; 11:38820-38828. [PMID: 35493231 PMCID: PMC9044239 DOI: 10.1039/d1ra07435k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/29/2021] [Indexed: 11/21/2022] Open
Abstract
One key challenge in oligonucleotide sequence sensing is to achieve multiplexed DNA detection in one sensor. Herein, a simple and efficient fluorescent biosensing platform is constructed to simultaneously detect multiplexed DNA depending on porous organic polymer (POP) nanospheres. The developed sensor is based on the concept that the POP nanospheres can efficiently quench the fluorescence emission of dye-labeled single-stranded DNA (ssDNA). Fluorescence quenching is achieved by the non-covalent assembly of multiple probes on the surface of POP nanospheres through electrostatic attraction and π–π stacking interactions, in which the electrostatic attraction plays a more critical role than π–π stacking. The formed dsDNA could be released off the surface of POP via hybridizing with the target DNA. Consequently, the target DNA can be quickly detected by fluorescence recovery. The biosensor could sensitively and specifically identify three target DNAs in the range of 0.1 to 36 nM, and the lowest detection limits are 50 pM, 100 pM, and 50 pM, respectively. It is noteworthy that the proposed platform is successfully applied to detect DNA in human serum. We perceive that the proposed sensing system represents a simple and sensitive strategy towards simultaneous and multiplexed assays for DNA monitoring and early clinical diagnosis. This communication reports a simple and efficient fluorescent biosensing platform to simultaneously detect multiplexed DNA depending on porous organic polymer (POP) nanospheres by electrostatic attraction and π–π stacking interaction.![]()
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Affiliation(s)
- Yujie Sun
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing 211816, China
| | - Zhenzhong Lu
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing 211816, China
| | - Wenlin Ma
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing 211816, China
| | - Rui Wang
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing 211816, China
| | - Chengwu Zhang
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing 211816, China
| | - Jinhua Liu
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing 211816, China
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35
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Nappi M, Hofer A, Balasubramanian S, Gaunt MJ. Selective Chemical Functionalization at N6-Methyladenosine Residues in DNA Enabled by Visible-Light-Mediated Photoredox Catalysis. J Am Chem Soc 2020; 142:21484-21492. [PMID: 33305571 PMCID: PMC7760100 DOI: 10.1021/jacs.0c10616] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Indexed: 12/18/2022]
Abstract
Selective chemistry that modifies the structure of DNA and RNA is essential to understanding the role of epigenetic modifications. We report a visible-light-activated photocatalytic process that introduces a covalent modification at a C(sp3)-H bond in the methyl group of N6-methyl deoxyadenosine and N6-methyl adenosine, epigenetic modifications of emerging importance. A carefully orchestrated reaction combines reduction of a nitropyridine to form a nitrosopyridine spin-trapping reagent and an exquisitely selective tertiary amine-mediated hydrogen-atom abstraction at the N6-methyl group to form an α-amino radical. Cross-coupling of the putative α-amino radical with nitrosopyridine leads to a stable conjugate, installing a label at N6-methyl-adenosine. We show that N6-methyl deoxyadenosine-containing oligonucleotides can be enriched from complex mixtures, paving the way for applications to identify this modification in genomic DNA and RNA.
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Affiliation(s)
- Manuel Nappi
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Alexandre Hofer
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Shankar Balasubramanian
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
- Cancer
Research UK Cambridge Institute, University
of Cambridge, Cambridge CB2 0RE, United Kingdom
- School
of Clinical Medicine, University of
Cambridge, Cambridge CB2 0SP, United Kingdom
| | - Matthew J. Gaunt
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
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36
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Chakrapani A, Vaňková Hausnerová V, Ruiz-Larrabeiti O, Pohl R, Krásný L, Hocek M. Photocaged 5-(Hydroxymethyl)pyrimidine Nucleoside Phosphoramidites for Specific Photoactivatable Epigenetic Labeling of DNA. Org Lett 2020; 22:9081-9085. [PMID: 33156631 DOI: 10.1021/acs.orglett.0c03462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
5-Hydroxymethylcytosine and uracil are epigenetic nucleobases, but their biological roles are still unclear. We present the synthesis of 2-nitrobenzyl photocaged 5-hydroxymethyl-2'-deoxycytidine and uridine 3'-O-phosphoramidites and their use in automated solid-phase synthesis of oligonucleotides (ONs) modified at specific positions. The ONs were used as primers for PCR to construct DNA templates modified in the promoter region that allowed switching of transcription through photochemical uncaging.
