1
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Espadas G, Llovera L, Ollivier A, Tuorto F, Novoa EM, Sabidó E. Spectral libraries from nucleobases and deoxyribonucleosides facilitate the identification of ribonucleosides by nano-flow liquid chromatography-tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9759. [PMID: 38680121 DOI: 10.1002/rcm.9759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/05/2024] [Accepted: 03/31/2024] [Indexed: 05/01/2024]
Abstract
RATIONALE The study addresses the challenge of identifying RNA post-transcriptional modifications when commercial standards are not available to generate reference spectral libraries. It proposes employing homologous nucleobases and deoxyribonucleosides as alternative reference spectral libraries to aid in identifying modified ribonucleosides and distinguishing them from their positional isomers when the standards are unavailable. METHODS Complete sets of ribonucleoside, deoxyribonucleoside and nucleobase standards were analyzed using high-performance nano-flow liquid chromatography coupled to an Orbitrap Eclipse Tribrid mass spectrometer. Spectral libraries were constructed from homologous nucleobases and deoxyribonucleosides using targeted MS2 and neutral-loss-triggered MS3 methods, and collision energies were optimized. The feasibility of using these libraries for identifying modified ribonucleosides and their positional isomers was assessed through comparison of spectral fragmentation patterns. RESULTS Our analysis reveals that both MS2 and neutral-loss-triggered MS3 methods yielded rich spectra with similar fragmentation patterns across ribonucleosides, deoxyribonucleosides and nucleobases. Moreover, we demonstrate that spectra from nucleobases and deoxyribonucleosides, generated at optimized collision energies, exhibited sufficient similarity to those of modified ribonucleosides to enable their use as reference spectra for accurate identification of positional isomers within ribonucleoside families. CONCLUSIONS The study demonstrates the efficacy of utilizing homologous nucleobases and deoxyribonucleosides as interchangeable reference spectral libraries for identifying modified ribonucleosides and their positional isomers. This approach offers a valuable solution for overcoming limitations posed by the unavailability of commercial standards, enhancing the analysis of RNA post-transcriptional modifications via mass spectrometry.
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Affiliation(s)
- Guadalupe Espadas
- Center for Genomics Regulation, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Laia Llovera
- Center for Genomics Regulation, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Alexane Ollivier
- Center for Genomics Regulation, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Francesca Tuorto
- Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Eva Maria Novoa
- Center for Genomics Regulation, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Eduard Sabidó
- Center for Genomics Regulation, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
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2
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Peters-Clarke TM, Quan Q, Anderson BJ, McGee WM, Lohr E, Hebert AS, Westphall MS, Coon JJ. Phosphorothioate RNA Analysis by NETD Tandem Mass Spectrometry. Mol Cell Proteomics 2024; 23:100742. [PMID: 38401707 PMCID: PMC11047293 DOI: 10.1016/j.mcpro.2024.100742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/19/2024] [Indexed: 02/26/2024] Open
Abstract
Therapeutic RNAs are routinely modified during their synthesis to ensure proper drug uptake, stability, and efficacy. Phosphorothioate (PS) RNA, molecules in which one or more backbone phosphates are modified with a sulfur atom in place of standard nonbridging oxygen, is one of the most common modifications because of ease of synthesis and pharmacokinetic benefits. Quality assessment of RNA synthesis, including modification incorporation, is essential for drug selectivity and performance, and the synthetic nature of the PS linkage incorporation often reveals impurities. Here, we present a comprehensive analysis of PS RNA via tandem mass spectrometry (MS). We show that activated ion-negative electron transfer dissociation MS/MS is especially useful in diagnosing PS incorporation, producing diagnostic a- and z-type ions at PS linkage sites, beyond the standard d- and w-type ions. Analysis using resonant and beam-type collision-based activation reveals that, overall, more intense sequence ions and base-loss ions result when a PS modification is present. Furthermore, we report increased detection of b- and x-type product ions at sites of PS incorporation, in addition to the standard c- and y-type ions. This work reveals that the gas-phase chemical stability afforded by sulfur alters RNA dissociation and necessitates inclusion of additional product ions for MS/MS of PS RNA.
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Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Qiuwen Quan
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Benton J Anderson
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Emily Lohr
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alexander S Hebert
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA
| | - Michael S Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA; Morgridge Institute for Research, Madison, Wisconsin, USA.
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3
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Baek A, Rayhan A, Lee GE, Golconda S, Yu H, Kim S, Limbach PA, Addepalli B, Kim S. Mapping m 6A Sites on HIV-1 RNA Using Oligonucleotide LC-MS/MS. Methods Protoc 2024; 7:7. [PMID: 38251200 PMCID: PMC10801558 DOI: 10.3390/mps7010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/23/2024] Open
Abstract
The biological significance of chemical modifications to the ribonucleic acid (RNA) of human immunodeficiency virus type-1 (HIV-1) has been recognized. However, our understanding of the site-specific and context-dependent roles of these chemical modifications remains limited, primarily due to the absence of nucleotide-resolution mapping of modification sites. In this study, we present a method for achieving nucleotide-resolution mapping of chemical modification sites on HIV-1 RNA using liquid chromatography and tandem mass spectrometry (LC-MS/MS). LC-MS/MS, a powerful tool capable of directly analyzing native RNAs, has proven effective for mapping RNA modifications in small RNA molecules, including ribosomal RNA and transfer RNA. However, longer RNAs have posed challenges, such as the 9 Kb HIV-1 virion RNA, due to the complexity of and ambiguity in mass differences among RNase T1-cleaved RNA fragments in LC-MS/MS data. Here, we introduce a new target RNA enrichment method to isolate small local RNA fragments of HIV-1 RNA that potentially harbor site-specific N6-methyladenosine (m6A) modifications. In our initial trial, we used target-specific DNA probes only and encountered insufficient RNA fragmentation due to inefficient S1 digestion near the target site. Recognizing that inefficient S1 digestion by HIV-1 RNA is likely due to the formation of secondary structures in proximity to the target site, we designed multiple DNA probes annealing to various sites of HIV-1 RNA to better control the structures of RNA substrates for S1 digestion. The use of these non-target DNA probes significantly improved the isolation of more homogeneous target RNA fragments of approximately 50 bases in length. Oligonucleotide LC-MS/MS analysis of these isolated target RNA fragments successfully separated and detected both m6A-methylated and non-methylated oligomers at the two m6A-predicted sites. The principle of this new target enrichment strategy holds promise and should be broadly applicable to the analysis of any lengthy RNA that was previously deemed infeasible for investigation using oligonucleotide LC-MS/MS.
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Affiliation(s)
- Alice Baek
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; (A.B.); (G.-E.L.); (S.G.); (H.Y.); (S.K.)
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Asif Rayhan
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (A.R.); (P.A.L.)
| | - Ga-Eun Lee
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; (A.B.); (G.-E.L.); (S.G.); (H.Y.); (S.K.)
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Sarah Golconda
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; (A.B.); (G.-E.L.); (S.G.); (H.Y.); (S.K.)
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Hannah Yu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; (A.B.); (G.-E.L.); (S.G.); (H.Y.); (S.K.)
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Shihyoung Kim
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; (A.B.); (G.-E.L.); (S.G.); (H.Y.); (S.K.)
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Patrick A. Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (A.R.); (P.A.L.)
| | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (A.R.); (P.A.L.)
| | - Sanggu Kim
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; (A.B.); (G.-E.L.); (S.G.); (H.Y.); (S.K.)
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
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4
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Deng L, Kumar J, Rose R, McIntyre W, Fabris D. Analyzing RNA posttranscriptional modifications to decipher the epitranscriptomic code. MASS SPECTROMETRY REVIEWS 2024; 43:5-38. [PMID: 36052666 DOI: 10.1002/mas.21798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
The discovery of RNA silencing has revealed that non-protein-coding sequences (ncRNAs) can cover essential roles in regulatory networks and their malfunction may result in severe consequences on human health. These findings have prompted a general reassessment of the significance of RNA as a key player in cellular processes. This reassessment, however, will not be complete without a greater understanding of the distribution and function of the over 170 variants of the canonical ribonucleotides, which contribute to the breathtaking structural diversity of natural RNA. This review surveys the analytical approaches employed for the identification, characterization, and detection of RNA posttranscriptional modifications (rPTMs). The merits of analyzing individual units after exhaustive hydrolysis of the initial biopolymer are outlined together with those of identifying their position in the sequence of parent strands. Approaches based on next generation sequencing and mass spectrometry technologies are covered in depth to provide a comprehensive view of their respective merits. Deciphering the epitranscriptomic code will require not only mapping the location of rPTMs in the various classes of RNAs, but also assessing the variations of expression levels under different experimental conditions. The fact that no individual platform is currently capable of meeting all such demands implies that it will be essential to capitalize on complementary approaches to obtain the desired information. For this reason, the review strived to cover the broadest possible range of techniques to provide readers with the fundamental elements necessary to make informed choices and design the most effective possible strategy to accomplish the task at hand.
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Affiliation(s)
- L Deng
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - J Kumar
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - R Rose
- Department of Advanced Research Technologies, New York University Langone Health Center, New York, USA
| | - W McIntyre
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Daniele Fabris
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
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5
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Herbert C, Ohrnberger CL, Quinlisk E, Addepalli B, Limbach PA. Characterizing Benzo[a]pyrene Adducts in Transfer RNAs Using Liquid Chromatography Coupled with Tandem Mass Spectrometry (LC-MS/MS). Biomedicines 2023; 11:3270. [PMID: 38137491 PMCID: PMC10741534 DOI: 10.3390/biomedicines11123270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
The activated forms of the environmental pollutant benzo[a]pyrene (B[a]P), such as benzo[a]pyrene diol epoxide (BPDE), are known to cause damage to genomic DNA and proteins. However, the impact of BPDE on ribonucleic acid (RNA) remains unclear. To understand the full spectrum of potential BPDE-RNA adducts formed, we reacted ribonucleoside standards with BPDE and characterized the reaction products using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). To understand the potential types of adducts that could form with biological RNAs, eukaryotic transfer RNAs (tRNAs) were also reacted with BPDE. The isolation and analysis of the modified and adducted ribonucleosides using LC-MS/MS revealed several BPDE derivatives of post-transcriptional modifications. The approach outlined in this work enables the identification of RNA adducts from BPDE, which can pave the way for understanding the potential impacts of such adducts on the higher-order structure and function of modified RNAs.
