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Motorin Y, Helm M. General Principles and Limitations for Detection of RNA Modifications by Sequencing. Acc Chem Res 2024; 57:275-288. [PMID: 38065564 PMCID: PMC10851944 DOI: 10.1021/acs.accounts.3c00529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 02/07/2024]
Abstract
Among the many analytical methods applied to RNA modifications, a particularly pronounced surge has occurred in the past decade in the field of modification mapping. The occurrence of modifications such as m6A in mRNA, albeit known since the 1980s, became amenable to transcriptome-wide analyses through the advent of next-generation sequencing techniques in a rather sudden manner. The term "mapping" here refers to detection of RNA modifications in a sequence context, which has a dramatic impact on the interpretation of biological functions. As a consequence, an impressive number of mapping techniques were published, most in the perspective of what now has become known as "epitranscriptomics". While more and more different modifications were reported to occur in mRNA, conflicting reports and controversial results pointed to a number of technical and theoretical problems rooted in analytics, statistics, and reagents. Rather than finding the proverbial needle in a haystack, the tasks were to determine how many needles of what color in what size of a haystack one was looking at.As the authors of this Account, we think it important to outline the limitations of different mapping methods since many life scientists freshly entering the field confuse the accuracy and precision of modification mapping with that of normal sequencing, which already features numerous caveats by itself. Indeed, we propose here to qualify a specific mapping method by the size of the transcriptome that can be meaningfully analyzed with it.We here focus on high throughput sequencing by Illumina technology, referred to as RNA-Seq. We noted with interest the development of methods for modification detection by other high throughput sequencing platforms that act directly on RNA, e.g., PacBio SMRT and nanopore sequencing, but those are not considered here.In contrast to approaches relying on direct RNA sequencing, current Illumina RNA-Seq protocols require prior conversion of RNA into DNA. This conversion relies on reverse transcription (RT) to create cDNA; thereafter, the cDNA undergoes a sequencing-by-synthesis type of analysis. Thus, a particular behavior of RNA modified nucleotides during the RT-step is a prerequisite for their detection (and quantification) by deep sequencing, and RT properties have great influence on the detection efficiency and reliability. Moreover, the RT-step requires annealing of a synthetic primer, a prerequisite with a crucial impact on library preparation. Thus, all RNA-Seq protocols must feature steps for the introduction of primers, primer landing sites, or adapters on both the RNA 3'- and 5'-ends.
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Affiliation(s)
- Yuri Motorin
- Université
de Lorraine, UMR7365 IMoPA CNRS-UL
and UAR2008/US40 IBSLor CNRS-Inserm, Biopole UL, Nancy F54000, France
| | - Mark Helm
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, Germany
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2
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D’Ambrosi S, García-Vílchez R, Kedra D, Vitali P, Macias-Cámara N, Bárcena L, Gonzalez-Lopez M, Aransay AM, Dietmann S, Hurtado A, Blanco S. Global and single-nucleotide resolution detection of 7-methylguanosine in RNA. RNA Biol 2024; 21:1-18. [PMID: 38566310 PMCID: PMC10993922 DOI: 10.1080/15476286.2024.2337493] [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] [Accepted: 03/27/2024] [Indexed: 04/04/2024] Open
Abstract
RNA modifications, including N-7-methylguanosine (m7G), are pivotal in governing RNA stability and gene expression regulation. The accurate detection of internal m7G modifications is of paramount significance, given recent associations between altered m7G deposition and elevated expression of the methyltransferase METTL1 in various human cancers. The development of robust m7G detection techniques has posed a significant challenge in the field of epitranscriptomics. In this study, we introduce two methodologies for the global and accurate identification of m7G modifications in human RNA. We introduce borohydride reduction sequencing (Bo-Seq), which provides base resolution mapping of m7G modifications. Bo-Seq achieves exceptional performance through the optimization of RNA depurination and scission, involving the strategic use of high concentrations of NaBH4, neutral pH and the addition of 7-methylguanosine monophosphate (m7GMP) during the reducing reaction. Notably, compared to NaBH4-based methods, Bo-Seq enhances the m7G detection performance, and simplifies the detection process, eliminating the necessity for intricate chemical steps and reducing the protocol duration. In addition, we present an antibody-based approach, which enables the assessment of m7G relative levels across RNA molecules and biological samples, however it should be used with caution due to limitations associated with variations in antibody quality between batches. In summary, our novel approaches address the pressing need for reliable and accessible methods to detect RNA m7G methylation in human cells. These advancements hold the potential to catalyse future investigations in the critical field of epitranscriptomics, shedding light on the complex regulatory roles of m7G in gene expression and its implications in cancer biology.
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Affiliation(s)
- Silvia D’Ambrosi
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Raquel García-Vílchez
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Salamanca, Spain
| | - Darek Kedra
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, Salamanca, Spain
| | - Patrice Vitali
- Molecular, Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Nuria Macias-Cámara
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Laura Bárcena
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Monika Gonzalez-Lopez
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Ana M. Aransay
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Sabine Dietmann
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Antonio Hurtado
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, Salamanca, Spain
| | - Sandra Blanco
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Salamanca, Spain
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3
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Ghasemi M, Debnath PC, Kim B, Pournoury M, Khazaeinezhad R, Hosseinzadeh Kassani S, Yeom DI, Oh K. Highly nonlinear optic nucleic acid thin-solid film to generate short pulse laser. Sci Rep 2023; 13:17494. [PMID: 37840076 PMCID: PMC10577146 DOI: 10.1038/s41598-023-44242-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/05/2023] [Indexed: 10/17/2023] Open
Abstract
Using aqueous precursors, we report successfully fabricating thin-solid films of two nucleic acids, ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). We investigated the potential of these films deposited on a fiber optic platform as all-fiber integrated saturable absorbers (SAs) for ultrafast nonlinear optics. RNA-SA performances were comparable to those of DNA-SA in terms of its nonlinear transmission, modulation depth, and saturation intensity. Upon insertion of these devices into an Erbium-doped fiber ring-laser cavity, both RNA and DNA SAs enabled efficient passive Q-switching operation. RNA-SA application further facilitated robust mode-locking and generated a transform-limited soliton pulse, exhibiting a pulse duration of 633 femtoseconds. A detailed analysis of these pulsed laser characteristics compared RNA and DNA fiber optic SAs with other nonlinear optic materials. The findings of this research establish the feasibility of utilizing RNA as a saturable absorber in ultrafast laser systems with an equal or higher potential as DNA, which presents novel possibilities for the nonlinear photonic applications of nucleic acid thin solid films.
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Affiliation(s)
- Marjan Ghasemi
- Photonic Device Physics Laboratory, Department of Physics, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 120-749, South Korea
| | - Pulak Chandra Debnath
- Department of Physics and Energy Systems Research, Ajou University, Suwon, 443-749, South Korea
| | - Byungjoo Kim
- Department of Laser and Electron Beam Technologies, Korea Institute of Machinery and Materials (KIMM), 156, Gajeongbuk-ro, Yuseong-gu, Daejeon, 34103, Republic of Korea
| | - Marzieh Pournoury
- Department of Electrical and Electronic Engineering, Yonsei University, Seoul, 03722, South Korea
| | - Reza Khazaeinezhad
- Beckman Laser Institute, University of California, Irvine, Irvine, CA, 92697, USA
| | | | - Dong-Il Yeom
- Department of Physics and Energy Systems Research, Ajou University, Suwon, 443-749, South Korea
| | - Kyunghwan Oh
- Photonic Device Physics Laboratory, Department of Physics, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 120-749, South Korea.
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4
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Du D, He J, Ju C, Wang C, Li H, He F, Zhou M. When N7-methyladenosine modification meets cancer: Emerging frontiers and promising therapeutic opportunities. Cancer Lett 2023; 562:216165. [PMID: 37028699 DOI: 10.1016/j.canlet.2023.216165] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/22/2023] [Accepted: 04/01/2023] [Indexed: 04/08/2023]
Abstract
N7-methylguanosine (m7G) methylation, one of the most common RNA modifications in eukaryotes, has recently gained considerable attention. The biological functions of m7G modification in RNAs, including tRNA, rRNA, mRNA, and miRNA, remain largely unknown in human diseases. Owing to rapid advances in high-throughput technologies, increasing evidence suggests that m7G modification plays a critical role in cancer initiation and progression. As m7G modification and hallmarks of cancer are inextricably linked together, targeting m7G regulators may provide new possibilities for future cancer diagnoses and potential intervention targets. This review summarizes various detection methods for m7G modification, recent advances in m7G modification and tumor biology regarding their interplay and regulatory mechanisms. We conclude with an outlook on the future of diagnosing and treating m7G-related diseases.