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Affiliation(s)
- Aswathi Chakrapani
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Viola Vaňková Hausnerová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Olatz Ruiz-Larrabeiti
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
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37
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Bell RT, Wolf YI, Koonin EV. Modified base-binding EVE and DCD domains: striking diversity of genomic contexts in prokaryotes and predicted involvement in a variety of cellular processes. BMC Biol 2020; 18:159. [PMID: 33148243 PMCID: PMC7641849 DOI: 10.1186/s12915-020-00885-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/01/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND DNA and RNA of all cellular life forms and many viruses contain an expansive repertoire of modified bases. The modified bases play diverse biological roles that include both regulation of transcription and translation, and protection against restriction endonucleases and antibiotics. Modified bases are often recognized by dedicated protein domains. However, the elaborate networks of interactions and processes mediated by modified bases are far from being completely understood. RESULTS We present a comprehensive census and classification of EVE domains that belong to the PUA/ASCH domain superfamily and bind various modified bases in DNA and RNA. We employ the "guilt by association" approach to make functional inferences from comparative analysis of bacterial and archaeal genomes, based on the distribution and associations of EVE domains in (predicted) operons and functional networks of genes. Prokaryotes encode two classes of EVE domain proteins, slow-evolving and fast-evolving ones. Slow-evolving EVE domains in α-proteobacteria are embedded in conserved operons, potentially involved in coupling between translation and respiration, cytochrome c biogenesis in particular, via binding 5-methylcytosine in tRNAs. In β- and γ-proteobacteria, the conserved associations implicate the EVE domains in the coordination of cell division, biofilm formation, and global transcriptional regulation by non-coding 6S small RNAs, which are potentially modified and bound by the EVE domains. In eukaryotes, the EVE domain-containing THYN1-like proteins have been reported to inhibit PCD and regulate the cell cycle, potentially, via binding 5-methylcytosine and its derivatives in DNA and/or RNA. We hypothesize that the link between PCD and cytochrome c was inherited from the α-proteobacterial and proto-mitochondrial endosymbiont and, unexpectedly, could involve modified base recognition by EVE domains. Fast-evolving EVE domains are typically embedded in defense contexts, including toxin-antitoxin modules and type IV restriction systems, suggesting roles in the recognition of modified bases in invading DNA molecules and targeting them for restriction. We additionally identified EVE-like prokaryotic Development and Cell Death (DCD) domains that are also implicated in defense functions including PCD. This function was inherited by eukaryotes, but in animals, the DCD proteins apparently were displaced by the extended Tudor family proteins, whose partnership with Piwi-related Argonautes became the centerpiece of the Piwi-interacting RNA (piRNA) system. CONCLUSIONS Recognition of modified bases in DNA and RNA by EVE-like domains appears to be an important, but until now, under-appreciated, common denominator in a variety of processes including PCD, cell cycle control, antivirus immunity, stress response, and germline development in animals.
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Affiliation(s)
- Ryan T Bell
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
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38
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Huang X, Zhang L, Wei L, Wang M, Li B, Guo B, Ma M. One-Pot Derivatization for Wide-Scope Detection of Nucleobases and Deoxyribosides in Natural Medicinal Foods with Liquid Chromatography-Tandem Mass Spectrometry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:10200-10212. [PMID: 32853523 DOI: 10.1021/acs.jafc.0c03328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A new chemical labeling-based LC-MS/MS approach was developed for quantitative profiling of nine canonical bases and deoxynucleosides (dNs) in natural products. Using 2-bromo-1-(4-dimethylamino-phenyl)-ethaone (BrDPE) as the tagging reagent, a previously unexploited N-alkylpyrimidine derivative (Nad) was created for one-pot labeling of widescope nucleobases via a flexible bromophilic substitution under mild conditions. The derivatization notably improved the LC-MS detection sensitivity by 31-107 fold, enabling a fast dilute-and-shoot analysis of highly diluted samples. The optimized and validated method demonstrated satisfactory accuracy (87-107%), precision (RSDs < 7.5%), and recovery (89-105%) for matrix-matched standard addition. The method was applied to simultaneously determine all target analytes and four uncanonical analogues and base-modified species in seven traditional health foods, which differ in contents by up to 600-fold for discrimination among samples. Further, the base-labeled Nads exhibit a unique fragmentation signature that could be used for untargeted screening of nucleobase-containing metabolites by simplified LC-MS/MS workflow to improve quality evaluation of natural medicinal products.