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Affiliation(s)
| | | | | | | | - Patrick A. Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, 301 Clifton Court, Cincinnati, OH 45221-0172, USA; (C.H.)
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6
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Kelley M, Holmes CJ, Herbert C, Rayhan A, Joves J, Uhran M, Frigard R, Singh K, Limbach PA, Addepalli B, Benoit JB. Tyrosine transfer RNA levels and modifications during blood-feeding and vitellogenesis in the mosquito, Aedes aegypti. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569187. [PMID: 38076852 PMCID: PMC10705485 DOI: 10.1101/2023.11.29.569187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Mosquitoes such as Aedes aegypti must consume a blood meal for the nutrients necessary for egg production. Several transcriptome and proteome changes occur post blood meal that likely corresponds with codon usage alterations. Transfer RNA (tRNA) is the adapter molecule that reads messenger RNA (mRNA) codons to add the appropriate amino acid during protein synthesis. Chemical modifications to tRNA enhance codons' decoding, improving the accuracy and efficiency of protein synthesis. Here, we examined tRNA modifications and transcripts associated with the blood meal and subsequent periods of vitellogenesis in A. aegypti. More specifically, we assessed tRNA transcript abundance and modification levels in the fat body at critical times post blood-feeding. Based on a combination of alternative codon usage and identification of particular modifications, we identified that increased transcription of tyrosine tRNAs is likely critical during the synthesis of egg yolk proteins in the fat body following a blood meal. Altogether, changes in both the abundance and modification of tRNA are essential factors in the process of vitellogenin production after blood-feeding in mosquitoes.
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Affiliation(s)
- Melissa Kelley
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211
| | | | - Cassandra Herbert
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45211
| | - Asif Rayhan
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45211
| | - Judd Joves
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211
| | - Melissa Uhran
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211
| | - Ronja Frigard
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211
| | - Khwahish Singh
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211
| | | | | | - Joshua B. Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211
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7
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Zheng J, Wang H. Highly Efficient Gel Electrophoresis for Accurate Quantification of Nucleic Acid Modifications via in-Gel Digestion with UHPLC-MS/MS. Anal Chem 2023; 95:13407-13411. [PMID: 37642231 DOI: 10.1021/acs.analchem.3c02418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Gel electrophoresis is a powerful technique for the characterization of sequences, sizes and conformations of nucleic acids due to its remarkable separation efficiency. In parallel, liquid chromatography-mass spectrometry (LC-MS) has established itself as a staple tool for the meticulous characterization and accurate quantification of a multitude of DNA modifications. In this study, we devised an in-gel digestion method for coupling gel electrophoresis with LC-MS/MS. This process involves the enzymatic digestion of DNA within the gel by nucleases and release single nucleosides, which subsequently serve as a preprocessing step for (LC-MS/MS) analysis. We demonstrated that ethylenediaminetetraacetic acid (EDTA) in the routine gel electrophoresis buffer reduced the enzymatic digestion efficiency, while Mg2+ could mitigate this inhibition. We further showed EDTA-free gel electrophoresis and the process of digestion of genomic DNA and plasmid DNA within a gel was fluorescently imaged, proving the efficient digestion of DNA. By this improvement, the efficiency of an in-gel digestion could reach 60% or more of the control, compared with direct in-solution digestion. The measured abundances of DNA modifications (5-methylcytosine and N6-methyladenine) via in-gel digestion are consistent with that measured by in-solution digestion. Collectively, we showed an in-gel digestion method, which is a very useful pretreatment technique for the precise quantification of epigenetic modifications in diverse DNA molecules.
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Affiliation(s)
- Jing Zheng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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8
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Li J, Xiao Z, Wang D, Jia L, Nie S, Zeng X, Hu W. The screening, identification, design and clinical application of tumor-specific neoantigens for TCR-T cells. Mol Cancer 2023; 22:141. [PMID: 37649123 PMCID: PMC10466891 DOI: 10.1186/s12943-023-01844-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development of tumor immunotherapies, including adoptive cell therapies (ACTs), cancer vaccines and antibody-based therapies, particularly for solid tumors. With the development of next-generation sequencing and bioinformatics technology, the rapid identification and prediction of tumor-specific antigens (TSAs) has become possible. Compared with tumor-associated antigens (TAAs), highly immunogenic TSAs provide new targets for personalized tumor immunotherapy and can be used as prospective indicators for predicting tumor patient survival, prognosis, and immune checkpoint blockade response. Here, the identification and characterization of neoantigens and the clinical application of neoantigen-based TCR-T immunotherapy strategies are summarized, and the current status, inherent challenges, and clinical translational potential of these strategies are discussed.
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Affiliation(s)
- Jiangping Li
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
| | - Zhiwen Xiao
- Department of Otolaryngology Head and Neck Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, People's Republic of China
| | - Donghui Wang
- Department of Radiation Oncology, The Third Affiliated Hospital Sun Yat-Sen University, Guangzhou, 510630, People's Republic of China
| | - Lei Jia
- International Health Medicine Innovation Center, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Shihong Nie
- Department of Radiation Oncology, West China Hospital, Sichuan University, Cancer Center, Chengdu, 610041, People's Republic of China
| | - Xingda Zeng
- Department of Parasitology of Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Wei Hu
- Division of Vascular Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, People's Republic of China
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9
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Lauman R, Kim HJ, Pino LK, Scacchetti A, Xie Y, Robison F, Sidoli S, Bonasio R, Garcia BA. Expanding the Epitranscriptomic RNA Sequencing and Modification Mapping Mass Spectrometry Toolbox with Field Asymmetric Waveform Ion Mobility and Electrochemical Elution Liquid Chromatography. Anal Chem 2023; 95:5187-5195. [PMID: 36916610 PMCID: PMC10190205 DOI: 10.1021/acs.analchem.2c04114] [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] [Indexed: 03/15/2023]
Abstract
Post-transcriptional modifications of RNA strongly influence the RNA structure and function. Recent advances in RNA sequencing and mass spectrometry (MS) methods have identified over 140 of these modifications on a wide variety of RNA species. Most next-generation sequencing approaches can only map one RNA modification at a time, and while MS can assign multiple modifications simultaneously in an unbiased manner, MS cannot accurately catalog and assign RNA modifications in complex biological samples due to limitations in the fragment length and coverage depth. Thus, a facile method to identify novel RNA modifications while simultaneously locating them in the context of their RNA sequences is still lacking. We combined two orthogonal modes of RNA ion separation before MS identification: high-field asymmetric ion mobility separation (FAIMS) and electrochemically modulated liquid chromatography (EMLC). FAIMS RNA MS increases both coverage and throughput, while EMLC LC-MS orthogonally separates RNA molecules of different lengths and charges. The combination of the two methods offers a broadly applicable platform to improve the length and depth of MS-based RNA sequencing while providing contextual access to the analysis of RNA modifications.
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Affiliation(s)
- Richard Lauman
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetic Institute and Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Hee Jong Kim
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Lindsay K. Pino
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Alessandro Scacchetti
- Epigenetic Institute and Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Yixuan Xie
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Faith Robison
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Roberto Bonasio
- Epigenetic Institute and Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
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10
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Crittenden CM, Lanzillotti MB, Chen B. Top-Down Mass Spectrometry of Synthetic Single Guide Ribonucleic Acids Enabled by Facile Sample Clean-Up. Anal Chem 2023; 95:3180-3186. [PMID: 36606446 DOI: 10.1021/acs.analchem.2c03030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In recent years, CRISPR-Cas9 genome editing has become an important technology in biomedical research and has demonstrated tremendous therapeutic potential. With Cas9 endonuclease, the use of single guide ribonucleic acids (sgRNAs) allows for sequence-specific cutting on target double-stranded deoxyribonucleic acids. Therefore, the design and quality of sgRNAs can greatly affect the efficiency and specificity of genome editing. Mass spectrometry (MS) has been a powerful tool to detect molecular features and sequence a variety of biomolecules; however, as the sizes of oligonucleotides get larger, it becomes more challenging to desalt samples and achieve high-quality intact spectra with effective fragmentation. Here, we develop a simple but effective online column-based clean-up method (reversed-phase column in a size exclusion mode) that removes formulation salts and metal adducts from larger oligonucleotides upon entering the mass spectrometer in a consistent manner. Using the top-down approach without any nuclease digestion, we characterized and sequenced 100-nucleotide-long sgRNAs by higher-energy collision dissociation (HCD), collision-induced dissociation (CID), ultraviolet photodissociation (UVPD), and activated electron photodetachment (a-EPD). In a single 10 min liquid chromatography-tandem MS (LC-MS/MS) run, CID yielded the best sequence coverage, of 67%. When adding complementary UVPD and a-EPD runs, we achieved 80% overall sequence coverage and 100% cleavages for the variable sequence, the first 20 nucleotides from the 5' end. This LC-MS/MS platform provides a facile top-down workflow to analyze and sequence larger chemically modified oligonucleotides with no sample treatment.
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Affiliation(s)
- Christopher M Crittenden
- Small Molecule Analytical Chemistry, Genentech Inc., South San Francisco, California 94080, United States
| | | | - Bifan Chen
- Small Molecule Analytical Chemistry, Genentech Inc., South San Francisco, California 94080, United States
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11
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Detection technologies for RNA modifications. Exp Mol Med 2022; 54:1601-1616. [PMID: 36266445 PMCID: PMC9636272 DOI: 10.1038/s12276-022-00821-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/21/2022] [Accepted: 05/18/2022] [Indexed: 12/29/2022] Open
Abstract
To date, more than 170 chemical modifications have been characterized in RNA, providing a new layer of gene expression regulation termed the 'epitranscriptome'. RNA modification detection methods and tools advance the functional studies of the epitranscriptome. According to the detection throughput and principles, existing RNA modification detection technologies can be categorized into four classes, including quantification methods, locus-specific detection methods, next-generation sequencing-based detection technologies and nanopore direct RNA sequencing-based technologies. In this review, we summarize the current knowledge about these RNA modification detection technologies and discuss the challenges for the existing detection tools, providing information for a comprehensive understanding of the epitranscriptome.
