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Sun Q, Li H, Lin Z, Cao G, Yang D, Tang D, Chen X, Pan Y, Guo M. Mass-Spectrometry-Based Assay at Single-Base Resolution for Simultaneously Detecting m 6A and m 6Am in RNA. Anal Chem 2024. [PMID: 38913599 DOI: 10.1021/acs.analchem.3c04003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The methylation modifications of adenosine, especially N6-methyladenosine (m6A) and N6, 2'-odimethyladenosine (m6Am), play vital roles in various biological, physiological, and pathological processes. However, current methods for detecting these modifications at single-base resolution have limitations. Mass spectrometry (MS), a highly accurate and sensitive technique, can be utilized to differentiate between m6A and m6Am by analyzing the molecular weight differences in their fragments during tandem MS analysis. In this study, we present an MS-based method that allows for the simultaneous determination of m6A and m6Am sites in targeted RNA fragments at single-nucleotide resolution. The approach involves the utilization of tandem MS in conjunction with targeted RNA enrichment and enzymatic digestion, eliminating the need for PCR amplification. By employing this strategy, we can accurately identify m6A and m6Am sites in targeted RNA fragments with high confidence. To evaluate the effectiveness of our method, we applied it to detect m6A and m6Am sites in cell and tissue samples. Furthermore, we verified the accuracy of our approach by performing CRISPR/Cas9-mediated knockout of the corresponding methyltransferases. Overall, our MS-based method offers a reliable and precise means for the simultaneous detection of m6A and m6Am modifications in targeted RNA fragments, providing valuable insights into the functional characterization of these modifications in various biological contexts.
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Affiliation(s)
- Qiang Sun
- College of Pharmacy, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
- Center for RNA Medicine, International Institutes of Medicine, the Fourth Affiliated Hospital of School of Medicine and Internation School of Medicine, Zhejiang University, Yiwu 310027, Zhejiang, China
| | - Haijuan Li
- College of Pharmacy, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
| | - Ziwei Lin
- College of Pharmacy, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
| | - Guodong Cao
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Dongzhi Yang
- College of Pharmacy, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
| | - Daoquan Tang
- College of Pharmacy, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
| | - Xi Chen
- College of Pharmacy, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
| | - Yuanjiang Pan
- Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, China
| | - Mengzhe Guo
- College of Pharmacy, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
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2
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Heel SV, Juen F, Bartosik K, Micura R, Kreutz C, Breuker K. Resolving the intricate binding of neomycin B to multiple binding motifs of a neomycin-sensing riboswitch aptamer by native top-down mass spectrometry and NMR spectroscopy. Nucleic Acids Res 2024; 52:4691-4701. [PMID: 38567725 PMCID: PMC11077050 DOI: 10.1093/nar/gkae224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 03/05/2024] [Accepted: 03/25/2024] [Indexed: 05/09/2024] Open
Abstract
Understanding small molecule binding to RNA can be complicated by an intricate interplay between binding stoichiometry, multiple binding motifs, different occupancies of different binding motifs, and changes in the structure of the RNA under study. Here, we use native top-down mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy to experimentally resolve these factors and gain a better understanding of the interactions between neomycin B and the 40 nt aptamer domain of a neomycin-sensing riboswitch engineered in yeast. Data from collisionally activated dissociation of the 1:1, 1:2 and 1:3 RNA-neomycin B complexes identified a third binding motif C of the riboswitch in addition to the two motifs A and B found in our previous study, and provided occupancies of the different binding motifs for each complex stoichiometry. Binding of a fourth neomycin B molecule was unspecific according to both MS and NMR data. Intriguingly, all major changes in the aptamer structure can be induced by the binding of the first neomycin B molecule regardless of whether it binds to motif A or B as evidenced by stoichiometry-resolved MS data together with titration data from 1H NMR spectroscopy in the imino proton region. Specific binding of the second and third neomycin B molecules further stabilizes the riboswitch aptamer, thereby allowing for a gradual response to increasing concentrations of neomycin B, which likely leads to a fine-tuning of the cellular regulatory mechanism.
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Affiliation(s)
- Sarah Viola Heel
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Fabian Juen
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Karolina Bartosik
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
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3
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赵 刚, 李 华, 张 鸿, 肖 克, 杨 辉, 李 子, 傅 崇. [m 6A methylase WTAP participates in renal ischemia-reperfusion injury by regulating FOXO1 expression]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2023; 43:2035-2042. [PMID: 38189389 PMCID: PMC10774094 DOI: 10.12122/j.issn.1673-4254.2023.12.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Indexed: 01/09/2024]
Abstract
OBJECTIVE To investigate the expression of WTAP, a m6A methylase, in a mouse model of renal ischemia-reperfusion (I/R) injury and the effect of WTAP knockdown on biological behavior of renal tubular epithelial cells exposed to I/R injury. METHODS Sixteen C57BL/6 mice with renal I/R injury or sham operation (n=8) were examined for blood urea nitrogen (BUN) and creatinine (Scr) levels to assess renal function, and renal pathologies were observed with HE staining. The expressions of WTAP and FOXO1 proteins in the kidneys of the mice were detected using immunohistochemistry. Human renal tubular epithelial cells (HK-2) were transfected with si-WTAP or si-NC followed by hypoxia-reoxygenation (H/R) exposure, Protein and mRNA expression were assessed by Western blot and qRT-PCR, and changes and changes in cell viability and apoptosis were assessed using CCK8 assay and TUNEL staining, respectively; LDH release level and caspase-3 activity of the cells were measured using commercial assay kits. FOXO1 m6A modification sites were predicted using SRAMP website (http://www.cuilab.cn/sramp/), and the interaction between WTAP and FOXO1 mRNA was analyzed with RIP experiment; the level of FOXO1 modified by m6A was detected by MeRIP-qPCR. RESULTS Compared with sham-operated mice, the mice with renal I/R injury showed significantly increased Scr and BUN levels (P < 0.001) and renal expressions of WTAP mRNA and protein (P < 0.001). In cultured HK-2 cells, H/R exposure significantly decreased the cell viability (P < 0.001) and increased cellular LDH release (P < 0.001) and expressions of WTAP mRNA and protein (P < 0.001). WTAP knockdown obviously reduced the cell damage induced by I/R injury and significantly decreased the mRNA and protein levels of FOXO1 in the cells (P < 0.001). RIP experiment confirmed WTAP binding to FOXO1 mRNA, and inhibition of WTAP expression significantly reduced FOXO1 m6A level in HK-2 cells (P < 0.001). CONCLUSION WTAP expression is up-regulated in the kidneys of mice with renal I/R injury and in HK-2 cells with H/R exposure. Inhibition of WTAP alleviates H/R-induced apoptotic damage in HK-2 cells possibly by inhibiting FOXO1 expression.