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5
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Chen Y, Zhang Y, Wang B, Fan Q, Yang Q, Xu J, Dai H, Xu F, Wang C. Blood Clot Scaffold Loaded with Liposome Vaccine and siRNAs Targeting PD-L1 and TIM-3 for Effective DC Activation and Cancer Immunotherapy. ACS NANO 2023; 17:760-774. [PMID: 36520665 DOI: 10.1021/acsnano.2c10797] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Tumor vaccines have been showing a relatively weak response rate in cancer patients, while deficiencies in delivery efficiency to dendritic cells (DCs), as well as DC-intrinsic immunosuppressive signals, contribute to a great extent. In this work, we report an implantable blood clot loaded with liposomes-protamine-hyaluronic acid nanoparticles (LPH NPs) containing vaccine (LPH-vaccine) and LPH NPs containing siRNA (LPH-siRNA) for synergistic DC recruitment and activation. The subcutaneously implanted blood clot scaffold can recruit abundant immune cells, particularly DCs, to form a DC-rich environment in vivo. Within the scaffold, LPH-vaccine effectively delivers antigens and adjuvants to the recruited DCs and induces the maturation of DCs. More importantly, LPH-siRNA that targets programmed death-ligand 1 (PD-L1) and T cell immunoglobulin and mucin-containing molecule 3 (TIM-3) can reduce immunosuppressive signals in mature DCs and prevent the DCs from expressing a regulatory program in the scaffold. The activated DCs correlate with an improved magnitude and efficacy of T cell priming, resulting in the production of tumor antigen-specific T cells in multiple mouse models. Our strategy can also be used for patient-tailored therapy by change of tumor neoantigens, suggesting a promising strategy for cancer therapy in the clinic.
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Affiliation(s)
- Yitong Chen
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu215123, China
| | - Yue Zhang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu215123, China
| | - Beilei Wang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu215123, China
| | - Qin Fan
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing210023, China
| | - Qianyu Yang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu215123, China
| | - Jialu Xu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu215123, China
| | - Huaxing Dai
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu215123, China
| | - Fang Xu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu215123, China
| | - Chao Wang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu215123, China
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6
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Watts JA, Grunseich C, Rodriguez Y, Liu Y, Li D, Burdick J, Bruzel A, Crouch RJ, Mahley RW, Wilson S, Cheung V. A common transcriptional mechanism involving R-loop and RNA abasic site regulates an enhancer RNA of APOE. Nucleic Acids Res 2022; 50:12497-12514. [PMID: 36453989 PMCID: PMC9757052 DOI: 10.1093/nar/gkac1107] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/30/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022] Open
Abstract
RNA is modified by hundreds of chemical reactions and folds into innumerable shapes. However, the regulatory role of RNA sequence and structure and how dysregulation leads to diseases remain largely unknown. Here, we uncovered a mechanism where RNA abasic sites in R-loops regulate transcription by pausing RNA polymerase II. We found an enhancer RNA, AANCR, that regulates the transcription and expression of apolipoprotein E (APOE). In some human cells such as fibroblasts, AANCR is folded into an R-loop and modified by N-glycosidic cleavage; in this form, AANCR is a partially transcribed nonfunctional enhancer and APOE is not expressed. In contrast, in other cell types including hepatocytes and under stress, AANCR does not form a stable R-loop as its sequence is not modified, so it is transcribed into a full-length enhancer that promotes APOE expression. DNA sequence variants in AANCR are associated significantly with APOE expression and Alzheimer's Disease, thus AANCR is a modifier of Alzheimer's Disease. Besides AANCR, thousands of noncoding RNAs are regulated by abasic sites in R-loops. Together our data reveal the essentiality of the folding and modification of RNA in cellular regulation and demonstrate that dysregulation underlies common complex diseases such as Alzheimer's disease.
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Affiliation(s)
- Jason A Watts
- Department of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Epigenetics and Stem Cell Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Christopher Grunseich
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yesenia Rodriguez
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Yaojuan Liu
- Department of Pediatrics and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dongjun Li
- Department of Pediatrics and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Joshua T Burdick
- Department of Pediatrics and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alan Bruzel
- Department of Pediatrics and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robert J Crouch
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert W Mahley
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Departments of Pathology and Medicine, University of California, San Francisco, CA, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Vivian G Cheung
- Department of Pediatrics and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
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7
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Hauf S, Rotrattanadumrong R, Yokobayashi Y. Analysis of the Sequence Preference of Saporin by Deep Sequencing. ACS Chem Biol 2022; 17:2619-2630. [PMID: 35969718 PMCID: PMC9486812 DOI: 10.1021/acschembio.2c00531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/29/2022] [Indexed: 01/19/2023]
Abstract
Ribosome-inactivating proteins (RIPs) are RNA:adenosine glycosidases that inactivate eukaryotic ribosomes by depurinating the sarcin-ricin loop (SRL) in 28S rRNA. The GAGA sequence at the top of the SRL or at the top of a hairpin loop is assumed to be their target motif. Saporin is a RIP widely used to develop immunotoxins for research and medical applications, but its sequence specificity has not been investigated. Here, we combine the conventional aniline cleavage assay for depurinated nucleic acids with high-throughput sequencing to study sequence-specific depurination of oligonucleotides caused by saporin. Our data reveal the sequence preference of saporin for different substrates and show that the GAGA motif is not efficiently targeted by this protein, neither in RNA nor in DNA. Instead, a preference of saporin for certain hairpin DNAs was observed. The observed sequence-specific activity of saporin may be relevant to antiviral or apoptosis-inducing effects of RIPs. The developed method could also be useful for studying the sequence specificity of depurination by other RIPs or enzymes.
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Affiliation(s)
- Samuel Hauf
- Nucleic Acid Chemistry and
Engineering Unit, Okinawa Institute of Science
and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Rachapun Rotrattanadumrong
- Nucleic Acid Chemistry and
Engineering Unit, Okinawa Institute of Science
and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and
Engineering Unit, Okinawa Institute of Science
and Technology Graduate University, Onna, Okinawa 904-0495, Japan
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8
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Zhao J, Gong Y. Amiloride-modulated phosphorescence turn-off/on method for the detection of abasic site-containing dsRNA based on uridine triphosphate-capped Mn-doped ZnS quantum dots. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104050] [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] Open
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9
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Cong D, Li Y, Ludford PT, Tor Y. Isomorphic Fluorescent Nucleosides Facilitate Real-Time Monitoring of RNA Depurination by Ribosome Inactivating Proteins. Chemistry 2022; 28:e202200994. [PMID: 35390188 PMCID: PMC9233005 DOI: 10.1002/chem.202200994] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Indexed: 09/07/2024]
Abstract
Ribosome-inactivating proteins, a family of highly cytotoxic proteins, interfere with protein synthesis by depurinating a specific adenosine residue within the conserved α-sarcin/ricin loop of eukaryotic ribosomal RNA. Besides being biological warfare agents, certain RIPs have been promoted as potential therapeutic tools. Monitoring their deglycosylation activity and their inhibition in real time have remained, however, elusive. Herein, we describe the enzymatic preparation and utility of consensus RIP hairpin substrates in which specific G residues, next to the depurination site, are surgically replaced with tz G and th G, fluorescent G analogs. By strategically modifying key positions with responsive fluorescent surrogate nucleotides, RIP-mediated depurination can be monitored in real time by steady-state fluorescence spectroscopy. Subtle differences observed in preferential depurination sites provide insight into the RNA folding as well as RIPs' substrate recognition features.
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Affiliation(s)
- Deyuan Cong
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Yao Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Paul T Ludford
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
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10
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Owens MC, Zhang C, Liu KF. Recent technical advances in the study of nucleic acid modifications. Mol Cell 2021; 81:4116-4136. [PMID: 34480848 PMCID: PMC9109655 DOI: 10.1016/j.molcel.2021.07.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/20/2021] [Accepted: 07/28/2021] [Indexed: 12/30/2022]
Abstract
Enzyme-mediated chemical modifications of nucleic acids are indispensable regulators of gene expression. Our understanding of the biochemistry and biological significance of these modifications has largely been driven by an ever-evolving landscape of technologies that enable accurate detection, mapping, and manipulation of these marks. Here we provide a summary of recent technical advances in the study of nucleic acid modifications with a focus on techniques that allow accurate detection and mapping of these modifications. For each modification discussed (N6-methyladenosine, 5-methylcytidine, inosine, pseudouridine, and N4-acetylcytidine), we begin by introducing the "gold standard" technique for its mapping and detection, followed by a discussion of techniques developed to address any shortcomings of the gold standard. By highlighting the commonalities and differences of these techniques, we hope to provide a perspective on the current state of the field and to lay out a guideline for development of future technologies.
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Affiliation(s)
- Michael C Owens
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Celia Zhang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathy Fange Liu
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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11
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Bartee D, Thalalla Gamage S, Link CN, Meier JL. Arrow pushing in RNA modification sequencing. Chem Soc Rev 2021; 50:9482-9502. [PMID: 34259263 DOI: 10.1039/d1cs00214g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Methods to accurately determine the location and abundance of RNA modifications are critical to understanding their functional role. In this review, we describe recent efforts in which chemical reactivity and next-generation sequencing have been integrated to detect modified nucleotides in RNA. For eleven exemplary modifications, we detail chemical, enzymatic, and metabolic labeling protocols that can be used to differentiate them from canonical nucleobases. By emphasizing the molecular rationale underlying these detection methods, our survey highlights new opportunities for chemistry to define the role of RNA modifications in disease.
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Affiliation(s)
- David Bartee
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 538 Chandler St, Frederick, MD 21702, USA.
| | - Supuni Thalalla Gamage
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 538 Chandler St, Frederick, MD 21702, USA.
| | - Courtney N Link
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 538 Chandler St, Frederick, MD 21702, USA.
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 538 Chandler St, Frederick, MD 21702, USA.