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12
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Santos IC, Lanzillotti M, Shilov I, Basanta-Sanchez M, Roushan A, Lawler R, Tang W, Bern M, Brodbelt JS. Ultraviolet Photodissociation and Activated Electron Photodetachment Mass Spectrometry for Top-Down Sequencing of Modified Oligoribonucleotides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:510-520. [PMID: 35157441 DOI: 10.1021/jasms.1c00340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
With the increased development of new RNA-based therapeutics, the need for robust analytical methods for confirming sequences and mapping modifications has accelerated. Characterizing modified ribonucleic acids using mass spectrometry is challenging because diagnostic fragmentation may be suppressed for modified nucleotides, thus hampering complete sequence coverage and the confident localization of modifications. Ultraviolet photodissociation (UVPD) has shown great potential for the characterization of nucleic acids due to extensive backbone fragmentation. Activated electron photodetachment dissociation (a-EPD) has also been used as an alternative to capitalize on the dominant charge-reduction pathway prevalent in UVPD, facilitate dissociation, and produce high abundances of fragment ions. Here, we compare higher-energy collisional activation (HCD), UVPD using 193 and 213 nm photons, and a-EPD for the top-down sequencing of modified nucleic acids, including methylated, phosphorothioate, and locked nucleic acid-modified DNA. The presence of these modifications alters the fragmentation pathways observed upon UVPD and a-EPD, and extensive backbone cleavage is observed that results in the production of fragment ions that retain the modifications and allow them to be pinpointed. LNA and 2'-O-methoxy phosphorothioate modifications caused a significant suppression of fragmentation for UVPD but not for a-EPD, whereas phosphorothioate bonds did not cause any significant suppression for either method. The incorporation of 2'-O-methyl modifications suppressed fragmentation of the antisense strand of patisiran, which resulted in some gaps in sequence coverage. However, UVPD provided the highest sequence coverage when compared to a-EPD.
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Affiliation(s)
- Inês C Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Michael Lanzillotti
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Ignat Shilov
- Protein Metrics Inc., 20863 Stevens Creek Boulevard, Cupertino, California 95014, United States
| | - Maria Basanta-Sanchez
- Protein Metrics Inc., 20863 Stevens Creek Boulevard, Cupertino, California 95014, United States
| | - Abhishek Roushan
- Protein Metrics Inc., 20863 Stevens Creek Boulevard, Cupertino, California 95014, United States
| | - Rose Lawler
- Protein Metrics Inc., 20863 Stevens Creek Boulevard, Cupertino, California 95014, United States
| | - Wilfred Tang
- Protein Metrics Inc., 20863 Stevens Creek Boulevard, Cupertino, California 95014, United States
| | - Marshall Bern
- Protein Metrics Inc., 20863 Stevens Creek Boulevard, Cupertino, California 95014, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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13
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Turathum B, Gao EM, Grataitong K, Liu YB, Wang L, Dai X, Chian RC. Dysregulated sphingolipid metabolism and autophagy in granulosa cells of women with endometriosis. Front Endocrinol (Lausanne) 2022; 13:906570. [PMID: 35992117 PMCID: PMC9381821 DOI: 10.3389/fendo.2022.906570] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
We evaluated metabolic profiles between cumulus cells (CCs) and mural granulosa cells (MGCs) derived from women with endometriosis to identify their correlations with oocyte quality. CCs and MGCs were collected from women with and without endometriosis undergoing in vitro fertilization/intracytoplasmic sperm injection treatment. The metabolomics of CCs and MGCs were measured by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) followed by a quantitative polymerase chain reaction to further confirm the genes involved in the metabolic results. LC-MS/MS analysis revealed differences in 24 metabolites of CCs and 71 metabolites of MGCs between groups. Among them, five metabolites were upregulated and 19 metabolites were downregulated in CCs with endometriosis, whereas three metabolites were upregulated and 68 metabolites were downregulated in MGCs with endometriosis. Metabolites related to sphingolipid metabolism, which included palmitic acid (PA) and docosahexaenoic acid, increased significantly only in CCs with endometriosis, whereas sphingosine and PA were significantly downregulated in MGCs with endometriosis compared with CCs and MGCs without endometriosis. Gene expression involved in ceramide synthesis (CERS1, SPTL1, and SMPD1) and autophagy (BECN1, LAMP, and PC3) were significantly higher in CCs with endometriosis according to FASN, BECN1, and LAMP protein expressions. However, gene expression involved in ceramide synthesis (SPHK1, ASAH1, and SGPP1) and autophagy (BECN1, LAMP, and PC3) were significantly lower in MGCs with endometriosis, whereas CERS1 and UGCG expression increased. There are differences in sphingolipid metabolites in CCs and MGCs with endometriosis compared with women without endometriosis. These differences seem to be involved in the regulation of autophagic cell death in preovulatory follicles.
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Affiliation(s)
- Bongkoch Turathum
- Centre for Reproductive Medicine, Shanghai 10th People Hospital of Tongji University, Shanghai, China
- Department of Basic Medical Science, Faculty of Medicine Vajira Hospital, Navamindradhiraj University, Bangkok, Thailand
| | - Er-Meng Gao
- Centre for Reproductive Medicine, Shanghai 10th People Hospital of Tongji University, Shanghai, China
- Shanghai Clinical College, Anhui Medical University, Hefei, China
| | - Khwanthana Grataitong
- Department of Basic Medical Science, Faculty of Medicine Vajira Hospital, Navamindradhiraj University, Bangkok, Thailand
| | - Yu-Bing Liu
- Centre for Reproductive Medicine, Shanghai 10th People Hospital of Tongji University, Shanghai, China
| | - Ling Wang
- Centre for Reproductive Medicine, Shanghai 10th People Hospital of Tongji University, Shanghai, China
| | - Xue Dai
- Centre for Reproductive Medicine, Shanghai 10th People Hospital of Tongji University, Shanghai, China
| | - Ri-Cheng Chian
- Centre for Reproductive Medicine, Shanghai 10th People Hospital of Tongji University, Shanghai, China
- Shanghai Clinical College, Anhui Medical University, Hefei, China
- *Correspondence: Ri-Cheng Chian,
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14
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Guo G, Pan K, Fang S, Ye L, Tong X, Wang Z, Xue X, Zhang H. Advances in mRNA 5-methylcytosine modifications: Detection, effectors, biological functions, and clinical relevance. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:575-593. [PMID: 34631286 PMCID: PMC8479277 DOI: 10.1016/j.omtn.2021.08.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
5-methylcytosine (m5C) post-transcriptional modifications affect the maturation, stability, and translation of the mRNA molecule. These modifications play an important role in many physiological and pathological processes, including stress response, tumorigenesis, tumor cell migration, embryogenesis, and viral replication. Recently, there has been a better understanding of the biological implications of m5C modification owing to the rapid development and optimization of detection technologies, including liquid chromatography-tandem mass spectrometry (LC-MS/MS) and RNA-BisSeq. Further, predictive models (such as PEA-m5C, m5C-PseDNC, and DeepMRMP) for the identification of potential m5C modification sites have also emerged. In this review, we summarize the current experimental detection methods and predictive models for mRNA m5C modifications, focusing on their advantages and limitations. We systematically surveyed the latest research on the effectors related to mRNA m5C modifications and their biological functions in multiple species. Finally, we discuss the physiological effects and pathological significance of m5C modifications in multiple diseases, as well as their therapeutic potential, thereby providing new perspectives for disease treatment and prognosis.
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Affiliation(s)
- Gangqiang Guo
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kan Pan
- First Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Su Fang
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lele Ye
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xinya Tong
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zhibin Wang
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiangyang Xue
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Huidi Zhang
- Department of Nephrology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
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15
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Grünberg S, Wolf EJ, Jin J, Ganatra MB, Becker K, Ruse C, Taron CH, Corrêa IR, Yigit E. Enhanced expression and purification of nucleotide-specific ribonucleases MC1 and Cusativin. Protein Expr Purif 2021; 190:105987. [PMID: 34637916 DOI: 10.1016/j.pep.2021.105987] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/25/2021] [Accepted: 10/04/2021] [Indexed: 12/13/2022]
Abstract
Combinations of ribonucleases (RNases) are commonly used to digest RNA into oligoribonucleotide fragments prior to liquid chromatography-mass spectrometry (LC-MS) analysis. The distribution of the RNase target sequences or nucleobase sites within an RNA molecule is critical for achieving a high mapping coverage. Cusativin and MC1 are nucleotide-specific endoribonucleases encoded in the cucumber and bitter melon genomes, respectively. Their high specificity for cytidine (Cusativin) and uridine (MC1) make them ideal molecular biology tools for RNA modification mapping. However, heterogenous recombinant expression of either enzyme has been challenging because of their high toxicity to expression hosts and the requirement of posttranslational modifications. Here, we present two highly efficient and time-saving protocols that overcome these hurdles and enhance the expression and purification of these RNases. We first purified MC1 and Cusativin from bacteria by expressing and shuttling both enzymes to the periplasm as MBP-fusion proteins in T7 Express lysY/IqE. coli strain at low temperature. The RNases were enriched using amylose affinity chromatography, followed by a subsequent purification via a C-terminal 6xHIS tag. This fast, two-step purification allows for the purification of highly active recombinant RNases significantly surpassing yields reported in previous studies. In addition, we expressed and purified a Cusativin-CBD fusion enzyme in P. pastoris using chitin magnetic beads. Both Cusativin variants exhibited a similar sequence preference, suggesting that neither posttranslational modifications nor the epitope-tags have a substantial effect on the sequence specificity of the enzyme.
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Affiliation(s)
| | - Eric J Wolf
- New England Biolabs, Inc, 240 County Rd, Ipswich, MA, 01938, USA
| | - Jingming Jin
- New England Biolabs, Inc, 240 County Rd, Ipswich, MA, 01938, USA
| | - Mehul B Ganatra
- New England Biolabs, Inc, 240 County Rd, Ipswich, MA, 01938, USA
| | - Kelly Becker
- New England Biolabs, Inc, 240 County Rd, Ipswich, MA, 01938, USA
| | - Cristian Ruse
- New England Biolabs, Inc, 240 County Rd, Ipswich, MA, 01938, USA
| | | | - Ivan R Corrêa
- New England Biolabs, Inc, 240 County Rd, Ipswich, MA, 01938, USA
| | - Erbay Yigit
- New England Biolabs, Inc, 240 County Rd, Ipswich, MA, 01938, USA.