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Affiliation(s)
- 刚刚 赵
- 西安医学院第一附属医院泌尿外科,陕西 西安 710000Department of Urology, First Affiliated Hospital of Xi'an Medical University, Xi'an 710000, China
| | - 华锋 李
- 西安医学院第一附属医院泌尿外科,陕西 西安 710000Department of Urology, First Affiliated Hospital of Xi'an Medical University, Xi'an 710000, China
| | - 鸿毅 张
- 西安医学院第一附属医院泌尿外科,陕西 西安 710000Department of Urology, First Affiliated Hospital of Xi'an Medical University, Xi'an 710000, China
| | - 克兵 肖
- 西安医学院第一附属医院泌尿外科,陕西 西安 710000Department of Urology, First Affiliated Hospital of Xi'an Medical University, Xi'an 710000, China
| | - 辉 杨
- 西安医学院第一附属医院泌尿外科,陕西 西安 710000Department of Urology, First Affiliated Hospital of Xi'an Medical University, Xi'an 710000, China
| | - 子峰 李
- 西安医学院第一附属医院泌尿外科,陕西 西安 710000Department of Urology, First Affiliated Hospital of Xi'an Medical University, Xi'an 710000, China
| | - 崇德 傅
- 西安航天总医院泌尿外科,陕西 西安 710100Department of Urology, Xi'an Aerospace General Hospital, Xi'an 710000, China
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4
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Thaler J, Syroegin EA, Breuker K, Polikanov YS, Micura R. Practical Synthesis of N-Formylmethionylated Peptidyl-tRNA Mimics. ACS Chem Biol 2023; 18:2233-2239. [PMID: 37433044 PMCID: PMC10594587 DOI: 10.1021/acschembio.3c00237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/22/2023] [Indexed: 07/13/2023]
Abstract
Hydrolysis-resistant RNA-peptide conjugates that mimic peptidyl-tRNAs are frequently needed for structural and functional studies of protein synthesis in the ribosome. Such conjugates are accessible by chemical solid-phase synthesis, allowing for the utmost flexibility of both the peptide and the RNA sequence. Commonly used protection group strategies, however, have severe limitations with respect to generating the characteristic Nα-formylmethionyl terminus because the formyl group of the conjugate synthesized at the solid support is easily cleaved during the final basic deprotection/release step. In this study, we demonstrate a simple solution to the problem by coupling appropriately activated Nα-formyl methionine to the fully deprotected conjugate. The structural integrity of the obtained Nα-formylmethionyl conjugate─and hence the chemoselectivity of the reaction─were verified by Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry sequence analysis. Additionally, we confirmed the applicability of our procedure for structural studies by obtaining two structures of the ribosome in complex with either fMAI-nh-ACCA or fMFI-nh-ACCA in the P site and ACC-PMN in the A site of the bacterial ribosome at 2.65 and 2.60 Å resolution, respectively. In summary, our approach for hydrolysis-resistant Nα-formylated RNA-peptide conjugates is synthetically straightforward and opens up new avenues to explore ribosomal translation with high-precision substrate mimics.
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Affiliation(s)
- Julia Thaler
- Institute
of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Egor A. Syroegin
- Department
of Biological Sciences, University of Illinois
at Chicago, Chicago, Illinois 60607, United States
| | - Kathrin Breuker
- Institute
of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Yury S. Polikanov
- Department
of Biological Sciences, University of Illinois
at Chicago, Chicago, Illinois 60607, United States
- Department
of Pharmaceutical Sciences, University of
Illinois at Chicago, Chicago, Illinois 60607, United States
- Center
for Biomolecular Sciences, University of
Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Ronald Micura
- Institute
of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
- Center
for Biomolecular Sciences, University of
Illinois at Chicago, Chicago, Illinois 60607, United States
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5
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Heel SV, Bartosik K, Juen F, Kreutz C, Micura R, Breuker K. Native Top-Down Mass Spectrometry Uncovers Two Distinct Binding Motifs of a Functional Neomycin-Sensing Riboswitch Aptamer. J Am Chem Soc 2023. [PMID: 37420313 PMCID: PMC10360057 DOI: 10.1021/jacs.3c02774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
Understanding how ligands bind to ribonucleic acids (RNA) is important for understanding RNA recognition in biological processes and drug development. Here, we have studied neomycin B binding to neomycin-sensing riboswitch aptamer constructs by native top-down mass spectrometry (MS) using electrospray ionization (ESI) and collisionally activated dissociation (CAD). Our MS data for a 27 nt aptamer construct reveal the binding site and ligand interactions, in excellent agreement with the structure derived from nuclear magnetic resonance (NMR) studies. Strikingly, for an extended 40 nt aptamer construct, which represents the sequence with the highest regulatory factor for riboswitch function, we identified two binding motifs for neomycin B binding, one corresponding to the bulge-loop motif of the 27 nt construct and the other one in the minor groove of the lower stem, which according to the MS data are equally populated. By replacing a noncanonical with a canonical base pair in the lower stem of the 40 nt aptamer, we can reduce binding to the minor groove motif from ∼50 to ∼30%. Conversely, the introduction of a CUG/CUG motif in the lower stem shifts the binding equilibrium in favor of minor groove binding. The MS data reveal site-specific and stoichiometry-resolved information on aminoglycoside binding to RNA that is not directly accessible by other methods and underscore the role of noncanonical base pairs in RNA recognition by aminoglycosides.