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12
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Marchand V, Bourguignon-Igel V, Helm M, Motorin Y. Mapping of 7-methylguanosine (m 7G), 3-methylcytidine (m 3C), dihydrouridine (D) and 5-hydroxycytidine (ho 5C) RNA modifications by AlkAniline-Seq. Methods Enzymol 2021; 658:25-47. [PMID: 34517949 DOI: 10.1016/bs.mie.2021.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Precise and reliable mapping of modified nucleotides in RNA is a challenging task in epitranscriptomics analysis. Only deep sequencing-based methods are able to provide both, a single-nucleotide resolution and sufficient selectivity and sensitivity. A number of protocols employing specific chemical reagents to distinguish modified RNA nucleotides from canonical parental residues have already proven their performance. We developed a deep-sequencing analytical pipeline for simultaneous detection of several modified nucleotides of different nature (methylation, hydroxylation, reduction) in RNA. The AlkAniline-Seq protocol uses intrinsic fragility of the N-glycosidic bond present in certain modified residues (7-methylguanosine (m7G), 3-methylcytidine (m3C), dihydrouridine (D) and 5-hydroxycytidine (ho5C)) to induce cleavage under heat combined with alkaline conditions. The resulting RNA abasic site is decomposed by aniline-driven β-elimination and creates a 5'-phosphate (5'-P) at the adjacent N+1 residue. This 5'-P is the crucial entry point for a highly selective ligation of sequencing adapters during the subsequent Illumina library preparation protocol. AlkAniline-Seq protocol has a very low background, and is both highly sensitive and specific. Applications of AlkAniline-Seq include mapping of m7G, m3C, D, and ho5C in variety of cellular RNAs, including in particular rRNAs and tRNAs.
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Affiliation(s)
- Virginie Marchand
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core facility, Nancy, France
| | - Valérie Bourguignon-Igel
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core facility, Nancy, France; Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, France
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Mainz, Germany
| | - Yuri Motorin
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core facility, Nancy, France; Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, France.
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13
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Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker. Comput Struct Biotechnol J 2021; 19:3293-3302. [PMID: 34188778 PMCID: PMC8207216 DOI: 10.1016/j.csbj.2021.05.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/14/2021] [Accepted: 05/20/2021] [Indexed: 12/18/2022] Open
Abstract
Ribonucleotides (rNTPs) are predicted to be incorporated into the genome at a rate of up to 3 million times per cell division, making rNTPs the most common non-standard nucleotide in the human genome. Typically, misinserted ribonucleotides are repaired by the ribonucleotide excision repair (RER) pathway, which is initiated by RNase H2 cleavage. However, rNTPs are susceptible to spontaneous depurination generating abasic ribonucleotides (rAPs), which are unable to be processed by RNase H2. Additionally, rAPs have been found in nascent RNA and coupled to R-loops. Recent work identified that base excision repair (BER) protein AP-Endonuclease 1 (APE1) is responsible for the initial processing of rAPs embedded in DNA and in R-loops. APE1 is a well characterized AP endonuclease that cleaves 5' of abasic sites, but its ability to cleave at rAPs remains poorly understood. Here, we utilize enzyme kinetics, X-ray crystallography, and molecular dynamics simulations to provide insight into rAP processing by APE1. Enzyme kinetics were used to determine pre-steady-state rates of APE1 cleavage on DNA substrates containing rAP, revealing a decrease in activity compared to cleavage at a canonical deoxy-AP substrate. Using X-ray crystallography, we identified novel contacts between the rAP and the APE1 active site. We demonstrate that the rAP sugar pucker is accommodated in the active site in a C3'-endo conformation, influencing its position and contributing to a decrease in activity compared to the deoxy-AP site. Together, this work provides molecular level insights into rAP processing by APE1 and advances our understanding of ribonucleotide processing within genomic DNA.
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14
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Tanaka M, Chock PB. Oxidative Modifications of RNA and Its Potential Roles in Biosystem. Front Mol Biosci 2021; 8:685331. [PMID: 34055897 PMCID: PMC8149912 DOI: 10.3389/fmolb.2021.685331] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
Elevated level of oxidized RNA was detected in vulnerable neurons in Alzheimer patients. Subsequently, several diseases and pathological conditions were reported to be associated with RNA oxidation. In addition to several oxidized derivatives, cross-linking and unique strand breaks are generated by RNA oxidation. With a premise that dysfunctional RNA mediated by oxidation is the pathogenetic molecular mechanism, intensive investigations have revealed the mechanism for translation errors, including premature termination, which gives rise to aberrant polypeptides. To this end, we and others revealed that mRNA oxidation could compromise its translational activity and fidelity. Under certain conditions, oxidized RNA can also induce several signaling pathways, to mediate inflammatory response and induce apoptosis. In this review, we focus on the oxidative modification of RNA and its resulting effect on protein synthesis as well as cell signaling. In addition, we will also discuss the potential roles of enzymatic oxidative modification of RNA in mediating cellular effects.
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Affiliation(s)
- Mikiei Tanaka
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - P Boon Chock
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
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15
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Cao J, Shu X, Feng XH, Liu J. Mapping messenger RNA methylations at single base resolution. Curr Opin Chem Biol 2021; 63:28-37. [PMID: 33684855 DOI: 10.1016/j.cbpa.2021.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 01/14/2021] [Accepted: 02/01/2021] [Indexed: 12/29/2022]
Abstract
The messenger RNA (mRNA) methylations in mammalian cells have been found to contain N6-methyladenosine (m6A), N6-2'-O-dimethyladenosine (m6Am), 7-methylguanosine (m7G), 1-methyladenosine (m1A), 5-methylcytosine (m5C), and 2'-O-methylation (2'-OMe). Their regulatory functions in control of mRNA fate and gene expression are being increasingly uncovered. To unambiguously understand the critical roles of mRNA methylations in physiological and pathological processes, mapping these methylations at single base resolution is highly required. Here, we will review the progresses made in methylation sequencing methodologies developed mainly in recent two years, with an emphasis on chemical labeling-assisted single base resolution methods, and discuss the problems and prospects as well.
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Affiliation(s)
- Jie Cao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Xiao Shu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Xin-Hua Feng
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jianzhao Liu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China; Life Sciences Institute, Zhejiang University, Hangzhou, China.
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16
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Pourshahian S. THERAPEUTIC OLIGONUCLEOTIDES, IMPURITIES, DEGRADANTS, AND THEIR CHARACTERIZATION BY MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:75-109. [PMID: 31840864 DOI: 10.1002/mas.21615] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Oligonucleotides are an emerging class of drugs that are manufactured by solid-phase synthesis. As a chemical class, they have unique product-related impurities and degradants, characterization of which is an essential step in drug development. The synthesis cycle, impurities produced during the synthesis and degradation products are presented and discussed. The use of liquid chromatography combined with mass spectrometry for characterization and quantification of product-related impurities and degradants is reviewed. In addition, sequence determination of oligonucleotides by gas-phase fragmentation and indirect mass spectrometric methods is discussed. © 2019 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Soheil Pourshahian
- Janssen Pharmaceutical Companies of Johnson & Johnson, South San Francisco, CA, 94080
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17
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Catalytic mechanism of the mismatch-specific DNA glycosylase methyl-CpG-binding domain 4. Biochem J 2020; 477:1601-1612. [PMID: 32297632 DOI: 10.1042/bcj20200125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 12/15/2022]
Abstract
Thymine:guanine base pairs are major promutagenic mismatches occurring in DNA metabolism. If left unrepaired, these mispairs can cause C to T transition mutations. In humans, T:G mismatches are repaired in part by mismatch-specific DNA glycosylases such as methyl-CpG-binding domain 4 (hMBD4) and thymine-DNA glycosylase. Unlike lesion-specific DNA glycosylases, T:G-mismatch-specific DNA glycosylases specifically recognize both bases of the mismatch and remove the thymine but only from mispairs with guanine. Despite the advances in biochemical and structural characterizations of hMBD4, the catalytic mechanism of hMBD4 remains elusive. Herein, we report two structures of hMBD4 processing T:G-mismatched DNA. A high-resolution crystal structure of Asp560Asn hMBD4-T:G complex suggests that hMBD4-mediated glycosidic bond cleavage occurs via a general base catalysis mechanism assisted by Asp560. A structure of wild-type hMBD4 encountering T:G-containing DNA shows the generation of an apurinic/apyrimidinic (AP) site bearing the C1'-(S)-OH. The inversion of the stereochemistry at the C1' of the AP-site indicates that a nucleophilic water molecule approaches from the back of the thymine substrate, suggesting a bimolecular displacement mechanism (SN2) for hMBD4-catalyzed thymine excision. The AP-site is stabilized by an extensive hydrogen bond network in the MBD4 catalytic site, highlighting the role of MBD4 in protecting the genotoxic AP-site.