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16
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Amalric A, Bastide A, Attina A, Choquet A, Vialaret J, Lehmann S, David A, Hirtz C. Quantifying RNA modifications by mass spectrometry: a novel source of biomarkers in oncology. Crit Rev Clin Lab Sci 2021; 59:1-18. [PMID: 34473579 DOI: 10.1080/10408363.2021.1958743] [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: 02/01/2023]
Abstract
Despite significant progress in targeted therapies, cancer recurrence remains a major cause of mortality worldwide. Identification of accurate biomarkers, through molecular profiling in healthy and cancer patient samples, will improve diagnosis and promote personalized medicine. While genetic and epigenetic alterations of DNA are currently exploited as cancer biomarkers, their robustness is limited by tumor heterogeneity. Recently, cancer-associated changes in RNA marks have emerged as a promising source of diagnostic and prognostic biomarkers. RNA epigenetics (also known as epitranscriptomics) is an emerging field in which at least 150 chemical modifications in all types of RNA (mRNA, tRNA, lncRNA, rRNA, and microRNA) have been detected. These modifications fine-tune gene expression in both physiological and pathological processes. A growing number of studies have established links between specific modified nucleoside levels in solid/liquid biopsies, and cancer onset and progression. In this review, we highlight the potential role of epitranscriptomic markers in refining cancer diagnosis and/or prognosis. RNA modification patterns may contain important information for establishing an initial diagnosis, monitoring disease evolution, and predicting response to treatment. Furthermore, recent developments in mass spectrometry allow reliable quantification of RNA marks in solid biopsies and biological fluids. We discuss the great potential of mass spectrometry for identifying epitranscriptomic biomarker signatures in cancer diagnosis. While there are various methods to quantify modified nucleosides, most are unable to detect and quantify more than one type of RNA modification at a time. Mass spectrometry analyses, especially GC-MS/MS and LC-MS/MS, overcome this limitation and simultaneously detect modified nucleosides by multiple reaction monitoring. Indeed, several groups are currently validating mass spectrometry methods that quantify several nucleosides at one time in liquid biopsies. The challenge now is to exploit these powerful analytical tools to establish epitranscriptomic signatures that should open new perspectives in personalized medicine. This review summarizes the growing clinical field of analysis of RNA modifications and discusses pre-analytical and analytical approaches, focusing in particular on the development of new mass spectrometry tools and their clinical applications.
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Affiliation(s)
- Amandine Amalric
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, France.,University of Montpellier, IRMB-PPC, INM, CHU Montpellier, INSERM CNRS, Montpellier, France
| | - Amandine Bastide
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Aurore Attina
- University of Montpellier, IRMB-PPC, INM, CHU Montpellier, INSERM CNRS, Montpellier, France
| | - Armelle Choquet
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Jerome Vialaret
- University of Montpellier, IRMB-PPC, INM, CHU Montpellier, INSERM CNRS, Montpellier, France
| | - Sylvain Lehmann
- University of Montpellier, IRMB-PPC, INM, CHU Montpellier, INSERM CNRS, Montpellier, France
| | - Alexandre David
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, France.,University of Montpellier, IRMB-PPC, INM, CHU Montpellier, INSERM CNRS, Montpellier, France
| | - Christophe Hirtz
- University of Montpellier, IRMB-PPC, INM, CHU Montpellier, INSERM CNRS, Montpellier, France
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17
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Gao Y, Fang J. RNA 5-methylcytosine modification and its emerging role as an epitranscriptomic mark. RNA Biol 2021; 18:117-127. [PMID: 34288807 DOI: 10.1080/15476286.2021.1950993] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
5-methylcytosine (m5C) is identified as an abundant and conserved modification in various RNAs, including tRNAs, mRNAs, rRNAs, and other non-coding RNAs. The application of high-throughput sequencing and mass spectrometry allowed for the detection of m5C at a single-nucleotide resolution and at a global abundance separately; this contributes to a better understanding of m5C modification and its biological functions. m5C modification plays critical roles in diverse aspects of RNA processing, including tRNA stability, rRNA assembly, and mRNA translation. Notably, altered m5C modifications and mutated RNA m5C methyltransferases are associated with diverse pathological processes, such as nervous system disorders and cancers. This review may provide new sights of molecular mechanism and functional importance of m5C modification.
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Affiliation(s)
- Yaqi Gao
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jingyuan Fang
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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18
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Kösters M, Leufken J, Leidel SA. SMITER-A Python Library for the Simulation of LC-MS/MS Experiments. Genes (Basel) 2021; 12:396. [PMID: 33799543 PMCID: PMC8000309 DOI: 10.3390/genes12030396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 12/24/2022] Open
Abstract
SMITER (Synthetic mzML writer) is a Python-based command-line tool designed to simulate liquid-chromatography-coupled tandem mass spectrometry LC-MS/MS runs. It enables the simulation of any biomolecule amenable to mass spectrometry (MS) since all calculations are based on chemical formulas. SMITER features a modular design, allowing for an easy implementation of different noise and fragmentation models. By default, SMITER uses an established noise model and offers several methods for peptide fragmentation, and two models for nucleoside fragmentation and one for lipid fragmentation. Due to the rich Python ecosystem, other modules, e.g., for retention time (RT) prediction, can easily be implemented for the tailored simulation of any molecule of choice. This facilitates the generation of defined gold-standard LC-MS/MS datasets for any type of experiment. Such gold standards, where the ground truth is known, are required in computational mass spectrometry to test new algorithms and to improve parameters of existing ones. Similarly, gold-standard datasets can be used to evaluate analytical challenges, e.g., by predicting co-elution and co-fragmentation of molecules. As these challenges hinder the detection or quantification of co-eluents, a comprehensive simulation can identify and thus, prevent such difficulties before performing actual MS experiments. SMITER allows the creation of such datasets easily, fast, and efficiently.
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Affiliation(s)
| | | | - Sebastian A. Leidel
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences (DCBP), University of Bern, Freiestrasse 3, 3012 Bern, Switzerland; (M.K.); (J.L.)
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19
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Yoluç Y, Ammann G, Barraud P, Jora M, Limbach PA, Motorin Y, Marchand V, Tisné C, Borland K, Kellner S. Instrumental analysis of RNA modifications. Crit Rev Biochem Mol Biol 2021; 56:178-204. [PMID: 33618598 DOI: 10.1080/10409238.2021.1887807] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Organisms from all domains of life invest a substantial amount of energy for the introduction of RNA modifications into nearly all transcripts studied to date. Instrumental analysis of RNA can focus on the modified residues and reveal the function of these epitranscriptomic marks. Here, we will review recent advances and breakthroughs achieved by NMR spectroscopy, sequencing, and mass spectrometry of the epitranscriptome.
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Affiliation(s)
- Yasemin Yoluç
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Gregor Ammann
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Pierre Barraud
- Expression génétique microbienne, UMR 8261, CNRS, Institut de biologie physico-chimique, IBPC, Université de Paris, Paris, France
| | - Manasses Jora
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Patrick A Limbach
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Yuri Motorin
- Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, France
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, Epitranscriptomics and RNA Sequencing Core facility, UM S2008, IBSLor, Nancy, France
| | - Carine Tisné
- Expression génétique microbienne, UMR 8261, CNRS, Institut de biologie physico-chimique, IBPC, Université de Paris, Paris, France
| | - Kayla Borland
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Stefanie Kellner
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany.,Institute of Pharmaceutical Chemistry, Goethe-University, Frankfurt, Germany
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20
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Bi F, Xu Y, Chen G, Wang P. Anti-inflammatory and Anti-endoplasmic reticulum stress Effects of catalpol Against myocardial ischemia-reperfusion injury in streptozotocin-induced diabetic rats. AN ACAD BRAS CIENC 2020; 92:e20191148. [PMID: 33237136 DOI: 10.1590/0001-3765202020191148] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/14/2020] [Indexed: 01/19/2023] Open
Abstract
The current study was designed to investigate the effects and the mechanism of catalpol on myocardial ischemia-reperfusion (MI/R) injury in a diabetic rat model. Male Sprague-Dawley rats were divided into DM + sham, DM +I/R, and DM +I/R + C groups and diabetes was induced using single injections of streptozotocin (STZ; 70 mg/kg; i.p). After confirming the induction of diabetes, rats were administered physiological saline and catalpol (10 mg/kg; i.p.) daily for 28 days. Subsequently, rats were subjected to left anterior descending (LAD) coronary artery occlusion for 30 min followed by reperfusion for 2 h. Haemodynamic parameters were recorded throughout surgery, and following sacrifice, hearts were isolated for biochemical, histopathological, and molecular analyses. Catalpol treatment significantly ameliorated MI/R injury by improving cardiac function, normalizing myocardial enzyme activities and markers of oxidative stress, and by maintaining myocardial architecture. Furthermore, expression levels of the inflammatory cytokines TNF-α and IL-6 were decreased in biochemical and immunohistochemical studies. Additionally, the cardioprotective effects of catalpol were partly related to reductions in myocardial endoplasmic reticulum stress (ERS). In conclusion, catalpol exerts cardioprotective effects in diabetic rats by attenuating inflammation and inhibiting ERS.
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Affiliation(s)
- Fangjie Bi
- Heart Center, Zibo Central Hospital, 255400 Shandong, China
| | - Yujia Xu
- Department of Echocardiography, Zibo Central Hospital, 255400 Shandong, China
| | - Guangxin Chen
- Department of Emergency, Zibo Central Hospital, 255400 Shandong, China
| | - Pan Wang
- Department of Pain Treatment, Zibo Central Hospital, 255400 Shandong, China
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21
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Matzov D, Taoka M, Nobe Y, Yamauchi Y, Halfon Y, Asis N, Zimermann E, Rozenberg H, Bashan A, Bhushan S, Isobe T, Gray MW, Yonath A, Shalev-Benami M. Cryo-EM structure of the highly atypical cytoplasmic ribosome of Euglena gracilis. Nucleic Acids Res 2020; 48:11750-11761. [PMID: 33091122 PMCID: PMC7672448 DOI: 10.1093/nar/gkaa893] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/21/2020] [Accepted: 10/21/2020] [Indexed: 12/11/2022] Open
Abstract
Ribosomal RNA is the central component of the ribosome, mediating its functional and architectural properties. Here, we report the cryo-EM structure of a highly divergent cytoplasmic ribosome from the single-celled eukaryotic alga Euglena gracilis. The Euglena large ribosomal subunit is distinct in that it contains 14 discrete rRNA fragments that are assembled non-covalently into the canonical ribosome structure. The rRNA is substantially enriched in post-transcriptional modifications that are spread far beyond the catalytic RNA core, contributing to the stabilization of this highly fragmented ribosome species. A unique cluster of five adenosine base methylations is found in an expansion segment adjacent to the protein exit tunnel, such that it is positioned for interaction with the nascent peptide. As well as featuring distinctive rRNA expansion segments, the Euglena ribosome contains four novel ribosomal proteins, localized to the ribosome surface, three of which do not have orthologs in other eukaryotes.