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Affiliation(s)
- Xingrong Huang
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha 410081, China
| | - Lu Zhang
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha 410081, China
| | - Lijuan Wei
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha 410081, China
| | - Meiling Wang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Bowen Li
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha 410081, China
| | - Bin Guo
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha 410081, China
| | - Ming Ma
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha 410081, China
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39
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Ganz D, Harijan D, Wagenknecht HA. Labelling of DNA and RNA in the cellular environment by means of bioorthogonal cycloaddition chemistry. RSC Chem Biol 2020; 1:86-97. [PMID: 34458750 PMCID: PMC8341813 DOI: 10.1039/d0cb00047g] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022] Open
Abstract
Labelling of nucleic acids as biologically important cellular components is a crucial prerequisite for the visualization and understanding of biological processes. Efficient bioorthogonal chemistry and in particular cycloadditions fullfill the requirements for cellular applications. The broadly applied Cu(i)-catalyzed azide-alkyne cycloaddition (CuAAC), however, is limited to labellings in vitro and in fixed cells due to the cytotoxicity of copper salts. Currently, there are three types of copper-free cycloadditions used for nucleic acid labelling in the cellular environment: (i) the ring-strain promoted azide-alkyne cycloaddition (SPAAC), (ii) the "photoclick" 1,3-dipolar cycloadditions, and (iii) the Diels-Alder reactions with inverse electron demand (iEDDA). We review only those building blocks for chemical synthesis on solid phase of DNA and RNA and for enzymatic DNA and RNA preparation, which were applied for labelling of DNA and RNA in situ or in vivo, i.e. in the cellular environment, in fixed or in living cells, by the use of bioorthogonal cycloaddition chemistry. Additionally, we review the current status of orthogonal dual and triple labelling of DNA and RNA in vitro to demonstrate their potential for future applications in situ or in vivo.
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Affiliation(s)
- Dorothée Ganz
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Dennis Harijan
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
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40
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Herbert A. ALU non-B-DNA conformations, flipons, binary codes and evolution. ROYAL SOCIETY OPEN SCIENCE 2020; 7:200222. [PMID: 32742689 PMCID: PMC7353975 DOI: 10.1098/rsos.200222] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/18/2020] [Indexed: 05/08/2023]
Abstract
ALUs contribute to genetic diversity by altering DNA's linear sequence through retrotransposition, recombination and repair. ALUs also have the potential to form alternative non-B-DNA conformations such as Z-DNA, triplexes and quadruplexes that alter the read-out of information from the genome. I suggest here these structures enable the rapid reprogramming of cellular pathways to offset DNA damage and regulate inflammation. The experimental data supporting this form of genetic encoding is presented. ALU sequence motifs that form non-B-DNA conformations under physiological conditions are called flipons. Flipons are binary switches. They are dissipative structures that trade energy for information. By efficiently targeting cellular machines to active genes, flipons expand the repertoire of RNAs compiled from a gene. Their action greatly increases the informational capacity of linearly encoded genomes. Flipons are programmable by epigenetic modification, synchronizing cellular events by altering both chromatin state and nucleosome phasing. Different classes of flipon exist. Z-flipons are based on Z-DNA and modify the transcripts compiled from a gene. T-flipons are based on triplexes and localize non-coding RNAs that direct the assembly of cellular machines. G-flipons are based on G-quadruplexes and sense DNA damage, then trigger the appropriate protective responses. Flipon conformation is dynamic, changing with context. When frozen in one state, flipons often cause disease. The propagation of flipons throughout the genome by ALU elements represents a novel evolutionary innovation that allows for rapid change. Each ALU insertion creates variability by extracting a different set of information from the neighbourhood in which it lands. By elaborating on already successful adaptations, the newly compiled transcripts work with the old to enhance survival. Systems that optimize flipon settings through learning can adapt faster than with other forms of evolution. They avoid the risk of relying on random and irreversible codon rewrites.