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18
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Marchand V, Pichot F, Neybecker P, Ayadi L, Bourguignon-Igel V, Wacheul L, Lafontaine DLJ, Pinzano A, Helm M, Motorin Y. HydraPsiSeq: a method for systematic and quantitative mapping of pseudouridines in RNA. Nucleic Acids Res 2020; 48:e110. [PMID: 32976574 PMCID: PMC7641733 DOI: 10.1093/nar/gkaa769] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/02/2020] [Accepted: 09/06/2020] [Indexed: 12/16/2022] Open
Abstract
Developing methods for accurate detection of RNA modifications remains a major challenge in epitranscriptomics. Next-generation sequencing-based mapping approaches have recently emerged but, often, they are not quantitative and lack specificity. Pseudouridine (ψ), produced by uridine isomerization, is one of the most abundant RNA modification. ψ mapping classically involves derivatization with soluble carbodiimide (CMCT), which is prone to variation making this approach only semi-quantitative. Here, we developed 'HydraPsiSeq', a novel quantitative ψ mapping technique relying on specific protection from hydrazine/aniline cleavage. HydraPsiSeq is quantitative because the obtained signal directly reflects pseudouridine level. Furthermore, normalization to natural unmodified RNA and/or to synthetic in vitro transcripts allows absolute measurements of modification levels. HydraPsiSeq requires minute amounts of RNA (as low as 10-50 ng), making it compatible with high-throughput profiling of diverse biological and clinical samples. Exploring the potential of HydraPsiSeq, we profiled human rRNAs, revealing strong variations in pseudouridylation levels at ∼20-25 positions out of total 104 sites. We also observed the dynamics of rRNA pseudouridylation throughout chondrogenic differentiation of human bone marrow stem cells. In conclusion, HydraPsiSeq is a robust approach for the systematic mapping and accurate quantification of pseudouridines in RNAs with applications in disease, aging, development, differentiation and/or stress response.
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Affiliation(s)
- Virginie Marchand
- Université de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
| | - Florian Pichot
- Université de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
- Institute of Pharmaceutical and Biomedical Science, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Paul Neybecker
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
| | - Lilia Ayadi
- Université de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
| | - Valérie Bourguignon-Igel
- Université de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
| | - Ludivine Wacheul
- RNA Molecular Biology, ULB-Cancer Research Center (U-CRC), Center for Microscopy and Molecular Imaging (CMMI), Fonds de la Recherche Scientifique (F.R.S./FNRS), and Université Libre de Bruxelles (ULB), BioPark campus, B-6041 Gosselies, Belgium
| | - Denis L J Lafontaine
- RNA Molecular Biology, ULB-Cancer Research Center (U-CRC), Center for Microscopy and Molecular Imaging (CMMI), Fonds de la Recherche Scientifique (F.R.S./FNRS), and Université Libre de Bruxelles (ULB), BioPark campus, B-6041 Gosselies, Belgium
| | - Astrid Pinzano
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Science, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Yuri Motorin
- Université de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
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19
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Abstract
RNA abasic sites and the mechanisms involved in their regulation are mostly unknown; in contrast, DNA abasic sites are well-studied. We found surprisingly that, in yeast and human cells, RNA abasic sites are prevalent. When a base is lost from RNA, the remaining ribose is found as a closed-ring or an open-ring sugar with a reactive C1' aldehyde group. Using primary amine-based reagents that react with the aldehyde group, we uncovered evidence for abasic sites in nascent RNA, messenger RNA, and ribosomal RNA from yeast and human cells. Mass spectroscopic analysis confirmed the presence of RNA abasic sites. The RNA abasic sites were found to be coupled to R-loops. We show that human methylpurine DNA glycosylase cleaves N-glycosidic bonds on RNA and that human apurinic/apyrimidinic endonuclease 1 incises RNA abasic sites in RNA-DNA hybrids. Our results reveal that, in yeast and human cells, there are RNA abasic sites, and we identify a glycosylase that generates these sites and an AP endonuclease that processes them.
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20
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21
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Takeshita T, Kanaly RA. In vitro DNA/RNA Adductomics to Confirm DNA Damage Caused by Benzo[ a]pyrene in the Hep G2 Cell Line. Front Chem 2019; 7:491. [PMID: 31338364 PMCID: PMC6629907 DOI: 10.3389/fchem.2019.00491] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/25/2019] [Indexed: 11/13/2022] Open
Abstract
In the development of new chemical substances, genetic toxicity evaluations are a high priority for safety risk management. Evaluation of the possibility of compound carcinogenicity with accuracy and at reasonable cost in the early stages of development by in vitro techniques is preferred. Currently, DNA damage-related in vitro genotoxicity tests are widely-used screening tools after which next generation toxicity testing may be applied to confirm DNA damage. DNA adductomics may be used to evaluate DNA damage in vitro, however confirmation of DNA adduct identities through comparison to authentic standards may be time-consuming and expensive processes. Considering this, a streamlined method for confirming putative DNA adducts that are detected by DNA adductomics may be useful. With this aim, in vitro DNA adductome methods in conjunction with in vitro RNA adductome methods may be proposed as a DNA adductome verification approach by which to eliminate false positive annotations. Such an approach was evaluated by conducting in vitro assays whereby Hep G2 cell lines that were exposed to or not exposed to benzo[a]pyrene were digested to their respective 2'-deoxynucleosides or ribonucleosides and analyzed by liquid chromatography electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) by comparative DNA and RNA adductomics through neutral loss targeting of the [M + H]+ > [M + H - 116]+ or [M + H]+ > [M + H -132]+ transitions over predetermined ranges. Comparisons of DNA adductome maps revealed putative DNA adducts that were detected in exposed cells but not in unexposed cells. Similarly, comparisons of RNA adductome maps revealed putative RNA adducts in exposed cells but not in unexposed cells. Taken together these experiments revealed that analogous forms of putative damage had occurred in both DNA and RNA which supported that putative DNA adducts detected by DNA adductomics were DNA adducts. High resolution mass spectrometry (HRMS) was utilized to confirm that putative nucleic acid adducts detected in both DNA and RNA were derived from benzo[a]pyrene exposure and these putative adducts were identified as 7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene- (B[a]PDE)-type adducts. Overall, this study demonstrates the usefulness of utilizing DNA/RNA adductomics to screen for nucleic acid damage.
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Affiliation(s)
| | - Robert A. Kanaly
- Department of Life and Environmental System Science, Graduate School of Nanobiosciences, Yokohama City University, Yokohama, Japan
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22
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Mungi CV, Bapat NV, Hongo Y, Rajamani S. Formation of Abasic Oligomers in Nonenzymatic Polymerization of Canonical Nucleotides. Life (Basel) 2019; 9:E57. [PMID: 31277469 PMCID: PMC6789551 DOI: 10.3390/life9030057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/30/2019] [Accepted: 07/01/2019] [Indexed: 12/02/2022] Open
Abstract
Polymerization of nucleotides under prebiotically plausible conditions has been a focus of several origins of life studies. Non-activated nucleotides have been shown to undergo polymerization under geothermal conditions when subjected to dry-wet cycles. They do so by a mechanism similar to acid-catalyzed ester-bond formation. However, one study showed that the low pH of these reactions resulted in predominantly depurination, thereby resulting in the formation of abasic sites in the oligomers. In this study, we aimed to systematically characterize the nature of the oligomers that resulted in reactions that involved one or more of the canonical ribonucleotides. All the reactions analyzed showed the presence of abasic oligomers, with purine nucleotides being affected the most due to deglycosylation. Even in the reactions that contained nucleotide mixtures, the presence of abasic oligomers was detected, which suggested that information transfer would be severely hampered due to losing the capacity to base pair via H-bonds. Importantly, the stability of the N-glycosidic linkage, under conditions used for dry-wet cycling, was also determined. Results from this study further strengthen the hypothesis that chemical evolution in a pre-RNA World would have been vital for the evolution of informational molecules of an RNA World. This is evident in the high degree of instability displayed by N-glycosidic bonds of canonical purine ribonucleotides under the same geothermal conditions that otherwise readily favors polymerization. Significantly, the resultant product characterization in the reactions concerned underscores the difficulty associated with analyzing complex prebiotically relevant reactions due to inherent limitation of current analytical methods.
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Affiliation(s)
- Chaitanya V. Mungi
- Indian Institute of Science Education and Research (IISER), Pune 411008, Maharashtra, India
| | - Niraja V. Bapat
- Indian Institute of Science Education and Research (IISER), Pune 411008, Maharashtra, India
| | - Yayoi Hongo
- ELSI, Tokyo-Tech (Earth-Life Science Institute, Tokyo Institute of Technology), 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- OIST, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Okinawa 904-0412, Japan
| | - Sudha Rajamani
- Indian Institute of Science Education and Research (IISER), Pune 411008, Maharashtra, India
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23
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Zhang LS, Liu C, Ma H, Dai Q, Sun HL, Luo G, Zhang Z, Zhang L, Hu L, Dong X, He C. Transcriptome-wide Mapping of Internal N 7-Methylguanosine Methylome in Mammalian mRNA. Mol Cell 2019; 74:1304-1316.e8. [PMID: 31031084 DOI: 10.1016/j.molcel.2019.03.036] [Citation(s) in RCA: 269] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 02/26/2019] [Accepted: 03/27/2019] [Indexed: 01/05/2023]
Abstract
N7-methylguanosine (m7G) is a positively charged, essential modification at the 5' cap of eukaryotic mRNA, regulating mRNA export, translation, and splicing. m7G also occurs internally within tRNA and rRNA, but its existence and distribution within eukaryotic mRNA remain to be investigated. Here, we show the presence of internal m7G sites within mammalian mRNA. We then performed transcriptome-wide profiling of internal m7G methylome using m7G-MeRIP sequencing (MeRIP-seq). To map this modification at base resolution, we developed a chemical-assisted sequencing approach that selectively converts internal m7G sites into abasic sites, inducing misincorporation at these sites during reverse transcription. This base-resolution m7G-seq enabled transcriptome-wide mapping of m7G in human tRNA and mRNA, revealing distribution features of the internal m7G methylome in human cells. We also identified METTL1 as a methyltransferase that installs a subset of m7G within mRNA and showed that internal m7G methylation could affect mRNA translation.