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Affiliation(s)
- Donna Matzov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Yuko Nobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Yoshio Yamauchi
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Yehuda Halfon
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nofar Asis
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ella Zimermann
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Haim Rozenberg
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anat Bashan
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shashi Bhushan
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Michael W Gray
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1X5
| | - Ada Yonath
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Moran Shalev-Benami
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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22
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Gonzalez G, Cui Y, Wang P, Wang Y. Normalized retention time for scheduled liquid chromatography-multistage mass spectrometry analysis of epitranscriptomic modifications. J Chromatogr A 2020; 1623:461181. [PMID: 32505282 PMCID: PMC7962276 DOI: 10.1016/j.chroma.2020.461181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 04/26/2020] [Accepted: 04/27/2020] [Indexed: 02/01/2023]
Abstract
Investigations into post-transcriptional modifications of RNA and their regulatory proteins have revealed pivotal roles of these modifications in cellular functions. A robust method for the quantitative analysis of modified nucleosides in RNA may facilitate the assessment about their functions in RNA biology and disease etiology. Here, we developed a sensitive nano-liquid chromatography-multistage mass spectrometry (nLC-MS3) method for profiling simultaneously 27 modified ribonucleosides. We employed normalized retention time (iRT) and scheduled selected-reaction monitoring (SRM) to achieve high-throughput analysis, where we assigned iRT values for modified ribonucleosides based on their relative elution times with respect to the four canonical ribonucleosides. The iRT scores allowed for reliable predictions of retention times for modified ribonucleosides with the use of two types of stationary phase materials and various mobile phase gradients. The method enabled the identification of 20 modified ribonucleosides with the use of the enzymatic digestion mixture of 2.5 ng total RNA and facilitated robust quantification of modified cytidine derivatives in total RNA. Together, we established a scheduled SRM-based method for high-throughput analysis of modified ribonucleosides with the use of a few nanograms of RNA.
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Affiliation(s)
| | - Yuxiang Cui
- Environmental Toxicology Graduate Program, United States
| | - Pengcheng Wang
- Environmental Toxicology Graduate Program, United States
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, United States; Department of Chemistry, University of California, Riverside, California 92521, United States.
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23
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Hagelskamp F, Borland K, Ramos J, Hendrick AG, Fu D, Kellner S. Broadly applicable oligonucleotide mass spectrometry for the analysis of RNA writers and erasers in vitro. Nucleic Acids Res 2020; 48:e41. [PMID: 32083657 PMCID: PMC7144906 DOI: 10.1093/nar/gkaa091] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 01/23/2020] [Accepted: 02/06/2020] [Indexed: 12/20/2022] Open
Abstract
RNAs are post-transcriptionally modified by dedicated writer or eraser enzymes that add or remove specific modifications, respectively. Mass spectrometry (MS) of RNA is a useful tool to study the modification state of an oligonucleotide (ON) in a sensitive manner. Here, we developed an ion-pairing reagent free chromatography for positive ion detection of ONs by low- and high-resolution MS, which does not interfere with other types of small compound analyses done on the same instrument. We apply ON-MS to determine the ONs from an RNase T1 digest of in vitro transcribed tRNA, which are purified after ribozyme-fusion transcription by automated size exclusion chromatography. The thus produced tRNAValAAC is substrate of the human tRNA ADAT2/3 enzyme and we confirm the deamination of adenosine to inosine and the formation of tRNAValIACin vitro by ON-MS. Furthermore, low resolution ON-MS is used to monitor the demethylation of ONs containing 1-methyladenosine by bacterial AlkB in vitro. The power of high-resolution ON-MS is demonstrated by the detection and mapping of modified ONs from native total tRNA digested with RNase T1. Overall, we present an oligonucleotide MS method which is broadly applicable to monitor in vitro RNA (de-)modification processes and native RNA.
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Affiliation(s)
- Felix Hagelskamp
- Department of Chemistry, Ludwig Maximilians University Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Kayla Borland
- Department of Chemistry, Ludwig Maximilians University Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Jillian Ramos
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY 14627, USA
| | - Alan G Hendrick
- STORM Therapeutics, Moneta Building, Babraham Research Campus, Cambridge CB22 3AT UK
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY 14627, USA
| | - Stefanie Kellner
- Department of Chemistry, Ludwig Maximilians University Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
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24
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Dremann DN, Chow CS. The use of electrospray ionization mass spectrometry to monitor RNA-ligand interactions. Methods Enzymol 2020; 623:315-337. [PMID: 31239052 DOI: 10.1016/bs.mie.2019.05.013] [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] [Indexed: 02/04/2023]
Abstract
RNAs are drawing increasing attention as potential therapeutic targets. A significant challenge in the RNA drug discovery process is identification of compounds that not only disrupt the natural functions of RNA by binding with high affinity, but also do so selectively. Assessing the binding mode of small molecules with RNA is important for understanding how they select their binding site and impart their mechanism of action. A number of complementary assays are often employed for analysis of the binding mode and to determine selectivity. One important technique that gives information about the binding affinity and stoichiometry is electrospray ionization mass spectrometry (ESI MS). More recent methods have also revealed the usefulness of ESI MS in determining the binding loci of small molecules on RNA.
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25
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Ou X, Ma B, Zhang R, Miao Z, Cheng A, Peppelenbosch MP, Pan Q. A simplified qPCR method revealing tRNAome remodeling upon infection by genotype 3 hepatitis E virus. FEBS Lett 2020; 594:2005-2015. [PMID: 32133647 DOI: 10.1002/1873-3468.13764] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/08/2020] [Accepted: 02/21/2020] [Indexed: 12/14/2022]
Abstract
The landscape of tRNA-viral codons regulates viral adaption at the translational level, presumably through adapting to host codon usage or modulating the host tRNAome. We found that the major zoonotic genotype of hepatitis E virus (HEV) has not adapted to host codon usage, prompting exploration of the effects of HEV infection on the host tRNAome. However, tRNAome quantification is largely impeded by the extremely short sequences of tRNAs and redundancy of tRNA genes. Here, we present a length-extension and stepwise simplified qPCR method that utilizes a universal DNA/RNA hybrid tRNA adaptor and degenerate primers. Using this novel methodology, we observe that HEV infection dramatically reprograms the hepatic tRNAome, which is likely to facilitate translation of viral RNAs. This tRNAome quantification method bears broad implications for future tRNA research and possibly tRNA-based diagnostics.
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Affiliation(s)
- Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Department of Gastroenterology and Hepatology, Erasmus MC - University Medical Center Rotterdam, The Netherlands
| | - Buyun Ma
- Department of Gastroenterology and Hepatology, Erasmus MC - University Medical Center Rotterdam, The Netherlands
| | - Ruyi Zhang
- Department of Gastroenterology and Hepatology, Erasmus MC - University Medical Center Rotterdam, The Netherlands
| | - Zhijiang Miao
- Department of Gastroenterology and Hepatology, Erasmus MC - University Medical Center Rotterdam, The Netherlands
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Maikel P Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC - University Medical Center Rotterdam, The Netherlands
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus MC - University Medical Center Rotterdam, The Netherlands
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26
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Meyer B, Immer C, Kaiser S, Sharma S, Yang J, Watzinger P, Weiß L, Kotter A, Helm M, Seitz HM, Kötter P, Kellner S, Entian KD, Wöhnert J. Identification of the 3-amino-3-carboxypropyl (acp) transferase enzyme responsible for acp3U formation at position 47 in Escherichia coli tRNAs. Nucleic Acids Res 2020; 48:1435-1450. [PMID: 31863583 PMCID: PMC7026641 DOI: 10.1093/nar/gkz1191] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 02/06/2023] Open
Abstract
tRNAs from all domains of life contain modified nucleotides. However, even for the experimentally most thoroughly characterized model organism Escherichia coli not all tRNA modification enzymes are known. In particular, no enzyme has been found yet for introducing the acp3U modification at position 47 in the variable loop of eight E. coli tRNAs. Here we identify the so far functionally uncharacterized YfiP protein as the SAM-dependent 3-amino-3-carboxypropyl transferase catalyzing this modification and thereby extend the list of known tRNA modification enzymes in E. coli. Similar to the Tsr3 enzymes that introduce acp modifications at U or m1Ψ nucleotides in rRNAs this protein contains a DTW domain suggesting that acp transfer reactions to RNA nucleotides are a general function of DTW domain containing proteins. The introduction of the acp3U-47 modification in E. coli tRNAs is promoted by the presence of the m7G-46 modification as well as by growth in rich medium. However, a deletion of the enzymes responsible for the modifications at position 46 and 47 in the variable loop of E. coli tRNAs did not lead to a clearly discernible phenotype suggesting that these two modifications play only a minor role in ensuring the proper function of tRNAs in E. coli.