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Affiliation(s)
- Sarah Viola Heel
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Karolina Bartosik
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Fabian Juen
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
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6
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Palasser M, Heel SV, Delsuc MA, Breuker K, van Agthoven MA. Ultra-Accurate Correlation between Precursor and Fragment Ions in Two-Dimensional Mass Spectrometry: Acetylated vs Trimethylated Histone Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:608-616. [PMID: 36930827 PMCID: PMC10080674 DOI: 10.1021/jasms.2c00319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/23/2023] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
Two-dimensional mass spectrometry (2D MS) is a method for tandem mass spectrometry in which precursor and fragment ions are correlated by manipulating ion radii rather than by ion isolation. A 2D mass spectrum contains the fragmentation patterns of all analytes in a sample, acquired in parallel. We report ultrahigh-resolution narrowband 2D mass spectra of a mixture of two histone peptides with the same sequence, one of which carries an acetylation and the other a trimethylation (m/z 0.006 difference). We reduced the distance between data points in the precursor ion dimension and compared the accuracy of the precursor-fragment correlation with the resolving power. We manage to perform label-free quantification on the histone peptide mixture and show that precursor and fragment ions can be accurately correlated even though the precursor ions are not resolved. Finally, we show that increasing the resolution of a 2D mass spectrum in the precursor ion dimension too far can lead to a decline in the signal-to-noise ratio.
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Affiliation(s)
- Michael Palasser
- Institute
for Organic Chemistry, University of Innsbruck, 80/82 Innrain, 6020 Innsbruck, Austria
| | - Sarah V. Heel
- Institute
for Organic Chemistry, University of Innsbruck, 80/82 Innrain, 6020 Innsbruck, Austria
| | - Marc-André Delsuc
- Institut
de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U596, UMR 7104, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch-Graffenstaden, France
- CASC4DE, Pôle API, 300 Bd. Sébastien
Grant, 67400 Illkirch-Graffenstaden, France
| | - Kathrin Breuker
- Institute
for Organic Chemistry, University of Innsbruck, 80/82 Innrain, 6020 Innsbruck, Austria
| | - Maria A. van Agthoven
- Institute
for Organic Chemistry, University of Innsbruck, 80/82 Innrain, 6020 Innsbruck, Austria
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7
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Geng Q, Cao X, Fan D, Wang Q, Wang X, Zhang M, Zhao L, Jiao Y, Deng T, Liu H, Zhou J, Lou Y, Liang J, Xiao C. Potential medicinal value of N6-methyladenosine in autoimmune diseases and tumours. Br J Pharmacol 2023. [PMID: 36624563 DOI: 10.1111/bph.16030] [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: 11/02/2022] [Revised: 12/23/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Autoimmune diseases (ADs) are closely related to malignant tumours. On the one hand, ADs can increase the incidence of tumours; on the other hand, malignant tumours can cause rheumatic disease-like manifestations. With the increasing depth of analysis into the mechanism of N6 -methyladenosine (m6A) modification, it has been found that changes in m6A-related modification enzymes are closely related to the occurrence and development of ADs and malignant tumours. In this review, we explore the pathogenesis of ADs and tumours based on m6A modification. According to systematic assessment of the similarities between ADs and tumours, m6A may represent a common target of both diseases. At present, most of the drugs targeting m6A are in the research and development stage, not in clinical trials. Therefore, advancing the development of drugs targeting m6A is of great significance for both the combined treatment of ADs and malignant tumours and improving the quality of life and prognosis of patients.
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Affiliation(s)
- Qishun Geng
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
- China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiaoxue Cao
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
- China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Danping Fan
- Beijing Key Laboratory of Research of Chinese Medicine on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, China
| | - Qiong Wang
- China-Japan Friendship Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Xing Wang
- China-Japan Friendship Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Mengxiao Zhang
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Lu Zhao
- China-Japan Friendship Hospital, Capital Medical University, Beijing, China
| | - Yi Jiao
- China-Japan Friendship Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Tingting Deng
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Honglin Liu
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Jing Zhou
- Department of Physiology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Yanni Lou
- Oncology Department of Integrated Traditional Chinese and Western Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Jing Liang
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Beijing, China
| | - Cheng Xiao
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
- China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Department of Emergency, China-Japan Friendship Hospital, Beijing, China
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8
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Palasser M, Breuker K. RNA Chemical Labeling with Site-Specific, Relative Quantification by Mass Spectrometry for the Structural Study of a Neomycin-Sensing Riboswitch Aptamer Domain. Chempluschem 2022; 87:e202200256. [PMID: 36220343 PMCID: PMC9828840 DOI: 10.1002/cplu.202200256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/14/2022] [Indexed: 01/12/2023]
Abstract
High-resolution mass spectrometry was used for the label-free, direct localization and relative quantification of CMC+ -modifications of a neomycin-sensing riboswitch aptamer domain in the absence and presence of the aminoglycoside ligands neomycin B, ribostamycin, and paromomycin. The chemical probing and MS data for the free riboswitch show high exposure to solvent of the uridine nucleobases U7, U8, U13, U14, U18 as part of the proposed internal and apical loops, but those of U10 and U21 as part of the proposed internal loop were found to be far less exposed than expected. Thus, our data are in better agreement with the proposed secondary structure of the riboswitch in complexes with aminoglycosides than with that of free RNA. For the riboswitch in complexes with neomycin B, ribostamycin, and paromomycin, we found highly similar CMC+ -modification patterns and excellent agreement with previous NMR studies. Differences between the chemical probing and MS data in the absence and presence of the aminoglycoside ligands were quantitative rather than qualitative (i. e., the same nucleobases were labeled, but to different extents) and can be rationalized by stabilization of both the proposed bulge and the apical loop by aminoglycoside binding. Our study shows that chemical probing and mass spectrometry can provide important structural information and complement other techniques such as NMR spectroscopy.