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Affiliation(s)
- Li-Sheng Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Chang Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Honghui Ma
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Qing Dai
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Hui-Lung Sun
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Guanzheng Luo
- The State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510060, China
| | - Zijie Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Linda Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Lulu Hu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Xueyang Dong
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA.
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24
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Waduge P, Sakakibara Y, Chow CS. Chemical probing for examining the structure of modified RNAs and ligand binding to RNA. Methods 2019; 156:110-120. [DOI: 10.1016/j.ymeth.2018.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/04/2018] [Accepted: 10/22/2018] [Indexed: 12/15/2022] Open
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25
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Ochkasova AS, Meschaninova MI, Venyaminova AG, Ivanov AV, Graifer DM, Karpova GG. The human ribosome can interact with the abasic site in mRNA via a specific peptide of the uS3 protein located near the mRNA entry channel. Biochimie 2018; 158:117-125. [PMID: 30594661 DOI: 10.1016/j.biochi.2018.12.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 12/25/2018] [Indexed: 12/12/2022]
Abstract
The small subunit ribosomal protein uS3 is a critically important player in the ribosome-mRNA interactions during translation and has numerous functions not directly related to protein synthesis in eukaryotes. A peculiar feature of the human uS3 protein is the ability of its fragment 55-64 exposed on the 40S subunit surface near the mRNA entry channel to form cross-links with 3'-terminal dialdehyde derivatives of various unstructured RNAs and with abasic sites in single-stranded DNAs. Here we showed that the ability of the above uS3 fragment to cross-link to abasic sites in DNAs is inherent only in mature cytoplasmic 40S subunits, but not nuclear pre-40S particles, which implies that it may be relevant to the ribosome-mRNA interplay. To clarify this issue, we investigated interactions of human ribosomes with synthetic mRNA analogues bearing an abasic site protected by a photocleavable group at the 3'-termini. We found that these mRNA analogues can form specific complexes with 80S ribosomes and 40S subunits, where the undamaged upstream part of the analogue is fixed in the mRNA binding channel by interaction with the P-site tRNA, and the downstream part located outside the ribosome is cross-linked to the uS3 fragment 55-64. The yield of cross-links of the mRNA analogues was rather high when their undamaged parts were bound to the mRNA channel prior to deprotection of the abasic site enabling its covalent attachment to the 40S subunit via the uS3 protein, but not vice versa. Based on our findings, one can assume that abasic sites, which can occur in mRNAs due to oxidative stress and ageing, are able to interact directly with the uS3 fragment exposed on the 40S subunit surface near the mRNA entry channel during translation. Consequently, the 40S subunit can be considered as a potential mRNA quality controller.
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Affiliation(s)
- Anastasia S Ochkasova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Maria I Meschaninova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Aliya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Anton V Ivanov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Dmitri M Graifer
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Galina G Karpova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia.
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26
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Marchand V, Ayadi L, Ernst FGM, Hertler J, Bourguignon‐Igel V, Galvanin A, Kotter A, Helm M, Lafontaine DLJ, Motorin Y. AlkAniline‐Seq: Profiling of m
7
G and m
3
C RNA Modifications at Single Nucleotide Resolution. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Virginie Marchand
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Lilia Ayadi
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Felix G. M. Ernst
- RNA Molecular BiologyULB-Cancer Research Center (U-CRC)Center for Microscopy and Molecular Imaging (CMMI)Fonds de la Recherche Scientifique (FRS)Université Libre de Bruxelles (ULB) BioPark campus Gosselies Belgium
| | - Jasmin Hertler
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Valérie Bourguignon‐Igel
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Adeline Galvanin
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Annika Kotter
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Mark Helm
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Denis L. J. Lafontaine
- RNA Molecular BiologyULB-Cancer Research Center (U-CRC)Center for Microscopy and Molecular Imaging (CMMI)Fonds de la Recherche Scientifique (FRS)Université Libre de Bruxelles (ULB) BioPark campus Gosselies Belgium
| | - Yuri Motorin
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
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27
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Marchand V, Ayadi L, Ernst FGM, Hertler J, Bourguignon‐Igel V, Galvanin A, Kotter A, Helm M, Lafontaine DLJ, Motorin Y. AlkAniline‐Seq: Profiling of m
7
G and m
3
C RNA Modifications at Single Nucleotide Resolution. Angew Chem Int Ed Engl 2018; 57:16785-16790. [DOI: 10.1002/anie.201810946] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Virginie Marchand
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Lilia Ayadi
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Felix G. M. Ernst
- RNA Molecular BiologyULB-Cancer Research Center (U-CRC)Center for Microscopy and Molecular Imaging (CMMI)Fonds de la Recherche Scientifique (FRS)Université Libre de Bruxelles (ULB) BioPark campus Gosselies Belgium
| | - Jasmin Hertler
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Valérie Bourguignon‐Igel
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Adeline Galvanin
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Annika Kotter
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Mark Helm
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Denis L. J. Lafontaine
- RNA Molecular BiologyULB-Cancer Research Center (U-CRC)Center for Microscopy and Molecular Imaging (CMMI)Fonds de la Recherche Scientifique (FRS)Université Libre de Bruxelles (ULB) BioPark campus Gosselies Belgium
| | - Yuri Motorin
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
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28
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Liu X, Chen Y, Fierke CA. Inner-Sphere Coordination of Divalent Metal Ion with Nucleobase in Catalytic RNA. J Am Chem Soc 2017; 139:17457-17463. [PMID: 29116782 PMCID: PMC6020041 DOI: 10.1021/jacs.7b08755] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Identification of the function of metal ions and the RNA moieties, particularly nucleobases, that bind metal ions is important in RNA catalysis. Here we combine single-atom and abasic substitutions to probe functions of conserved nucleobases in ribonuclease P (RNase P). Structural and biophysical studies of bacterial RNase P propose direct coordination of metal ions by the nucleobases of conserved uridine and guanosine in helix P4 of the RNA subunit (P RNA). To biochemically probe the function of metal ion interactions, we substituted the universally conserved bulged uridine (U51) in the P4 helix of circularly permuted Bacillus subtilis P RNA with 4-thiouridine, 4-deoxyuridine, and abasic modifications and G378/379 with 2-aminopurine, N7-deazaguanosine, and 6-thioguanosine. The functional group modifications of U51 decrease RNase P-catalyzed phosphodiester bond cleavage 16- to 23-fold, as measured by the single-turnover cleavage rate constant. The activity of the 4-thiouridine RNase P is partially rescued by addition of Cd(II) or Mn(II) ions. This is the first time a metal-rescue experiment provides evidence for inner-sphere divalent metal ion coordination with a nucleobase. Modifications of G379 modestly decrease the cleavage activity of RNase P, suggesting outer-sphere coordination of O6 on G379 to a metal ion. These data provide biochemical evidence for catalytically important interactions of the P4 helix of P RNA with metal ions, demonstrating that the bulged uridine coordinates at least one catalytic metal ion through an inner-sphere interaction. The combination of single-atom and abasic nucleotide substitutions provides a powerful strategy to probe functions of conserved nucleobases in large RNAs.
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Affiliation(s)
- Xin Liu
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Yu Chen
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Carol A. Fierke
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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29
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Malfatti MC, Balachander S, Antoniali G, Koh KD, Saint-Pierre C, Gasparutto D, Chon H, Crouch RJ, Storici F, Tell G. Abasic and oxidized ribonucleotides embedded in DNA are processed by human APE1 and not by RNase H2. Nucleic Acids Res 2017; 45:11193-11212. [PMID: 28977421 PMCID: PMC5737539 DOI: 10.1093/nar/gkx723] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 08/11/2017] [Indexed: 12/13/2022] Open
Abstract
Ribonucleoside 5′-monophosphates (rNMPs) are the most common non-standard nucleotides found in DNA of eukaryotic cells, with over 100 million rNMPs transiently incorporated in the mammalian genome per cell cycle. Human ribonuclease (RNase) H2 is the principal enzyme able to cleave rNMPs in DNA. Whether RNase H2 may process abasic or oxidized rNMPs incorporated in DNA is unknown. The base excision repair (BER) pathway is mainly responsible for repairing oxidized and abasic sites into DNA. Here we show that human RNase H2 is unable to process an abasic rNMP (rAP site) or a ribose 8oxoG (r8oxoG) site embedded in DNA. On the contrary, we found that recombinant purified human apurinic/apyrimidinic endonuclease-1 (APE1) and APE1 from human cell extracts efficiently process an rAP site in DNA and have weak endoribonuclease and 3′-exonuclease activities on r8oxoG substrate. Using biochemical assays, our results provide evidence of a human enzyme able to recognize and process abasic and oxidized ribonucleotides embedded in DNA.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, Udine, Italy
| | - Sathya Balachander
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, Udine, Italy
| | - Kyung Duk Koh
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,University of California, San Francisco, UCSF, School of Medicine, San Francisco, CA, USA
| | - Christine Saint-Pierre
- Chimie Reconnaissance & Etude Assemblages Biologiques, Université Grenoble Alpes, SPrAM UMR5819 CEA CNRS UGA, INAC/CEA, Grenoble, France
| | - Didier Gasparutto
- Chimie Reconnaissance & Etude Assemblages Biologiques, Université Grenoble Alpes, SPrAM UMR5819 CEA CNRS UGA, INAC/CEA, Grenoble, France
| | - Hyongi Chon
- Developmental Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Robert J Crouch
- Developmental Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, Udine, Italy
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30
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Antoniali G, Serra F, Lirussi L, Tanaka M, D'Ambrosio C, Zhang S, Radovic S, Dalla E, Ciani Y, Scaloni A, Li M, Piazza S, Tell G. Mammalian APE1 controls miRNA processing and its interactome is linked to cancer RNA metabolism. Nat Commun 2017; 8:797. [PMID: 28986522 PMCID: PMC5630600 DOI: 10.1038/s41467-017-00842-8] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 07/28/2017] [Indexed: 01/31/2023] Open
Abstract
Mammalian apurinic/apyrimidinic endonuclease 1 is a DNA repair enzyme involved in genome stability and expression of genes involved in oxidative stress responses, tumor progression and chemoresistance. However, the molecular mechanisms underlying the role of apurinic/apyrimidinic endonuclease 1 in these processes are still unclear. Recent findings point to a novel role of apurinic/apyrimidinic endonuclease 1 in RNA metabolism. Through the characterization of the interactomes of apurinic/apyrimidinic endonuclease 1 with RNA and other proteins, we demonstrate here a role for apurinic/apyrimidinic endonuclease 1 in pri-miRNA processing and stability via association with the DROSHA-processing complex during genotoxic stress. We also show that endonuclease activity of apurinic/apyrimidinic endonuclease 1 is required for the processing of miR-221/222 in regulating expression of the tumor suppressor PTEN. Analysis of a cohort of different cancers supports the relevance of our findings for tumor biology. We also show that apurinic/apyrimidinic endonuclease 1 participates in RNA-interactomes and protein-interactomes involved in cancer development, thus indicating an unsuspected post-transcriptional effect on cancer genes. APE1 plays an important role in the cellular response to oxidative stress, and mutations are linked to tumor progression and chemoresistance. Here, the authors characterize the interactions of APE1 with RNA and demonstrate a role in microRNA processing.