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Affiliation(s)
- Britta Meyer
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Carina Immer
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Steffen Kaiser
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5, 81377 Munich, Germany
| | - Sunny Sharma
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany.,Department of Cell Biology and Neurosciences, Rutgers University, Piscataway, NJ 08854, USA
| | - Jun Yang
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany.,Department of Cell Biology and Neurosciences, Rutgers University, Piscataway, NJ 08854, USA
| | - Peter Watzinger
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Lena Weiß
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Annika Kotter
- Institute of Pharmacy and Biochemistry, Johannes-Gutenberg-Universität Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes-Gutenberg-Universität Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Hans-Michael Seitz
- Institute for Geosciences, Research Unit Mineralogy, and Frankfurt Isotope and Element Research Center (FIERCE), Goethe-Universität Frankfurt, Altenhöferallee 1, 60438 Frankfurt/M., Germany
| | - Peter Kötter
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Stefanie Kellner
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5, 81377 Munich, Germany
| | - Karl-Dieter Entian
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany.,Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
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27
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Li X, Liang QX, Lin JR, Peng J, Yang JH, Yi C, Yu Y, Zhang QC, Zhou KR. Epitranscriptomic technologies and analyses. SCIENCE CHINA-LIFE SCIENCES 2020; 63:501-515. [DOI: 10.1007/s11427-019-1658-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 02/12/2020] [Indexed: 01/28/2023]
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28
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Thakur P, Estevez M, Lobue PA, Limbach PA, Addepalli B. Improved RNA modification mapping of cellular non-coding RNAs using C- and U-specific RNases. Analyst 2020; 145:816-827. [PMID: 31825413 PMCID: PMC7002195 DOI: 10.1039/c9an02111f] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Locating ribonucleoside modifications within an RNA sequence requires digestion of the RNA into oligoribonucleotides of amenable size for subsequent analysis by LC-MS (liquid chromatography-mass spectrometry). This approach, widely referred to as RNA modification mapping, is facilitated through ribonucleases (RNases) such as T1 (guanosine-specific), U2 (purine-selective) and A (pyrimidine-specific) among others. Sequence coverage by these enzymes depends on positioning of the recognized nucleobase (such as guanine or purine or pyrimidine) in the sequence and its ribonucleotide composition. Using E. coli transfer RNA (tRNA) and ribosomal RNA (rRNA) as model samples, we demonstrate the ability of complementary nucleobase-specific ribonucleases cusativin (C-specific) and MC1 (U-specific) to generate digestion products that facilitate confident mapping of modifications in regions such as G-rich and pyrimidine-rich segments of RNA, and to distinguish C to U sequence differences. These enzymes also increase the number of oligonucleotide digestion products that are unique to a specific RNA sequence. Further, with these additional RNases, multiple modifications can be localized with high confidence in a single set of experiments with minimal dependence on the individual tRNA abundance in a mixture. The sequence overlaps observed with these complementary digestion products and that of RNase T1 improved sequence coverage to 75% or above. A similar level of sequence coverage was also observed for the 2904 nt long 23S rRNA indicating their utility has no dependence on RNA size. Wide-scale adoption of these additional modification mapping tools could help expedite the characterization of modified RNA sequences to understand their structural and functional role in various living systems.
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Affiliation(s)
- Priti Thakur
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA.
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29
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Mapping of Posttranscriptional tRNA Modifications by Two-Dimensional Gel Electrophoresis Mass Spectrometry. Methods Mol Biol 2020; 2113:101-110. [PMID: 32006310 DOI: 10.1007/978-1-0716-0278-2_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
RNA modification mapping by mass spectrometry (MS) is based on the use of specific ribonucleases (RNases) that generate short oligonucleotide digestion products which are further separated by nano-liquid chromatography and analyzed by MS and MS/MS. Recent developments in MS instrumentation allow the possibility to deeply explore posttranscriptional modifications. Notably, development of nano-liquid chromatography and nano-electrospray drastically increases the detection sensitivity and allows the identification and sequencing of RNA digested fragments separated and extracted from two-dimensional polyacrylamide gels, as long as the mapping and characterization of ribonucleotide modifications.
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30
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Nakayama H, Yamauchi Y, Nobe Y, Sato K, Takahashi N, Shalev-Benami M, Isobe T, Taoka M. Method for Direct Mass-Spectrometry-Based Identification of Monomethylated RNA Nucleoside Positional Isomers and Its Application to the Analysis of Leishmania rRNA. Anal Chem 2019; 91:15634-15643. [DOI: 10.1021/acs.analchem.9b03735] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hiroshi Nakayama
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama 351-0198, Japan
| | - Yoshio Yamauchi
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan
| | - Yuko Nobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan
| | - Ko Sato
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan
| | - Nobuhiro Takahashi
- Department of Biotechnology, Global Innovation Research Institute, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo 183-8509, Japan
| | - Moran Shalev-Benami
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan
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31
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Lowenthal MS, Quittman E, Phinney KW. Absolute Quantification of RNA or DNA Using Acid Hydrolysis and Mass Spectrometry. Anal Chem 2019; 91:14569-14576. [PMID: 31638773 DOI: 10.1021/acs.analchem.9b03625] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Accurate, traceable quantification of ribonucleotide or deoxyribonucleotide oligomers is achievable using acid hydrolysis and isotope dilution mass spectrometry (ID-MS). In this work, formic acid hydrolysis is demonstrated to generate stoichiometric release of nucleobases from intact oligonucleotides, which then can be measured by ID-MS, facilitating true and precise absolute quantification of RNA, short linearized DNA, or genomic DNA. Surrogate nucleobases are quantified with a liquid chromatography-tandem mass spectrometry (LC-MS/MS) workflow, using multiple reaction monitoring (MRM). Nucleobases were chromatographically resolved using a novel cation-exchange separation, incorporating a pH gradient. Trueness of this quantitative assay is estimated from agreement among the surrogate nucleobases and by comparison to concentrations provided for commercial materials or Standard Reference Materials (SRMs) from the National Institute of Standards and Technology (NIST). Comparable concentration estimates using NanoDrop spectrophotometry or established from droplet-digital polymerase chain reaction (ddPCR) techniques agree well with the results. Acid hydrolysis-ID-LC-MS/MS provides excellent quantitative selectivity and accuracy while enabling traceability to mass unit. Additionally, this approach can be uniquely useful for quantifying modified nucleobases or mixtures.
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Affiliation(s)
- Mark S Lowenthal
- Biomolecular Measurement Division , National Institute of Standards and Technology , 100 Bureau Drive, Stop 8314 , Gaithersburg , Maryland 20899 , United States
| | - Eva Quittman
- Biomolecular Measurement Division , National Institute of Standards and Technology , 100 Bureau Drive, Stop 8314 , Gaithersburg , Maryland 20899 , United States
| | - Karen W Phinney
- Biomolecular Measurement Division , National Institute of Standards and Technology , 100 Bureau Drive, Stop 8314 , Gaithersburg , Maryland 20899 , United States
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32
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Konno M, Koseki J, Asai A, Yamagata A, Shimamura T, Motooka D, Okuzaki D, Kawamoto K, Mizushima T, Eguchi H, Takiguchi S, Satoh T, Mimori K, Ochiya T, Doki Y, Ofusa K, Mori M, Ishii H. Distinct methylation levels of mature microRNAs in gastrointestinal cancers. Nat Commun 2019; 10:3888. [PMID: 31467274 PMCID: PMC6715669 DOI: 10.1038/s41467-019-11826-1] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 08/06/2019] [Indexed: 02/07/2023] Open
Abstract
The biological significance of micro (mi)RNAs has traditionally been evaluated according to their RNA expression levels based on the assumption that miRNAs recognize and regulate their targets in an unvarying fashion. Here we show that a fraction of mature miRNAs including miR-17-5p, -21-5p, and -200c-3p and let-7a-5p harbor methyl marks that potentially alter their stability and target recognition. Importantly, methylation of these miRNAs was significantly increased in cancer tissues as compared to paired normal tissues. Furthermore, miR-17-5p methylation level in serum samples distinguished early pancreatic cancer patients from healthy controls with extremely high sensitivity and specificity. These findings provide a basis for diagnostic strategies for early-stage cancer and add a dimension to our understanding of miRNA biology. In cancer it is assumed that microRNAs recognise and regulate their targets uniformly. Here, the authors show that in gastrointestinal cancers methylation of microRNAs may impact their stability, and that levels of microRNA methylation are distinct in pancreatic cancer patients compared to healthy controls with potential diagnostic implications.
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Affiliation(s)
- Masamitsu Konno
- Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Jun Koseki
- Department of Cancer Profiling Discovery/ Medical Data Science, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Ayumu Asai
- Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.,Department of Cancer Profiling Discovery/ Medical Data Science, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Akira Yamagata
- Prophoenix Division, Food and Life-Science Laboratory, Idea Consultants, Inc., Osaka-city, Osaka, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Koichi Kawamoto
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Tsunekazu Mizushima
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Shuji Takiguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.,Department of Gastroenterological Surgery, Nagoya City University Graduate School of Medical Sciences and Medical School, Nagoya, Aichi, Japan
| | - Taroh Satoh
- Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Oita, Japan
| | - Takahiro Ochiya
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Ken Ofusa
- Prophoenix Division, Food and Life-Science Laboratory, Idea Consultants, Inc., Osaka-city, Osaka, Japan.
| | - Masaki Mori
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
| | - Hideshi Ishii
- Department of Cancer Profiling Discovery/ Medical Data Science, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
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33
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Tardu M, Jones JD, Kennedy RT, Lin Q, Koutmou KS. Identification and Quantification of Modified Nucleosides in Saccharomyces cerevisiae mRNAs. ACS Chem Biol 2019; 14:1403-1409. [PMID: 31243956 DOI: 10.1021/acschembio.9b00369] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Post-transcriptional modifications to messenger RNAs (mRNAs) have the potential to alter the biological function of this important class of biomolecules. The study of mRNA modifications is a rapidly emerging field, and the full complement of chemical modifications in mRNAs is not yet established. We sought to identify and quantify the modifications present in yeast mRNAs using an ultra-high performance liquid chromatography tandem mass spectrometry method to detect 40 nucleoside variations in parallel. We observe six modified nucleosides with high confidence in highly purified mRNA samples (N7-methylguanosine, N6-methyladenosine, 2'-O-methylguanosine, 2'-O-methylcytidine, N4-acetylcytidine, and 5-formylcytidine) and identify the yeast protein responsible for N4-acetylcytidine incorporation in mRNAs (Rra1). In addition, we find that mRNA modification levels change in response to heat shock, glucose starvation, and/or oxidative stress. This work expands the repertoire of potential chemical modifications in mRNAs and highlights the value of integrating mass spectrometry tools in the mRNA modification discovery and characterization pipeline.
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Affiliation(s)
- Mehmet Tardu
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Joshua D. Jones
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Robert T. Kennedy
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Qishan Lin
- Mass Spectrometry Consortium for Epitranscriptomics, University at Albany, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Kristin S. Koutmou
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
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34
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Leitner A, Dorn G, Allain FHT. Combining Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) Spectroscopy for Integrative Structural Biology of Protein-RNA Complexes. Cold Spring Harb Perspect Biol 2019; 11:11/7/a032359. [PMID: 31262947 DOI: 10.1101/cshperspect.a032359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Deciphering complex RNA-protein interactions on a (near-)atomic level is a hurdle that hinders advancing our understanding of fundamental processes in RNA metabolism and RNA-based gene regulation. To overcome challenges associated with individual structure determination methods, structural information derived from complementary biophysical methods can be combined in integrative structural biology approaches. Here, we review recent advances in such hybrid structural approaches with a focus on combining mass spectrometric analysis of cross-linked protein-RNA complexes and nuclear magnetic resonance (NMR) spectroscopy.