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Affiliation(s)
- Michael Palasser
- Institut of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80/826020InnsbruckAustria
| | - Kathrin Breuker
- Institut of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80/826020InnsbruckAustria
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9
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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: 11] [Impact Index Per Article: 5.5] [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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10
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Zhou M, Wang DO, Li W, Zheng J. RNA adduction derived from electrophilic species in vitro and in vivo. Chem Biol Interact 2022; 351:109748. [PMID: 34801539 DOI: 10.1016/j.cbi.2021.109748] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/30/2021] [Accepted: 11/10/2021] [Indexed: 11/03/2022]
Abstract
RNA molecules are essential for cell function by not only serving as genetic materials, but also providing cells with structural support and catalytic functions. Due to nucleophilicity of nucleobases, RNA molecules can react with electrophilic species thus to be "adducted". The electron-deficient agents potentially inducing adduction exist in a variety of natural sources including metabolic products of biomolecules. Although evident and readily detected in human tissue, RNA adduction remains poorly understood for their physiological and pathological function. In this article, we review a collection of exogenous and endogenous molecular species that participate in RNA adduction and elaborates on the chemical nature of their RNA adduction sites. Furthermore, we provide perspectives on the potential of RNA adducts as biomarkers of environmental insults. Finally, we project future investigations that are necessary for understanding the mechanisms of cellular toxicity of RNA adduction.
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Affiliation(s)
- Mengyue Zhou
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Guiyang, Guizhou, 550025, PR China
| | - Dan Ohtan Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, PR China; Center for Biosystems Dynamics Research, RIKEN, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Weiwei Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Guiyang, Guizhou, 550025, PR China
| | - Jiang Zheng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Provincial Key Laboratory of Pharmaceutics, Guizhou Medical University, Guiyang, Guizhou, 550025, PR China; Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou, 550025, PR China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, 110016, PR China.
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11
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Morgan TE, Floyd TG, Marzullo BP, Wootton CA, Barrow MP, Bristow AWT, Perrier S, O'Connor PB. Stochasticity of poly(2-oxazoline) oligomer hydrolysis determined by tandem mass spectrometry. Polym Chem 2022; 13:4162-4169. [PMID: 35923808 PMCID: PMC9294869 DOI: 10.1039/d2py00437b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/01/2022] [Indexed: 11/30/2022]
Abstract
Understanding modification of synthetic polymer structures is necessary for their accurate synthesis and potential applications. In this contribution, a series of partially hydrolyzed poly(2-oxazoline) species were produced forming poly[(2-polyoxazoline)-co-(ethylenimine)] (P(EtOx-co-EI)) copolymers; EI being the hydrolyzed product of Ox. Bulk mass spectrometry (MS) measurements accurately measured the EI content. Tandem mass spectrometry analysis of the EI content in the copolymer samples determined the distribution of each monomer within the copolymer and corresponded to a theoretically modelled random distribution. The EI distribution across the polymers was shown to be effected by the choice of terminus, with a permanent hydrolysis event observed at an OH terminus. A neighbouring group effect wasn't observed at the polymer length analysed (approximately 25-mer species), suggesting that previously observed neighbouring group effects require a larger polymer chain. Although clearly useful for random polymer distribution this approach may be applied to many systems containing non-specific modifications to determine if they are directed or random locations across peptides, proteins, polymers, and nucleic acids. Tandem mass spectrometry can be used to better understand modification sites of synthetic polymer structures providing more complete chemical knowledge which is necessary for their accurate synthesis and potential applications.![]()
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Affiliation(s)
- Tomos E Morgan
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK
| | - Thomas G Floyd
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK
| | - Bryan P Marzullo
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK
| | | | - Mark P Barrow
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK
| | - Anthony W T Bristow
- Chemical Development, Pharmaceutical Technology and Development, Operations, AstraZeneca Charter Way Macclesfield SK102NA UK
| | - Sébastien Perrier
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK
- Warwick Medical School, University of Warwick Coventry CV4 7AL UK
- Faculty of Pharmaceutical Sciences, Monash University 381 Royal Parade Parkville VIC 3052 Australia
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK
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12
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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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13
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Issah MA, Wu D, Zhang F, Zheng W, Liu Y, Fu H, Zhou H, Chen R, Shen J. Epigenetic modifications in acute myeloid leukemia: The emerging role of circular RNAs (Review). Int J Oncol 2021; 59:107. [PMID: 34792180 PMCID: PMC8651224 DOI: 10.3892/ijo.2021.5287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/13/2021] [Indexed: 11/06/2022] Open
Abstract
Canonical epigenetic modifications, which include histone modification, chromatin remodeling and DNA methylation, play key roles in numerous cellular processes. Epigenetics underlies how cells that posses DNA with similar sequences develop into different cell types with different functions in an organism. Earlier epigenetic research has primarily been focused at the chromatin level. However, the number of studies on epigenetic modifications of RNA, such as N1‑methyladenosine, 2'‑O‑ribosemethylation, inosine, 5‑methylcytidine, N6‑methyladenosine (m6A) and pseudouridine, has seen an increase. Circular RNAs (circRNAs), a type of RNA species that lacks a 5' cap or 3' poly(A) tail, are abundantly expressed in acute myeloid leukemia (AML) and may regulate disease progression. circRNAs possess various functions, including microRNA sponging, gene transcription regulation and RNA‑binding protein interaction. Furthermore, circRNAs are m6A methylated in other types of cancer, such as colorectal and hypopharyngeal squamous cell cancers. Therefore, the critical roles of circRNA epigenetic modifications, particularly m6A, and their possible involvement in AML are discussed in the present review. Epigenetic modification of circRNAs may become a diagnostic and therapeutic target for AML in the future.
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Affiliation(s)
- Mohammed Awal Issah
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Dansen Wu
- Medical Intensive Care Unit, Fujian Provincial Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Feng Zhang
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Weili Zheng
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Yanquan Liu
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Haiying Fu
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Huarong Zhou
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Rong Chen
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Jianzhen Shen
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
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14
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Zhang Z, Hug C, Tao Y, Bitsch F, Yang Y. Solving Complex Biologics Truncation Problems by Top-Down Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1928-1935. [PMID: 33395284 DOI: 10.1021/jasms.0c00343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
With increasing protein therapeutics being designed as non-mAb (non-monoclonal antibody) modalities, additional efforts and resources are required to develop and characterize such therapeutic proteins. Truncation is an emerging issue for manufacturing of non-mAb drug substances and requires sophisticated methods to investigate. In this paper, we describe two cases with complex truncation problems where traditional methods such as intact mass spectrometry led to inclusive or wrong identifications. Therefore, we developed an online top-down LC-MS (liquid chromatography-mass spectrometry) based workflow to study truncated drug substances, and we successfully identified the clipping locations. Compared to other orthogonal methods, this method provides a unique capability of solving protein clipping problems. The successful identification of truncated species and the high compatibility to routine intact MS make it a very valuable tool for resolving truncation problems during protein production in the pharmaceutical industry.