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Affiliation(s)
- Giulia Antoniali
- Department of Medicine, Laboratory of Molecular Biology and DNA repair, University of Udine, p.le M. Kolbe 4, Udine, 33100, Italy
| | - Fabrizio Serra
- Department of Medicine, Laboratory of Molecular Biology and DNA repair, University of Udine, p.le M. Kolbe 4, Udine, 33100, Italy.,Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, I.R.C.C.S., via Franco Gallini 2, Aviano (PN), 33081, Italy
| | - Lisa Lirussi
- Department of Medicine, Laboratory of Molecular Biology and DNA repair, University of Udine, p.le M. Kolbe 4, Udine, 33100, Italy.,Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Sykehusveien 27, Nordbyhagen, 1474, Norway
| | - Mikiei Tanaka
- Laboratory of Biochemistry, National Heart Lung and Blood Institute, National Institutes of Health, 50 South Drive, MSC-8012, Bethesda, MD, 20892-8012, USA
| | - Chiara D'Ambrosio
- Proteomics and Mass Spectrometry Laboratory, Institute for the Animal Production System in the Mediterranean Environment (ISPAAM) National Research Council (CNR) of Italy, via Argine 1085, Naples, 80147, Italy
| | - Shiheng Zhang
- Cancer Center of Daping Hospital, Third Military Medical University, Chongqing, 400042, China
| | | | - Emiliano Dalla
- Laboratorio Nazionale CIB, Area Science Park Padriciano, Trieste, 34149, Italy
| | - Yari Ciani
- Laboratorio Nazionale CIB, Area Science Park Padriciano, Trieste, 34149, Italy
| | - Andrea Scaloni
- Proteomics and Mass Spectrometry Laboratory, Institute for the Animal Production System in the Mediterranean Environment (ISPAAM) National Research Council (CNR) of Italy, via Argine 1085, Naples, 80147, Italy
| | - Mengxia Li
- Cancer Center of Daping Hospital, Third Military Medical University, Chongqing, 400042, China.
| | - Silvano Piazza
- Laboratorio Nazionale CIB, Area Science Park Padriciano, Trieste, 34149, Italy. .,Bioinformatics Core Facility, Centre for Integrative Biology, CIBIO, University of Trento, via Sommarive 18, Povo, Trento, TN, 38123, Italy.
| | - Gianluca Tell
- Department of Medicine, Laboratory of Molecular Biology and DNA repair, University of Udine, p.le M. Kolbe 4, Udine, 33100, Italy.
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31
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Wu Q, Fang J, Li S, Wei J, Yang Z, Zhao H, Zhao C, Cai Z. Interaction of bisphenol A 3,4-quinone metabolite with glutathione and ribonucleosides/deoxyribonucleosides in vitro. JOURNAL OF HAZARDOUS MATERIALS 2017; 323:195-202. [PMID: 26971050 DOI: 10.1016/j.jhazmat.2016.03.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/02/2016] [Accepted: 03/05/2016] [Indexed: 06/05/2023]
Abstract
Bisphenol A is a monomer used in the manufacture of polycarbonate plastic products, epoxy resin-based food can liners and flame retardants. To determine the genotoxic potential of bisphenol A, the mechanism of the reactions between the reactive electophilic bisphenol A 3,4-quinone (BPAQ) with glutathione and ribonucleosides/deoxyribonucleosides were studied. The obtained results demonstrated that BPAQ reacted with 2'-deoxyguanosine (dG)/guanosine (G), 2'-deoxyadenosine (dA)/adenosine (A), but not with 2'-deoxycytidine (dC)/cytidine (C) and thymidine (T)/uridine (U) in aqueous acetic acid. The reactions were accompanied by loss of deoxyribose, and the rate of depurination by deoxyribonucleoside adducts were faster than that of ribonucleoside adducts. In mixtures of ribonucleosides and deoxyribonucleosides treated with BPAQ, reactions occurred more readily with dG/G than dA/A. The structures of the modified bases were confirmed by electrospray ionization tandem mass spectrometry (ESI-MS/MS). We also found that BPAQ reacted readily with glutathione (GSH) in aqueous acetic acid, and characterized the BPAQ-GSH conjugate by ESI-MS/MS. The in vitro data of depurinating DNA/RNA adducts and BPAQ-GSH adducts may provide appropriate reference for the identification of BPAQ adducts in environmental and biological systems.
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Affiliation(s)
- Qian Wu
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
| | - Jing Fang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
| | - Shangfu Li
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
| | - Juntong Wei
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
| | - Zhiyi Yang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
| | - Hongzhi Zhao
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
| | - Chao Zhao
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China; School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, China.
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32
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Sassa A, Çağlayan M, Rodriguez Y, Beard WA, Wilson SH, Nohmi T, Honma M, Yasui M. Impact of Ribonucleotide Backbone on Translesion Synthesis and Repair of 7,8-Dihydro-8-oxoguanine. J Biol Chem 2016; 291:24314-24323. [PMID: 27660390 DOI: 10.1074/jbc.m116.738732] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 08/28/2016] [Indexed: 12/21/2022] Open
Abstract
Numerous ribonucleotides are incorporated into the genome during DNA replication. Oxidized ribonucleotides can also be erroneously incorporated into DNA. Embedded ribonucleotides destabilize the structure of DNA and retard DNA synthesis by DNA polymerases (pols), leading to genomic instability. Mammalian cells possess translesion DNA synthesis (TLS) pols that bypass DNA damage. The mechanism of TLS and repair of oxidized ribonucleotides remains to be elucidated. To address this, we analyzed the miscoding properties of the ribonucleotides riboguanosine (rG) and 7,8-dihydro-8-oxo-riboguanosine (8-oxo-rG) during TLS catalyzed by the human TLS pols κ and η in vitro The primer extension reaction catalyzed by human replicative pol α was strongly blocked by 8-oxo-rG. pol κ inefficiently bypassed rG and 8-oxo-rG compared with dG and 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxo-dG), whereas pol η easily bypassed the ribonucleotides. pol α exclusively inserted dAMP opposite 8-oxo-rG. Interestingly, pol κ preferentially inserted dCMP opposite 8-oxo-rG, whereas the insertion of dAMP was favored opposite 8-oxo-dG. In addition, pol η accurately bypassed 8-oxo-rG. Furthermore, we examined the activity of the base excision repair (BER) enzymes 8-oxoguanine DNA glycosylase (OGG1) and apurinic/apyrimidinic endonuclease 1 on the substrates, including rG and 8-oxo-rG. Both BER enzymes were completely inactive against 8-oxo-rG in DNA. However, OGG1 suppressed 8-oxo-rG excision by RNase H2, which is involved in the removal of ribonucleotides from DNA. These results suggest that the different sugar backbones between 8-oxo-rG and 8-oxo-dG alter the capacity of TLS and repair of 8-oxoguanine.