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41
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Yuan F, Yu Y, Zhou YL, Zhang XX. 5hmC-MIQuant: Ultrasensitive Quantitative Detection of 5-Hydroxymethylcytosine in Low-Input Cell-Free DNA Samples. Anal Chem 2019; 92:1605-1610. [DOI: 10.1021/acs.analchem.9b04920] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Fang Yuan
- Beijing National Laboratory
for Molecular Sciences,
MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yue Yu
- Beijing National Laboratory
for Molecular Sciences,
MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ying-Lin Zhou
- Beijing National Laboratory
for Molecular Sciences,
MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xin-Xiang Zhang
- Beijing National Laboratory
for Molecular Sciences,
MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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42
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Wang N, Bao H, Chen L, Liu Y, Li Y, Wu B, Huang H. Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK. Nucleic Acids Res 2019; 47:10388-10399. [PMID: 31504793 PMCID: PMC6821365 DOI: 10.1093/nar/gkz744] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/13/2019] [Accepted: 08/20/2019] [Indexed: 02/06/2023] Open
Abstract
HMCES and yedK were recently identified as sensors of abasic sites in ssDNA. In this study, we present multiple crystal structures captured in the apo-, nonspecific-substrate-binding, specific-substrate-binding, and product-binding states of yedK. In combination with biochemical data, we unveil the molecular basis of AP site sensing in ssDNA by yedK. Our results indicate that yedK has a strong preference for AP site-containing ssDNA over native ssDNA and that the conserved Glu105 residue is important for identifying AP sites in ssDNA. Moreover, our results reveal that a thiazolidine linkage is formed between yedK and AP sites in ssDNA, with the residues that stabilize the thiazolidine linkage important for the formation of DNA-protein crosslinks between yedK and the AP sites. We propose that our findings offer a unique platform to develop yedK and other SRAP domain-containing proteins as tools for detecting abasic sites in vitro and in vivo.
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Affiliation(s)
- Na Wang
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Hongyu Bao
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Liu Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yanhong Liu
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yue Li
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Baixing Wu
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Hongda Huang
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
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43
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Affiliation(s)
- Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry and Sauvage Center for Molecular Sciences, Wuhan University, Wuhan 430072, P.R. China
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Hocek M. Enzymatic Synthesis of Base-Functionalized Nucleic Acids for Sensing, Cross-linking, and Modulation of Protein-DNA Binding and Transcription. Acc Chem Res 2019; 52:1730-1737. [PMID: 31181911 DOI: 10.1021/acs.accounts.9b00195] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein-DNA interactions are important in replication, transcription, repair, as well as epigenetic modifications of DNA, which involve methylation and demethylation of DNA resulting in regulation of gene expression. Understanding of these processes and chemical tools for studying and perhaps even modulating them could be of great relevance and importance not only in chemical biology but also in real diagnostics and treatment of diseases. In the past decade, we have been working on development of synthesis of base-modified 2'-deoxyribo- or ribonucleoside triphosphates (dNTPs or NTPs) and their use in enzymatic synthesis of modified nucleic acids using DNA or RNA polymerases. These synthetic and enzymatic methods are briefly summarized with focus on recent development and outlining of scope, limitations, and further challenges. The main focus of this Account is on applications of base-modified nucleic acids in sensing of protein-DNA interactions, in covalent cross-linking to DNA-binding proteins ,and in modulation of protein-DNA binding and transcription. Several environment-sensitive fluorescent nucleotides were incorporated to DNA probes which responded to protein binding by light-up, changing of color, or lifetime of fluorescence. Using a cyclodextrin-peptide transporter, fluorescent nucleotides can be transported through the cell membrane and incorporated to genomic DNA. Several dNTPs bearing reactive groups (i.e., vinylsulfonamide or chloroacetamide) were used for polymerase synthesis of DNA reactive probes which cross-link to Cys, His, or Lys in peptides or proteins. An attractive challenge is to use DNA modifications and bioorthogonal reactions in the major groove of DNA for modulation and switching of protein-DNA interactions. We have systematically explored the influence of major-groove modifications on recognition and cleavage of DNA by restriction endonucleases and constructed simple chemical switches of DNA cleavage. Systematic study of the influence of major-groove modifications on transcription with bacterial RNA polymerases revealed not only that some modified bases are tolerated, but also that the presence of 5-hydroxymethyluracil or -cytosine can even enhance the transcription (350 or 250% compared to native DNA). Based on these results, we have constructed the first chemical switch of transcription based on photocaging of hydroxymethylpyrimidines in DNA by 2-nitrobenzyl protection (transcription off), photochemical deprotection of the DNA (transcription on), and enzymatic phosphorylation (only for 5-hydroxymethyluracil, transcription off). Although it has been so far demonstrated only in vitro, it is the proof-of-principle first step toward chemical epigenetics.
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Affiliation(s)
- Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
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