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Affiliation(s)
- Zhe Zhang
- NIBR Biologics Center, Novartis Institutes for BioMedical Research, 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Christian Hug
- NIBR Biologics Center, Novartis Institutes for BioMedical Research, Klybeckstrasse 141, CH-4057, Basel, Switzerland
| | - Yuanqi Tao
- NIBR Biologics Center, Novartis Institutes for BioMedical Research, 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Francis Bitsch
- NIBR Biologics Center, Novartis Institutes for BioMedical Research, Klybeckstrasse 141, CH-4057, Basel, Switzerland
| | - Yang Yang
- NIBR Biologics Center, Novartis Institutes for BioMedical Research, Klybeckstrasse 141, CH-4057, Basel, Switzerland
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15
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Flemmich L, Heel S, Moreno S, Breuker K, Micura R. A natural riboswitch scaffold with self-methylation activity. Nat Commun 2021; 12:3877. [PMID: 34162884 PMCID: PMC8222354 DOI: 10.1038/s41467-021-24193-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/04/2021] [Indexed: 11/12/2022] Open
Abstract
Methylation is a prevalent post-transcriptional modification encountered in coding and non-coding RNA. For RNA methylation, cells use methyltransferases and small organic substances as methyl-group donors, such as S-adenosylmethionine (SAM). SAM and other nucleotide-derived cofactors are viewed as evolutionary leftovers from an RNA world, in which riboswitches have regulated, and ribozymes have catalyzed essential metabolic reactions. Here, we disclose the thus far unrecognized direct link between a present-day riboswitch and its inherent reactivity for site-specific methylation. The key is O6-methyl pre-queuosine (m6preQ1), a potentially prebiotic nucleobase which is recognized by the native aptamer of a preQ1 class I riboswitch. Upon binding, the transfer of the ligand’s methyl group to a specific cytidine occurs, installing 3-methylcytidine (m3C) in the RNA pocket under release of pre-queuosine (preQ1). Our finding suggests that nucleic acid-mediated methylation is an ancient mechanism that has offered an early path for RNA epigenetics prior to the evolution of protein methyltransferases. Furthermore, our findings may pave the way for the development of riboswitch-descending methylation tools based on rational design as a powerful alternative to in vitro selection approaches. In humans, protein methyltransferase is responsible for RNA methylation using S-adenosylmethionine as a methyl group donor. Here the authors report a self-methylation activity of a bacterial riboswitch.
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Affiliation(s)
- Laurin Flemmich
- University of Innsbruck, Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Innrain 80-82, Innsbruck, 6020, Austria
| | - Sarah Heel
- University of Innsbruck, Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Innrain 80-82, Innsbruck, 6020, Austria
| | - Sarah Moreno
- University of Innsbruck, Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Innrain 80-82, Innsbruck, 6020, Austria
| | - Kathrin Breuker
- University of Innsbruck, Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Innrain 80-82, Innsbruck, 6020, Austria
| | - Ronald Micura
- University of Innsbruck, Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Innrain 80-82, Innsbruck, 6020, Austria.
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16
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Bereiter R, Himmelstoß M, Renard E, Mairhofer E, Egger M, Breuker K, Kreutz C, Ennifar E, Micura R. Impact of 3-deazapurine nucleobases on RNA properties. Nucleic Acids Res 2021; 49:4281-4293. [PMID: 33856457 PMCID: PMC8096147 DOI: 10.1093/nar/gkab256] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 03/29/2021] [Indexed: 11/13/2022] Open
Abstract
Deazapurine nucleosides such as 3-deazaadenosine (c3A) are crucial for atomic mutagenesis studies of functional RNAs. They were the key for our current mechanistic understanding of ribosomal peptide bond formation and of phosphodiester cleavage in recently discovered small ribozymes, such as twister and pistol RNAs. Here, we present a comprehensive study on the impact of c3A and the thus far underinvestigated 3-deazaguanosine (c3G) on RNA properties. We found that these nucleosides can decrease thermodynamic stability of base pairing to a significant extent. The effects are much more pronounced for 3-deazapurine nucleosides compared to their constitutional isomers of 7-deazapurine nucleosides (c7G, c7A). We furthermore investigated base pair opening dynamics by solution NMR spectroscopy and revealed significantly enhanced imino proton exchange rates. Additionally, we solved the X-ray structure of a c3A-modified RNA and visualized the hydration pattern of the minor groove. Importantly, the characteristic water molecule that is hydrogen-bonded to the purine N3 atom and always observed in a natural double helix is lacking in the 3-deazapurine-modified counterpart. Both, the findings by NMR and X-ray crystallographic methods hence provide a rationale for the reduced pairing strength. Taken together, our comparative study is a first major step towards a comprehensive understanding of this important class of nucleoside modifications.