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Affiliation(s)
- Akira Sassa
- From the Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan and
| | - Melike Çağlayan
- the Genome Integrity and Structural Biology Laboratory, National Institutes of Health, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Yesenia Rodriguez
- the Genome Integrity and Structural Biology Laboratory, National Institutes of Health, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - William A Beard
- the Genome Integrity and Structural Biology Laboratory, National Institutes of Health, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Samuel H Wilson
- the Genome Integrity and Structural Biology Laboratory, National Institutes of Health, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Takehiko Nohmi
- From the Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan and
| | - Masamitsu Honma
- From the Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan and
| | - Manabu Yasui
- From the Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan and
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Wang Y, Wong TY, Chan W. Quantitation of the DNA Adduct of Semicarbazide in Organs of Semicarbazide-Treated Rats by Isotope-Dilution Liquid Chromatography–Tandem Mass Spectrometry: A Comparative Study with the RNA Adduct. Chem Res Toxicol 2016; 29:1560-4. [DOI: 10.1021/acs.chemrestox.6b00232] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Yinan Wang
- Department of Chemistry, The Hong Kong University of Science and Technology, Room 4520, Academic Building, Clear Water Bay, Kowloon, Hong Kong
| | - Tin-Yan Wong
- Department of Chemistry, The Hong Kong University of Science and Technology, Room 4520, Academic Building, Clear Water Bay, Kowloon, Hong Kong
| | - Wan Chan
- Department of Chemistry, The Hong Kong University of Science and Technology, Room 4520, Academic Building, Clear Water Bay, Kowloon, Hong Kong
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34
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Imincan G, Pei F, Yu L, Jin H, Zhang L, Yang X, Zhang L, Tang X. Microenvironmental Effect of 2'-O-(1-Pyrenylmethyl)uridine Modified Fluorescent Oligonucleotide Probes on Sensitive and Selective Detection of Target RNA. Anal Chem 2016; 88:4448-55. [PMID: 27021236 DOI: 10.1021/acs.analchem.6b00227] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
2'-O-(1-Pyrenylmethyl)uridine modified oligoribonucleotides provide highly sensitive pyrene fluorescent probes for detecting specific nucleotide mutation of RNA targets. To develop more stable and cost-effective oligonucleotide probes, we investigated the local microenvironmental effects of nearby nucleobases on pyrene fluorescence in duplexes of RNAs and 2'-O-(1-pyrenylmethyl)uridine modified oligonucleotides. By incorporation of deoxyribonucleotides, ribonucleotides, 2'-MeO-nucleotides and 2'-F-nucleotides at both sides of 2'-O-(1-pyrenylmethyl)uridine (U(p)) in oligodeoxynucleotide probes, we synthesized a series of pyrene modified oligonucleotide probes. Their pyrene fluorescence emission spectra indicated that only two proximal nucleotides have a substantial effect on the pyrene fluorescence properties of these oligonucleotide probes hybridized with target RNA with an order of fluorescence sensitivity of 2'-F-nucleotides > 2'-MeO-nucleotides > ribonucleotides ≫ deoxyribonucleotides. While based on circular dichroism spectra, overall helix conformations (either A- or B-form) of the duplexes have marginal effects on the sensitivity of the probes. Instead, the local substitution reflected the propensity of the nucleotide sugar ring to adopt North type conformation and, accordingly, shifted their helix geometry toward a more A-type like conformation in local microenvironments. Thus, higher enhancement of pyrene fluorescence emission favored local A-type helix structures and more polar and hydrophobic environments (F > MeO > OH at 2' substitution) of duplex minor grooves of probes with the target RNA. Further dynamic simulation revealed that local microenvironmental effect of 2'-F-nucleotides or ribonucleotides was enough for pyrene moiety to move out of nucleobases to the minor groove of duplexes; in addition, 2'-F-nucleotide had less effect on π-stack of pyrene-modified uridine with upstream and downstream nucleobases. The present oligonucleotide probes successfully distinguished target RNA from single-mutated RNA analyte during an in vitro assay of RNA synthesis.
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Affiliation(s)
- Gülnur Imincan
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Fen Pei
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Lijia Yu
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Xiaoda Yang
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
| | - XinJing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University , Beijing, 100191, China
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35
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Effect of Depurination on Cellular and Viral RNA. MODIFIED NUCLEIC ACIDS IN BIOLOGY AND MEDICINE 2016. [DOI: 10.1007/978-3-319-34175-0_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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36
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Bartos P, Ebenryter-Olbinska K, Sochacka E, Nawrot B. The influence of the C5 substituent on the 2-thiouridine desulfuration pathway and the conformational analysis of the resulting 4-pyrimidinone products. Bioorg Med Chem 2015; 23:5587-94. [DOI: 10.1016/j.bmc.2015.07.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 07/14/2015] [Accepted: 07/15/2015] [Indexed: 11/29/2022]
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37
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Yang B, Jinnouchi A, Usui K, Katayama T, Fujii M, Suemune H, Aso M. Bioconjugation of Oligodeoxynucleotides Carrying 1,4-Dicarbonyl Groups via Reductive Amination with Lysine Residues. Bioconjug Chem 2015. [PMID: 26200210 DOI: 10.1021/acs.bioconjchem.5b00361] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We evaluated the efficacy of bioconjugation of oligodeoxynucleotides (ODNs) containing 1,4-dicarbonyl groups, a C4'-oxidized abasic site (OAS), and a newly designed 2'-methoxy analogue, via reductive amination with lysine residues. Dicarbonyls, aldehyde and ketone at C1- and C4-positions of deoxyribose in the ring-opened form of OAS allowed efficient reaction with amines. Kinetic studies indicated that reductive amination of OAS-containing ODNs with a proximal amine on the complementary strand proceeded 10 times faster than the corresponding reaction of an ODN containing an abasic site with C1-aldehyde. Efficient reductive amination between the DNA-binding domain of Escherichia coli DnaA protein and ODNs carrying OAS in the DnaA-binding sequence proceeded at the lysine residue in proximity to the phosphate group at the 5'-position of the OAS, in contrast to unsuccessful conjugation with abasic site ODNs, even though they have similar aldehydes. Theoretical calculation indicated that the C1-aldehyde of OAS was more accessible to the target lysine than that of the abasic site. These results demonstrate the potential utility of cross-linking strategies that use dicarbonyl-containing ODNs for the study of protein-nucleic acid interactions. Conjugation with a lysine-containing peptide that lacked specific affinity for ODN was also successful, further highlighting the advantages of 1,4-dicarbonyls.
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Affiliation(s)
- Bo Yang
- †Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Akiko Jinnouchi
- †Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Kazuteru Usui
- †Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Tsutomu Katayama
- †Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Masayuki Fujii
- ‡Department of Biological and Environmental Chemistry, School of Humanity-Oriented Science and Engineering, Kinki University, 11-6 Kayanomori, Iizuka, Fukuoka 820-8555, Japan
| | - Hiroshi Suemune
- †Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Mariko Aso
- †Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
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Fleming AM, Alshykhly O, Zhu J, Muller JG, Burrows CJ. Rates of chemical cleavage of DNA and RNA oligomers containing guanine oxidation products. Chem Res Toxicol 2015; 28:1292-300. [PMID: 25853314 PMCID: PMC4482417 DOI: 10.1021/acs.chemrestox.5b00096] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
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The nucleobase guanine in DNA (dG)
and RNA (rG) has the lowest
standard reduction potential of the bases, rendering it a major site
of oxidative damage in these polymers. Mapping the sites at which
oxidation occurs in an oligomer via chemical reagents utilizes hot
piperidine for cleaving oxidized DNA and aniline (pH 4.5) for cleaving
oxidized RNA. In the present studies, a series of time-dependent cleavages
of DNA and RNA strands containing various guanine lesions were examined
to determine the strand scission rate constants. The guanine base
lesions 8-oxo-7,8-dihydroguanine (OG), spiroiminodihydantoin
(Sp), 5-guanidinohydantoin (Gh), 2,2,4-triamino-2H-oxazol-5-one (Z), and 5-carboxamido-5-formamido-2-iminohydantoin
(2Ih) were evaluated in piperidine-treated DNA and aniline-treated
RNA. These data identified wide variability in the chemical lability
of the lesions studied in both DNA and RNA. Further, the rate constants
for cleaving lesions in RNA were generally found to be significantly
smaller than for lesions in DNA. The OG nucleotides were poorly cleaved
in DNA and RNA; Sp nucleotides were slowly cleaved in DNA and did
not cleave significantly in RNA; Gh and Z nucleotides cleaved in both
DNA and RNA at intermediate rates; and 2Ih oligonucleotides cleaved
relatively quickly in both DNA and RNA. The data are compared and
contrasted with respect to future experimental design.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Omar Alshykhly
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Judy Zhu
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - James G Muller
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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Leung EMK, Chan W. Comparison of DNA and RNA Adduct Formation: Significantly Higher Levels of RNA than DNA Modifications in the Internal Organs of Aristolochic Acid-Dosed Rats. Chem Res Toxicol 2015; 28:248-55. [DOI: 10.1021/tx500423m] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Elvis M. K. Leung
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Wan Chan
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
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40
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Self-Amplifying mRNA Vaccines. NONVIRAL VECTORS FOR GENE THERAPY - PHYSICAL METHODS AND MEDICAL TRANSLATION 2015; 89:179-233. [DOI: 10.1016/bs.adgen.2014.10.005] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Abstract
While primordial life is thought to have been RNA-based (Cech, Cold Spring Harbor Perspect. Biol. 4 (2012) a006742), all living organisms store genetic information in DNA, which is chemically more stable. Distinctions between the RNA and DNA worlds and our views of "DNA" synthesis continue to evolve as new details emerge on the incorporation, repair and biological effects of ribonucleotides in DNA genomes of organisms from bacteria through humans.
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Affiliation(s)
- Jessica S Williams
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, United States
| | - Thomas A Kunkel
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, United States.