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Affiliation(s)
- Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Georg Dorn
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
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35
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Ranjan N, Leidel SA. The epitranscriptome in translation regulation: mRNA and tRNA modifications as the two sides of the same coin? FEBS Lett 2019; 593:1483-1493. [PMID: 31206634 DOI: 10.1002/1873-3468.13491] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/07/2019] [Accepted: 06/11/2019] [Indexed: 12/17/2022]
Abstract
Translation of mRNA is a highly regulated process that is tightly coordinated with cotranslational protein maturation. Recently, mRNA modifications and tRNA modifications - the so called epitranscriptome - have added a new layer of regulation that is still poorly understood. Both types of modifications can affect codon-anticodon interactions, thereby affecting mRNA translation and protein synthesis in similar ways. Here, we describe an updated view on how the different types of modifications can be mapped, how they affect translation, how they trigger phenotypes and discuss how the combined action of mRNA and tRNA modifications coordinate translation in health and disease.
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Affiliation(s)
- Namit Ranjan
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
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36
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Motorin Y, Marchand V. Detection and Analysis of RNA Ribose 2'-O-Methylations: Challenges and Solutions. Genes (Basel) 2018; 9:genes9120642. [PMID: 30567409 PMCID: PMC6316082 DOI: 10.3390/genes9120642] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 12/11/2018] [Accepted: 12/13/2018] [Indexed: 02/07/2023] Open
Abstract
Ribose 2'-O-methylation is certainly one of the most common RNA modifications found in almost any type of cellular RNA. It decorates transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), small nuclear RNAs (snRNAs) (and most probably small nucleolar RNAs, snoRNAs), as well as regulatory RNAs like microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), and finally, eukaryotic messenger RNAs (mRNAs). Due to this exceptional widespread of RNA 2'-O-methylation, considerable efforts were made in order to precisely map these numerous modifications. Extensive studies of RNA 2'-O-methylation were also stimulated by the discovery of C/D-box snoRNA-guided machinery, which insures site-specific modification of hundreds 2'-O-methylated residues in archaeal and eukaryotic rRNAs and some other RNAs. In this brief review we discussed both traditional approaches of RNA biochemistry and also modern deep sequencing-based methods, used for detection/mapping and quantification of RNA 2'-O-methylations.
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Affiliation(s)
- Yuri Motorin
- UMR7365 IMoPA, Biopôle, CNRS-Lorraine University, 9 Avenue de la Forêt de Haye, 54505 Vandoeuvre-les-Nancy, France.
| | - Virginie Marchand
- UMS2008 IBSLor, Biopôle, CNRS-Lorraine University-INSERM, 9 Avenue de la Forêt de Haye, 54505 Vandoeuvre-les-Nancy, France.
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Solivio B, Yu N, Addepalli B, Limbach PA. Improving RNA modification mapping sequence coverage by LC-MS through a nonspecific RNase U2-E49A mutant. Anal Chim Acta 2018; 1036:73-79. [PMID: 30253839 PMCID: PMC6214470 DOI: 10.1016/j.aca.2018.08.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/31/2018] [Accepted: 08/03/2018] [Indexed: 11/21/2022]
Abstract
We report the identification and use of a mutant of the purine selective ribonuclease RNase U2 that randomly cleaves RNA in a manner that is directly compatible with RNA modification mapping by mass spectrometry. A number of RNase U2 mutants were generated using site-saturation mutagenesis. The enzyme activity and specificity were tested using oligonucleotide substrates, which revealed an RNase U2 E49A mutant with limited specificity and a tendency to undercut RNA. Using this mutant, RNA digestion conditions were optimized to yield long, overlapping digestion products, which improve sequence coverage in RNA modification mapping experiments. The analytical utility of this mutant was demonstrated by liquid chromatography tandem mass spectrometry (LC-MS/MS) mapping of several modified RNAs where 100% sequence coverage could be obtained using only a single enzymatic digestion. This new mutant facilitates more accurate and efficient RNA modification mapping than traditional highly base-specific RNases that are currently used.
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Affiliation(s)
- Beulah Solivio
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH, 45221-0172, United States
| | - Ningxi Yu
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH, 45221-0172, United States
| | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH, 45221-0172, United States
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH, 45221-0172, United States.
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Detection of ribonucleoside modifications by liquid chromatography coupled with mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:280-290. [PMID: 30414470 DOI: 10.1016/j.bbagrm.2018.10.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/20/2018] [Accepted: 10/27/2018] [Indexed: 12/21/2022]
Abstract
A small set of ribonucleoside modifications have been found in different regions of mRNA including the open reading frame. Accurate detection of these specific modifications is critical to understanding their modulatory roles in facilitating mRNA maturation, translation and degradation. While transcriptome-wide next-generation sequencing (NGS) techniques could provide exhaustive information about the sites of one specific or class of modifications at a time, recent investigations strongly indicate cautionary interpretation due to the appearance of false positives. Therefore, it is suggested that NGS-based modification data can only be treated as predicted sites and their existence need to be validated by orthogonal methods. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is an analytical technique that can yield accurate and reproducible information about the qualitative and quantitative characteristics of ribonucleoside modifications. Here, we review the recent advancements in LC-MS/MS technology that could help in securing accurate, gold-standard quality information about the resident post-transcriptional modifications of mRNA.
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Hamlow LA, Zhu Y, Devereaux ZJ, Cunningham NA, Berden G, Oomens J, Rodgers MT. Modified Quadrupole Ion Trap Mass Spectrometer for Infrared Ion Spectroscopy: Application to Protonated Thiated Uridines. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2125-2137. [PMID: 30136214 DOI: 10.1007/s13361-018-2047-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 05/17/2023]
Abstract
Modifications to a Paul-type quadrupole ion trap mass spectrometer providing optical access to the trapped ion cloud as well as hardware and software for coupling to a table-top IR optical parametric oscillator laser (OPO) are detailed. Critical experimental parameters for infrared multiple photon dissociation (IRMPD) on this instrument are characterized. IRMPD action spectra, collected in the hydrogen-stretching region with this instrument, complemented by spectra in the IR fingerprint region acquired at the FELIX facility, are employed to characterize the structures of the protonated forms of 2-thiouridine, [s2Urd+H]+, and 4-thiouridine, [s4Urd+H]+. The measured spectra are compared with predicted linear IR spectra calculated at the B3LYP/6-311+G(d,p) level of theory to determine the conformers populated in the experiments. This comparison indicates that thiation at the 2- or 4-positions shifts the protonation preference between the 2,4-H tautomer and 4-protonation in opposite directions versus canonical uridine, which displays a roughly equal preference for the 2,4-H tautomer and O4 protonation. As found for canonical uridine, protonation leads to a mixture of conformers exhibiting C2'-endo and C3'-endo sugar puckering with an anti nucleobase orientation being populated for both 2- and 4-thiated uridine. Graphical Abstract ᅟ.
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Affiliation(s)
- L A Hamlow
- Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, MI, 48202, USA
| | - Y Zhu
- Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, MI, 48202, USA
| | - Zachary J Devereaux
- Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, MI, 48202, USA
| | - N A Cunningham
- Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, MI, 48202, USA
| | - G Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - J Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - M T Rodgers
- Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, MI, 48202, USA.
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Xiong Y, Shi L, Wang L, Zhou Z, Wang C, Lin Y, Luo D, Qiu J, Chen D. Activation of sirtuin 1 by catalpol-induced down-regulation of microRNA-132 attenuates endoplasmic reticulum stress in colitis. Pharmacol Res 2017; 123:73-82. [DOI: 10.1016/j.phrs.2017.05.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/23/2017] [Accepted: 05/23/2017] [Indexed: 02/06/2023]
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Novel ribonuclease activity of cusativin from Cucumis sativus for mapping nucleoside modifications in RNA. Anal Bioanal Chem 2017; 409:5645-5654. [PMID: 28730304 DOI: 10.1007/s00216-017-0500-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/14/2017] [Accepted: 06/27/2017] [Indexed: 01/05/2023]
Abstract
A recombinant ribonuclease, cusativin, was characterized for its cytidine-specific cleavage ability of RNA to map chemical modifications. Following purification of native cusativin protein as described before (Rojo et al. Planta 194:328, 17), partial amino acid sequencing was carried out to identify the corresponding protein coding gene in cucumber genome. Cloning and heterologous expression of the identified gene in Escherichia coli resulted in successful production of active protein as a C-terminal His-tag fusion protein. The ribonuclease activity and cleavage specificity of the fusion protein were confirmed with a variety of tRNA isoacceptors and total tRNA. Characterization of cusativin digestion products by ion-pairing reverse-phase liquid chromatography coupled with mass spectrometry (IP-RP-LC-MS) analysis revealed cleavage of CpA, CpG, and CpU phosphodiester bonds at the 3'-terminus of cytidine under optimal digestion conditions. Ribose methylation or acetylation of cytosine inhibited RNA cleavage. The CpC phosphodiester bond was also resistant to cusativin-mediated RNA cleavage; a feature to our knowledge has not been reported for other nucleobase-specific ribonucleases. Here, we demonstrate the analytical utility of such a novel feature for obtaining high-sequence coverage and accurate mapping of modified residues in substrate RNAs. Graphical abstract Cytidine-specific novel ribonuclease activity of cusativin.
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Mapping Post-Transcriptional Modifications onto Transfer Ribonucleic Acid Sequences by Liquid Chromatography Tandem Mass Spectrometry. Biomolecules 2017; 7:biom7010021. [PMID: 28241457 PMCID: PMC5372733 DOI: 10.3390/biom7010021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 02/15/2017] [Indexed: 01/07/2023] Open
Abstract
Liquid chromatography, coupled with tandem mass spectrometry, has become one of the most popular methods for the analysis of post-transcriptionally modified transfer ribonucleic acids (tRNAs). Given that the information collected using this platform is entirely determined by the mass of the analyte, it has proven to be the gold standard for accurately assigning nucleobases to the sequence. For the past few decades many labs have worked to improve the analysis, contiguous to instrumentation manufacturers developing faster and more sensitive instruments. With biological discoveries relating to ribonucleic acid happening more frequently, mass spectrometry has been invaluable in helping to understand what is happening at the molecular level. Here we present a brief overview of the methods that have been developed and refined for the analysis of modified tRNAs by liquid chromatography tandem mass spectrometry.