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Affiliation(s)
- Raphael Bereiter
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Maximilian Himmelstoß
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Eva Renard
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Université de Strasbourg, Strasbourg, France
| | - Elisabeth Mairhofer
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Michaela Egger
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Eric Ennifar
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Université de Strasbourg, Strasbourg, France
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
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17
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Chen H, Ge XL, Zhang ZY, Liu M, Wu RY, Zhang XF, Xu LP, Cheng HY, Sun XC, Zhu HC. M 5C regulator-mediated methylation modification patterns and tumor microenvironment infiltration characterization in lung adenocarcinoma. Transl Lung Cancer Res 2021; 10:2172-2192. [PMID: 34164268 PMCID: PMC8182725 DOI: 10.21037/tlcr-21-351] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Background In recent years, immunotherapy has made great progress, and the regulatory role of epigenetics has been verified. However, the role of 5-methylcytosine (m5C) in the tumor microenvironment (TME) and immunotherapy response remains unclear. Methods Based on 11 m5C regulators, we evaluated the m5C modification patterns of 572 lung adenocarcinoma (LUAD) patients. The m5C score was constructed by principal component analysis (PCA) algorithms in order to quantify the m5C modification pattern of individual LUAD patients. Results Two m5C methylation modification patterns were identified according to 11 m5C regulators. The two patterns had a remarkably distinct TME immune cell infiltration characterization. Next, 226 differentially expressed genes (DEGs) related to the m5C phenotype were screened. Patients were divided into three different gene cluster subtypes based on these genes, which had different TME immune cell infiltration and prognosis characteristics. The m5C score was constructed to quantify the m5C modification pattern of individual LUAD patients. We found that the high m5C score group had a better prognosis. The role of the m5C score in predicting prognosis was also verified in the dataset GSE31210. Conclusions Our study revealed that m5C modification played a significant role in TME regulation of LUAD. Investigation of the m5C regulation mode may have some implications for tumor immunotherapy in the future.
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Affiliation(s)
- Hui Chen
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiao-Lin Ge
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhao-Yue Zhang
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ming Liu
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
| | - Rui-Yan Wu
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
| | - Xiao-Fei Zhang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
| | - Li-Ping Xu
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hong-Yan Cheng
- Department of Synthetic Internal Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xin-Chen Sun
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hong-Cheng Zhu
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
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18
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Schaefer MR. The Regulation of RNA Modification Systems: The Next Frontier in Epitranscriptomics? Genes (Basel) 2021; 12:genes12030345. [PMID: 33652758 PMCID: PMC7996938 DOI: 10.3390/genes12030345] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 12/12/2022] Open
Abstract
RNA modifications, long considered to be molecular curiosities embellishing just abundant and non-coding RNAs, have now moved into the focus of both academic and applied research. Dedicated research efforts (epitranscriptomics) aim at deciphering the underlying principles by determining RNA modification landscapes and investigating the molecular mechanisms that establish, interpret and modulate the information potential of RNA beyond the combination of four canonical nucleotides. This has resulted in mapping various epitranscriptomes at high resolution and in cataloguing the effects caused by aberrant RNA modification circuitry. While the scope of the obtained insights has been complex and exciting, most of current epitranscriptomics appears to be stuck in the process of producing data, with very few efforts to disentangle cause from consequence when studying a specific RNA modification system. This article discusses various knowledge gaps in this field with the aim to raise one specific question: how are the enzymes regulated that dynamically install and modify RNA modifications? Furthermore, various technologies will be highlighted whose development and use might allow identifying specific and context-dependent regulators of epitranscriptomic mechanisms. Given the complexity of individual epitranscriptomes, determining their regulatory principles will become crucially important, especially when aiming at modifying specific aspects of an epitranscriptome both for experimental and, potentially, therapeutic purposes.
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Affiliation(s)
- Matthias R Schaefer
- Centre for Anatomy & Cell Biology, Division of Cell-and Developmental Biology, Medical University of Vienna, Schwarzspanierstrasse 17, Haus C, 1st Floor, 1090 Vienna, Austria
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19
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Halper M, Delsuc MA, Breuker K, van Agthoven MA. Narrowband Modulation Two-Dimensional Mass Spectrometry and Label-Free Relative Quantification of Histone Peptides. Anal Chem 2020; 92:13945-13952. [PMID: 32960586 PMCID: PMC7581016 DOI: 10.1021/acs.analchem.0c02843] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Two-dimensional mass
spectrometry (2D MS) on a Fourier transform
ion cyclotron resonance (FT-ICR) mass analyzer allows for tandem mass
spectrometry without requiring ion isolation. In the ICR cell, the
precursor ion radii are modulated before fragmentation, which results
in modulation of the abundance of their fragments. The resulting 2D
mass spectrum enables a correlation between the precursor and fragment
ions. In a standard broadband 2D MS, the range of precursor ion cyclotron
frequencies is determined by the lowest mass-to-charge (m/z) ratio to be fragmented in the 2D MS experiment,
which leads to precursor ion m/z ranges that are much wider than necessary, thereby limiting the
resolving power for precursor ions and the accuracy of the correlation
between the precursor and fragment ions. We present narrowband modulation
2D MS, which increases the precursor ion resolving power by reducing
the precursor ion m/z range, with
the aim of resolving the fragment ion patterns of overlapping isotopic
distributions. In this proof-of-concept study, we compare broadband
and narrowband modulation 2D mass spectra of an equimolar mixture
of histone peptide isoforms. In narrowband modulation 2D MS, we were
able to separate the fragment ion patterns of all 13C isotopes
of the different histone peptide forms. We further demonstrate the
potential of narrowband 2D MS for label-free quantification of peptides.
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Affiliation(s)
- Matthias Halper
- Institute for Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Marc-André Delsuc
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U596, UMR 7104, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch-Graffenstaden, France.,CASC4DE, Pôle API, 300 Bd. Sébastien Grant, 67400 Illkirch-Graffenstaden, France
| | - Kathrin Breuker
- Institute for Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Maria A van Agthoven
- Institute for Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
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20
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Abstract
The discovery and analysis of modifications on proteins and nucleic acids has provided functional information that has rapidly accelerated the field of epigenetics. While protein post-translational modifications (PTMs), especially on histones, have been highlighted as critical components of epigenetics, the post-transcriptional modification of RNA has been a subject of more recently emergent interest. Multiple RNA modifications have been known to be present in tRNA and rRNA since the 1960s, but the exploration of mRNA, small RNA, and inducible tRNA modifications remains nascent. Sequencing-based methods have been essential to the field by creating the first epitranscriptome maps of m6A, m5C, hm5C, pseudouridine, and inosine; however, these methods possess significant limitations. Here, we discuss the past, present, and future of the application of mass spectrometry (MS) to the study of RNA modifications.