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42
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Kausar A, Mitran CJ, Li Y, Gibbs-Davis JM. Rapid, Isothermal DNA Self-Replication Induced by a Destabilizing Lesion. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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43
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Kausar A, Mitran CJ, Li Y, Gibbs-Davis JM. Rapid, isothermal DNA self-replication induced by a destabilizing lesion. Angew Chem Int Ed Engl 2013; 52:10577-81. [PMID: 23922255 DOI: 10.1002/anie.201303225] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Indexed: 11/07/2022]
Abstract
You spin me round: Using a destabilizing abasic site and high concentration of ligase, rapid DNA self-replication in an isothermal ligase chain reaction (LCR) was produced. Both destabilization and rapid ligation are essential for proper LCR replication. This method also provides insight into prebiotic nucleotide replication and is a potential amplification method for biodiagnostics.
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Affiliation(s)
- Abu Kausar
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2 (Canada) http://www.chem.ualberta.ca/∼gibbsdavis
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Liu J, Pendergraff H, Narayanannair KJ, Lackey JG, Kuchimanchi S, Rajeev KG, Manoharan M, Hu J, Corey DR. RNA duplexes with abasic substitutions are potent and allele-selective inhibitors of huntingtin and ataxin-3 expression. Nucleic Acids Res 2013; 41:8788-801. [PMID: 23887934 PMCID: PMC3794577 DOI: 10.1093/nar/gkt594] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Abasic substitutions within DNA or RNA are tools for evaluating the impact of absent nucleobases. Because of the importance of abasic sites in genetic damage, most research has involved DNA. Little information is available on the impact of abasic substitutions within RNA or on RNA interference (RNAi). Here, we examine the effect of abasic substitutions on RNAi and allele-selective gene silencing. Huntington's disease (HD) and Machado Joseph Disease (MJD) are severe neurological disorders that currently have no cure. HD and MJD are caused by an expansion of CAG repeats within one mRNA allele encoding huntingtin (HTT) and ataxin-3 (ATX-3) proteins. Agents that silence mutant HTT or ATX-3 expression would remove the cause of HD or MJD and provide an option for therapeutic development. We describe flexible syntheses for abasic substitutions and show that abasic RNA duplexes allele-selectively inhibit both mutant HTT and mutant ATX-3. Inhibition involves the RNAi protein argonaute 2, even though the abasic substitution disrupts the catalytic cleavage of RNA target by argonaute 2. Several different abasic duplexes achieve potent and selective inhibition, providing a broad platform for subsequent development. These findings introduce abasic substitutions as a tool for tailoring RNA duplexes for gene silencing.
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Affiliation(s)
- Jing Liu
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA, Department of Chemistry and Institute for Life Sciences, University of Southampton, Highfield, Southampton, SO17 1BJ, UK and Alnylam Pharmaceuticals, 300 Third St., Cambridge, MA 02142, USA
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45
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Rios AC, Tor Y. Refining the genetic alphabet: a late-period selection pressure? ASTROBIOLOGY 2012; 12:884-891. [PMID: 22984873 PMCID: PMC3444765 DOI: 10.1089/ast.2011.0789] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 08/04/2012] [Indexed: 06/01/2023]
Abstract
The transition from genomic ribonucleic acid (RNA) to deoxyribonucleic acid (DNA) in primitive cells may have created a selection pressure that refined the genetic alphabet, resulting from the global weakening of the N-glycosyl bonds. Hydrolytic rupture of these bonds, termed deglycosylation, leaves an abasic site that is the single greatest threat to the stability and integrity of genomic DNA. The rates of deglycosylation are highly dependent on the identity of the nucleobases. Modifications made to the bases, such as deamination, oxidation, and alkylation, can further increase deglycosylation reaction rates, suggesting that the native bases provide optimum N-glycosyl bond stability. To protect their genomes, cells have evolved highly specific enzymes called glycosylases, associated with DNA repair, that detect and remove these damaged bases. In RNA, however, the occurrence of many of these modified bases is deliberate. The dichotomous behavior that cells exhibit toward base modifications may have originated in the RNA world. Modified bases would have been advantageous for the functional and structural repertoire of catalytic RNAs. Yet in an early DNA world, the utility of these heterocycles was greatly diminished, and their presence posed a distinct liability to the stability of cells' genomes. A natural selection for bases exhibiting the greatest resistance to deglycosylation would have ensured the viability of early DNA life, along with the recruitment of DNA repair.
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Affiliation(s)
- Andro C Rios
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, California 92093, USA.
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46
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Tanaka M, Jaruga P, Küpfer PA, Leumann CJ, Dizdaroglu M, Sonntag WE, Chock PB. RNA oxidation catalyzed by cytochrome c leads to its depurination and cross-linking, which may facilitate cytochrome c release from mitochondria. Free Radic Biol Med 2012; 53:854-62. [PMID: 22683603 PMCID: PMC4319184 DOI: 10.1016/j.freeradbiomed.2012.05.044] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 04/16/2012] [Accepted: 05/29/2012] [Indexed: 12/11/2022]
Abstract
Growing evidence indicates that RNA oxidation is correlated with a number of age-related neurodegenerative diseases, and RNA oxidation has also been shown to induce dysfunction in protein synthesis. Here we study in vitro RNA oxidation catalyzed by cytochrome c (cyt c)/H(2)O(2) or by the Fe(II)/ascorbate/H(2)O(2) system. Our results reveal that the products of RNA oxidation vary with the oxidant used. Guanosine residues are preferentially oxidized by cyt c/H(2)O(2) relative to the Fe(II)/ascorbate/H(2)O(2) system. GC/MS and LC/MS analyses demonstrated that the guanine base was not only oxidized but also depurinated to form an abasic sugar moiety. Results from gel electrophoresis and HPLC analyses show that RNA formed a cross-linked complex with cyt c in an H(2)O(2) concentration-dependent manner. Furthermore, when cyt c was associated with liposomes composed of cardiolipin/phosphatidylcholine, and incubated with RNA and H(2)O(2), it was found cross-linked with the oxidized RNA and dissociated from the liposome. Results of the quantitative analysis indicate that the release of the cyt c from the liposome is facilitated by the formation of an RNA-cyt c cross-linked complex. Thus, RNA oxidation may facilitate the release of cyt c from the mitochondrial membrane to induce apoptosis in response to oxidative stress.
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Affiliation(s)
- Mikiei Tanaka
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Reynolds Oklahoma Center on Aging, Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Corresponding author. Fax: +1 301 295 3566. (M. Tanaka)
| | - Pawel Jaruga
- Chemical Science and Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Pascal A. Küpfer
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | - Christian J. Leumann
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | - Miral Dizdaroglu
- Chemical Science and Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - William E. Sonntag
- Reynolds Oklahoma Center on Aging, Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - P. Boon Chock
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Corresponding author. Fax: +1 301 451 5459. (P. Boon Chock)
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47
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Sato Y, Ichihashi T, Nishizawa S, Teramae N. Strong and Selective Binding of Amiloride to an Abasic Site in RNA Duplexes: Thermodynamic Characterization and MicroRNA Detection. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201790] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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48
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Sato Y, Ichihashi T, Nishizawa S, Teramae N. Strong and Selective Binding of Amiloride to an Abasic Site in RNA Duplexes: Thermodynamic Characterization and MicroRNA Detection. Angew Chem Int Ed Engl 2012; 51:6369-72. [DOI: 10.1002/anie.201201790] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Indexed: 01/04/2023]
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49
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Tanpure AA, Patheja P, Srivatsan SG. Label-free fluorescence detection of the depurination activity of ribosome inactivating protein toxins. Chem Commun (Camb) 2012; 48:501-3. [DOI: 10.1039/c1cc16667k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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50
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Ariza-Mateos A, Prieto-Vega S, Díaz-Toledano R, Birk A, Szeto H, Mena I, Berzal-Herranz A, Gómez J. RNA self-cleavage activated by ultraviolet light-induced oxidation. Nucleic Acids Res 2011; 40:1748-66. [PMID: 21989404 PMCID: PMC3287179 DOI: 10.1093/nar/gkr822] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A novel UV-C-light-induced ribozyme activity was discovered within the highly structured 5'-genomic regions of both Hepatitis C Virus (HCV) and the related Classic Swine Fever Virus (CSFV). Cleavage is mediated by exposure to UV-C light but not by exogenous oxygen radicals. It is also very selective, occurring at base positions HCV C(79) and CSFV A(45) in some molecules and at the immediately adjacent 5'-positions HCV U(78) and CSFV U(44) in others. Among other reaction products, the majority of biochemically active products detected contained 3'-phosphate and 5'-phosphate-end groups at the newly generated termini, along with a much lower amount of 3'-hydroxyl end group. While preservation of an E-loop RNA structure in the vicinity of the cleavage site was a requisite for HCV RNA self-cleavage, this was not the case for CSFV RNA. The short size of the reactive domains (~33 nt), which are compatible with primitive RNA motifs, and the lack of sequence homology, indicate that as-yet unidentified UV-activated ribozymes are likely to be found throughout structured RNAs, thereby providing clues to whether early RNA self-cleavage events were mediated by photosensitive RNA structures.
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Affiliation(s)
- Ascensión Ariza-Mateos
- Laboratory of RNA Archeology, Instituto de Parasitología y Biomedicina 'López-Neyra', CSIC, Armilla, 18100 Granada, Spain
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