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Limbach PA, June Paulines M. Going global: the new era of mapping modifications in RNA. WILEY INTERDISCIPLINARY REVIEWS. RNA 2017; 8:10.1002/wrna.1367. [PMID: 27251302 PMCID: PMC5133204 DOI: 10.1002/wrna.1367] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 04/22/2016] [Accepted: 04/28/2016] [Indexed: 12/30/2022]
Abstract
The post-transcriptional modification of RNA by the addition of one or more chemical groups has been known for over 50 years. These chemical modifications, once thought to be static, are now being discovered to play key regulatory roles in gene expression. The advent of massive parallel sequencing of RNA (RNA-seq) now allows us to probe the complexity of cellular RNA and how chemically altering RNA structure expands the RNA vocabulary. Here we present an overview of the various strategies and technologies that are available to profile RNA chemical modifications at the cellular level. These strategies can be characterized as targeted and untargeted approaches: targeted strategies are developed for one single chemical modification while untargeted strategies are more broadly applicable to a range of such chemical changes. Key for all of these approaches is the ability to locate modifications within the RNA sequence. While most of these methods are built upon an RNA-Seq pipeline, alternative approaches based on mass spectrometry or conventional DNA sequencing retain value in the overall analysis process. We also look forward toward future opportunities and technologies that may expand the types of modifications that can be globally profiled. Given the ever increasing recognition that these RNA chemical modifications play important biological roles, a variety of methods, preferably orthogonal approaches, will be required to globally identify, validate and quantify RNA chemical modifications found in the transcriptome. WIREs RNA 2017, 8:e1367. doi: 10.1002/wrna.1367 For further resources related to this article, please visit the WIREs website.
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Jiang J, Seo H, Chow CS. Post-transcriptional Modifications Modulate rRNA Structure and Ligand Interactions. Acc Chem Res 2016; 49:893-901. [PMID: 27064497 DOI: 10.1021/acs.accounts.6b00014] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Post-transcriptional modifications play important roles in modulating the functions of RNA species. The presence of modifications in RNA may directly alter its interactions with binding partners or cause structural changes that indirectly affect ligand recognition. Given the rapidly growing list of modifications identified in noncoding and mRNAs associated with human disease, as well as the dynamic control over modifications involved in various physiological processes, it is imperative to understand RNA structural modulation by these modifications. Among the RNA species, rRNAs provide numerous examples of modification types located in differing sequence and structural contexts. In addition, the modified rRNA motifs participate in a wide variety of ligand interactions, including those with RNA, protein, and small molecules. In fact, several classes of antibiotics exert their effects on protein synthesis by binding to functionally important and highly modified regions of the rRNAs. These RNA regions often display conservation in sequence, secondary structure, tertiary interactions, and modifications, trademarks of ideal drug-targeting sites. Furthermore, ligand interactions with such regions often favor certain modification-induced conformational states of the RNA. Our laboratory has employed a combination of biophysical methods such as nuclear magnetic resonance spectroscopy (NMR), circular dichroism, and UV melting to study rRNA modifications in functionally important motifs, including helix 31 (h31) and helix h44 (h44) of the small subunit rRNA and helix 69 (H69) of the large subunit rRNA. The modified RNA oligonucleotides used in these studies were generated by solid-phase synthesis with a variety of phosphoramidite chemistries. The natural modifications were shown to impact thermal stability, dynamic behavior, and tertiary structures of the RNAs, with additive or cooperative effects occurring with multiple, clustered modifications. Taking advantage of the structural diversity offered by specific modifications in the chosen rRNA motifs, phage display was used to select peptides that bind with moderate (low micromolar) affinity and selectivity to modified h31, h44, and H69. Interactions between peptide ligands and RNAs were monitored by biophysical methods, including electrospray ionization mass spectrometry (ESI-MS), NMR, and surface plasmon resonance (SPR). The peptides compare well with natural compounds such as aminoglycosides in their binding affinities to the modified rRNA constructs. Some candidates were shown to exhibit specificity toward different modification states of the rRNA motifs. The selected peptides may be further optimized for improved RNA targeting or used in screening assays for new drug candidates. In this Account, we hope to stimulate interest in bioorganic and biophysical approaches, which may be used to deepen our understanding of other functionally important, naturally modified RNAs beyond the rRNAs.
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Affiliation(s)
- Jun Jiang
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Hyosuk Seo
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Christine S. Chow
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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Abstract
A common feature of ribonucleic acids (RNAs) is that they can undergo a variety of chemical modifications. As nearly all of these chemical modifications result in an increase in the mass of the canonical nucleoside, mass spectrometry has long been a powerful approach for identifying and characterizing modified RNAs. Over the past several years, significant advances have been made in method development and software for interpreting tandem mass spectra resulting in approaches that can yield qualitative and quantitative information on RNA modifications, often at the level of sequence specificity. We discuss these advances along with instrumentation developments that have increased our ability to extract such information from relatively complex biological samples. With the increasing interest in how these modifications impact the epitranscriptome, mass spectrometry will continue to play an important role in bioanalytical investigations revolving around RNA.
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Affiliation(s)
- Collin Wetzel
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, PO Box 210172. and University of Cincinnati, Cincinnati, OH 45221-0172, USA.
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Post-Transcriptional Modifications of RNA: Impact on RNA Function and Human Health. MODIFIED NUCLEIC ACIDS IN BIOLOGY AND MEDICINE 2016. [DOI: 10.1007/978-3-319-34175-0_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Basanta-Sanchez M, Temple S, Ansari SA, D'Amico A, Agris PF. Attomole quantification and global profile of RNA modifications: Epitranscriptome of human neural stem cells. Nucleic Acids Res 2015; 44:e26. [PMID: 26438536 PMCID: PMC4756851 DOI: 10.1093/nar/gkv971] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/15/2015] [Indexed: 01/09/2023] Open
Abstract
Exploration of the epitranscriptome requires the development of highly sensitive and accurate technologies in order to elucidate the contributions of the more than 100 RNA modifications to cell processes. A highly sensitive and accurate ultra-high performance liquid chromatography—tandem mass spectrometry method was developed to simultaneously detect and quantify 28 modified and four major nucleosides in less than 20 min. Absolute concentrations were calculated using extinction coefficients of each of the RNA modifications studied. A comprehensive RNA modifications database of UV profiles and extinction coefficient is reported within a 2.3–5.2 % relative standard deviation. Excellent linearity was observed 0.99227–0.99999 and limit of detection values ranged from 63.75 attomoles to 1.21 femtomoles. The analytical performance was evaluated by analyzing RNA modifications from 100 ng of RNA from human pluripotent stem cell-derived neural cells. Modifications were detected at concentrations four orders of magnitude lower than the corresponding parental nucleosides, and as low as 23.01 femtograms, 64.09 attomoles. Direct and global quantitative analysis of RNA modifications are among the advantages of this new approach.
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Affiliation(s)
| | | | | | - Anna D'Amico
- The RNA Institute, University at Albany, Albany, NY, USA
| | - Paul F Agris
- The RNA Institute, University at Albany, Albany, NY, USA
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Addepalli B, Lesner NP, Limbach PA. Detection of RNA nucleoside modifications with the uridine-specific ribonuclease MC1 from Momordica charantia. RNA (NEW YORK, N.Y.) 2015; 21:1746-1756. [PMID: 26221047 PMCID: PMC4574751 DOI: 10.1261/rna.052472.115] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 06/28/2015] [Indexed: 06/06/2023]
Abstract
A codon-optimized recombinant ribonuclease, MC1 is characterized for its uridine-specific cleavage ability to map nucleoside modifications in RNA. The published MC1 amino acid sequence, as noted in a previous study, was used as a template to construct a synthetic gene with a natural codon bias favoring expression in Escherichia coli. Following optimization of various expression conditions, the active recombinant ribonuclease was successfully purified as a C-terminal His-tag fusion protein from E. coli [Rosetta 2(DE3)] cells. The isolated protein was tested for its ribonuclease activity against oligoribonucleotides and commercially available E. coli tRNA(Tyr I). Analysis of MC1 digestion products by ion-pairing reverse phase liquid-chromatography coupled with mass spectrometry (IP-RP-LC-MS) revealed enzymatic cleavage of RNA at the 5'-termini of uridine and pseudouridine, but cleavage was absent if the uridine was chemically modified or preceded by a nucleoside with a bulky modification. Furthermore, the utility of this enzyme to generate complementary digestion products to other common endonucleases, such as RNase T1, which enables the unambiguous mapping of modified residues in RNA is demonstrated.
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Affiliation(s)
- Balasubrahmanym Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, USA
| | - Nicholas P Lesner
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, USA Department of Chemistry, The College of Wooster, Wooster, Ohio 44691-2393, USA
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, USA
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Cao X, Limbach PA. Enhanced detection of post-transcriptional modifications using a mass-exclusion list strategy for RNA modification mapping by LC-MS/MS. Anal Chem 2015; 87:8433-40. [PMID: 26176336 PMCID: PMC4542202 DOI: 10.1021/acs.analchem.5b01826] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
There
has been a renewed appreciation for the dynamic nature of
ribonucleic acid (RNA) modifications and for the impact of modified
RNAs on organism health resulting in an increased emphasis on developing
analytical methods capable of detecting modifications within specific
RNA sequence contexts. Here we demonstrate that a DNA-based exclusion
list enhances data dependent liquid chromatography tandem mass spectrometry
(LC-MS/MS) detection of post-transcriptionally modified nucleosides
within specific RNA sequences. This approach is possible because all
post-transcriptional modifications of RNA, except pseudouridine, result
in a mass increase in the canonical nucleoside undergoing chemical
modification. Thus, DNA-based sequences reflect the state of the RNA
prior to or in the absence of modification. The utility of this exclusion
list strategy is demonstrated through the RNA modification mapping
of total tRNAs from the bacteria Escherichia coli, Lactococcus lactis, and Streptomyces griseus. Creation of a DNA-based exclusion list is shown to consistently
enhance the number of detected modified ribonuclease (RNase) digestion
products by ∼20%. All modified RNase digestion products that
were detected during standard data dependent acquisition (DDA) LC-MS/MS
were also detected when the DNA-based exclusion list was used. Consequently,
the increase in detected modified RNase digestion products is attributed
to new experimental information only obtained when using the exclusion
list. This exclusion list strategy should be broadly applicable to
any class of RNA and improves the utility of mass spectrometry approaches
for discovery-based analyses of RNA modifications, such as are required
for studies of the epitranscriptome.
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Affiliation(s)
- Xiaoyu Cao
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, Ohio 45221-0172, United States
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