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MESH Headings
- Animals
- Humans
- Mass Spectrometry
- Molecular Structure
- Nucleosides
- Nucleotides
- Protein Processing, Post-Translational
- RNA/chemistry
- RNA/genetics
- RNA/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
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Affiliation(s)
- Richard Lauman
- Biochemistry and Molecular Biophysics Graduate Group, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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21
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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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22
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Yao W, Han X, Ge M, Chen C, Xiao X, Li H, Hei Z. N 6-methyladenosine (m 6A) methylation in ischemia-reperfusion injury. Cell Death Dis 2020; 11:478. [PMID: 32581252 PMCID: PMC7314846 DOI: 10.1038/s41419-020-2686-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/30/2020] [Accepted: 06/15/2020] [Indexed: 12/21/2022]
Abstract
Ischemia-reperfusion (I/R) injury is common during surgery and often results in organ dysfunction. The mechanisms of I/R injury are complex, diverse, and not well understood. RNA methylation is a novel epigenetic modification that is involved in the regulation of various biological processes, such as immunity, response to DNA damage, tumorigenesis, metastasis, stem cell renewal, fat differentiation, circadian rhythms, cell development and differentiation, and cell division. Research on RNA modifications, specifically N6-methyladenosine (m6A), have confirmed that they are involved in the regulation of organ I/R injury. In this review, we summarized current understanding of the regulatory roles and significance of m6A RNA methylation in I/R injury in different organs.
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Affiliation(s)
- Weifeng Yao
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Xue Han
- Department of Anesthesiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China
| | - Mian Ge
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Chaojin Chen
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Xue Xiao
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Haobo Li
- Department of Corrigan-Minehan Heart Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.
| | - Ziqing Hei
- Department of Anesthesiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China.
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23
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Calderisi G, Glasner H, Breuker K. Radical Transfer Dissociation for De Novo Characterization of Modified Ribonucleic Acids by Mass Spectrometry. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Giovanni Calderisi
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität Innsbruck Innrain 80/82 6020 Innsbruck Austria
| | - Heidelinde Glasner
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität Innsbruck Innrain 80/82 6020 Innsbruck Austria
| | - Kathrin Breuker
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität Innsbruck Innrain 80/82 6020 Innsbruck Austria
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24
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Calderisi G, Glasner H, Breuker K. Radical Transfer Dissociation for De Novo Characterization of Modified Ribonucleic Acids by Mass Spectrometry. Angew Chem Int Ed Engl 2020; 59:4309-4313. [PMID: 31867820 PMCID: PMC7065001 DOI: 10.1002/anie.201914275] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Indexed: 12/20/2022]
Abstract
Mass spectrometry (MS) can reliably detect and localize all mass-altering modifications of ribonucleic acids (RNA), but current MS approaches that allow for simultaneous de novo sequencing and modification analysis generally require specialized instrumentation. Here we report a novel RNA dissociation technique, radical transfer dissociation (RTD), that can be used for the comprehensive de novo characterization of ribonucleic acids and their posttranscriptional or synthetic modifications. We demonstrate full sequence coverage for RNA consisting of up to 39 nucleotides and show that RTD is especially useful for RNA with highly labile modifications such as 5-hydroxymethylcytidine and 5-formylcytidine.
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Affiliation(s)
- Giovanni Calderisi
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität InnsbruckInnrain 80/826020InnsbruckAustria
| | - Heidelinde Glasner
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität InnsbruckInnrain 80/826020InnsbruckAustria
| | - Kathrin Breuker
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität InnsbruckInnrain 80/826020InnsbruckAustria
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25
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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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26
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Qi C, Ding J, Yuan B, Feng Y. Analytical methods for locating modifications in nucleic acids. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.02.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Fuchs E, Falschlunger C, Micura R, Breuker K. The effect of adenine protonation on RNA phosphodiester backbone bond cleavage elucidated by deaza-nucleobase modifications and mass spectrometry. Nucleic Acids Res 2019; 47:7223-7234. [PMID: 31276590 PMCID: PMC6698743 DOI: 10.1093/nar/gkz574] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/15/2019] [Accepted: 06/21/2019] [Indexed: 12/14/2022] Open
Abstract
The catalytic strategies of small self-cleaving ribozymes often involve interactions between nucleobases and the ribonucleic acid (RNA) backbone. Here we show that multiply protonated, gaseous RNA has an intrinsic preference for the formation of ionic hydrogen bonds between adenine protonated at N3 and the phosphodiester backbone moiety on its 5'-side that facilitates preferential phosphodiester backbone bond cleavage upon vibrational excitation by low-energy collisionally activated dissociation. Removal of the basic N3 site by deaza-modification of adenine was found to abrogate preferential phosphodiester backbone bond cleavage. No such effects were observed for N1 or N7 of adenine. Importantly, we found that the pH of the solution used for generation of the multiply protonated, gaseous RNA ions by electrospray ionization affects phosphodiester backbone bond cleavage next to adenine, which implies that the protonation patterns in solution are at least in part preserved during and after transfer into the gas phase. Our study suggests that interactions between protonated adenine and phosphodiester moieties of RNA may play a more important mechanistic role in biological processes than considered until now.
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Affiliation(s)
- Elisabeth Fuchs
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Christoph Falschlunger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
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28
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Meng S, Zhou H, Feng Z, Xu Z, Tang Y, Wu M. Epigenetics in Neurodevelopment: Emerging Role of Circular RNA. Front Cell Neurosci 2019; 13:327. [PMID: 31379511 PMCID: PMC6658887 DOI: 10.3389/fncel.2019.00327] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 07/03/2019] [Indexed: 01/16/2023] Open
Abstract
Canonical epigenetic modifications, including DNA methylation, histone modification and chromatin remodeling, play a role in numerous life processes, particularly neurodevelopment. Epigenetics explains the development of cells in an organism with the same DNA sequence into different cell types with various functions. However, previous studies on epigenetics have only focused on the chromatin level. Recently, epigenetic modifications of RNA, which mainly include 6-methyladenosine (m6A), pseudouridine, 5-methylcytidine (m5C), inosine (I), 2′-O-ribosemethylation, and 1-methyladenosine (m1A), have gained increasing attention. Circular RNAs (circRNAs), which are a type of non-coding RNA without a 5′ cap or 3′ poly (A) tail, are abundantly found in the brain and might respond to and regulate synaptic function. Also, circRNAs have various functions, such as microRNA sponge, regulation of gene transcription and interaction with RNA binding protein. In addition, circRNAs are methylated by N6-methyladenosine (m6A). In this review, we discuss the crucial roles of epigenetic modifications of circRNAs, such as m6A, in the genesis and development of neurons and in synaptic function and plasticity. Thus, this type of changes in circRNAs might be a therapeutic target in central nervous system (CNS) disorders and could aid the diagnosis and treatment of these disorders.
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Affiliation(s)
- Shujuan Meng
- Hunan Provincial Tumor Hospital, The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Hecheng Zhou
- Hunan Provincial Tumor Hospital, The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Ziyang Feng
- Hunan Provincial Tumor Hospital, The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Zihao Xu
- Hunan Provincial Tumor Hospital, The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Ying Tang
- Hunan Provincial Tumor Hospital, The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Minghua Wu
- Hunan Provincial Tumor Hospital, The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
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29
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Functions of RNA N6-methyladenosine modification in cancer progression. Mol Biol Rep 2019; 46:2567-2575. [PMID: 30911972 DOI: 10.1007/s11033-019-04655-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/07/2018] [Indexed: 01/05/2023]
Abstract
N6-methyladenosine (m6A) serves as a major RNA methylation modification and impacts the initiation and progression of various human cancers through diverse mechanisms. It has been reported that m6A RNA methylation is involved in different physiological and pathological processes, including stem cell differentiation and motility, immune response, cellular stress, tissue renewal and viral infection. In this review, the m6A modification and its regulatory functions in a few major cancers is introduced. The detection approaches for the m6A sites identification are discussed. Additionally, the potential of the RNA m6A modification in clinical application is discussed.
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30
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Functions of RNA N6-methyladenosine modification in cancer progression. Mol Biol Rep 2019; 46:1383-1391. [PMID: 30788764 DOI: 10.1007/s11033-018-4471-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/07/2018] [Indexed: 10/27/2022]
Abstract
N6-methyladenosine (m6A) serves as a major RNA methylation modification and impacts the initiation and progression of various human cancers through diverse mechanisms. It has been reported that m6A RNA methylation is involved in different physiological and pathological processes, including stem cell differentiation and motility, immune response, cellular stress, tissue renewal and viral infection. In this review, the m6A modification and its regulatory functions in a few major cancers is introduced. The detection approaches for the m6A sites identification are discussed. Additionally, the potential of the RNA m6A modification in clinical application is discussed.
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31
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Guo M, Liu D, Sha Q, Geng H, Liang J, Tang D. Succinic acid enhanced quantitative determination of blood modified nucleosides in the development of diabetic nephropathy based on hydrophilic interaction liquid chromatography mass spectrometry. J Pharm Biomed Anal 2019; 164:309-316. [DOI: 10.1016/j.jpba.2018.10.042] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/22/2018] [Accepted: 10/23/2018] [Indexed: 12/18/2022]
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32
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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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33
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Trixl L, Lusser A. The dynamic RNA modification 5-methylcytosine and its emerging role as an epitranscriptomic mark. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1510. [PMID: 30311405 PMCID: PMC6492194 DOI: 10.1002/wrna.1510] [Citation(s) in RCA: 189] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 08/30/2018] [Accepted: 09/17/2018] [Indexed: 12/11/2022]
Abstract
It is a well‐known fact that RNA is the target of a plethora of modifications which currently amount to over a hundred. The vast majority of these modifications was observed in the two most abundant classes of RNA, rRNA and tRNA. With the recent advance in mapping technologies, modifications have been discovered also in mRNA and in less abundant non‐coding RNA species. These developments have sparked renewed interest in elucidating the nature and functions of those “epitransciptomic” modifications in RNA. N6‐methyladenosine (m6A) is the best understood and most frequent mark of mRNA with demonstrated functions ranging from pre‐mRNA processing, translation, miRNA biogenesis to mRNA decay. By contrast, much less research has been conducted on 5‐methylcytosine (m5C), which was detected in tRNAs and rRNAs and more recently in poly(A)RNAs. In this review, we discuss recent developments in the discovery of m5C RNA methylomes, the functions of m5C as well as the proteins installing, translating and manipulating this modification. Although our knowledge about m5C in RNA transcripts is just beginning to consolidate, it has become clear that cytosine methylation represents a powerful mechanistic strategy to regulate cellular processes on an epitranscriptomic level. This article is categorized under:RNA Processing > RNA Editing and Modification RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications RNA Processing > tRNA Processing RNA Turnover and Surveillance > Regulation of RNA Stability
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Affiliation(s)
- Lukas Trixl
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
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34
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Schneeberger EM, Breuker K. Replacing H + by Na + or K + in phosphopeptide anions and cations prevents electron capture dissociation. Chem Sci 2018; 9:7338-7353. [PMID: 30542537 PMCID: PMC6237128 DOI: 10.1039/c8sc02470g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/07/2018] [Indexed: 01/29/2023] Open
Abstract
By successively replacing H+ by Na+ or K+ in phosphopeptide anions and cations, we show that the efficiency of fragmentation into c and z˙ or c˙ and z fragments from N-Cα backbone bond cleavage by negative ion electron capture dissociation (niECD) and electron capture dissociation (ECD) substantially decreases with increasing number of alkali ions attached. In proton-deficient phosphopeptide ions with a net charge of 2-, we observed an exponential decrease in electron capture efficiency with increasing number of Na+ or K+ ions attached, suggesting that electrons are preferentially captured at protonated sites. In proton-abundant phosphopeptide ions with a net charge of 3+, the electron capture efficiency was not affected by replacing up to four H+ ions with Na+ or K+ ions, but the yield of c, z˙ and c˙, z fragments from N-Cα backbone bond cleavage generally decreased next to Na+ or K+ binding sites. We interpret the site-specific decrease in fragmentation efficiency as Na+ or K+ binding to backbone amide oxygen in competition with interactions of protonated sites that would otherwise lead to backbone cleavage into c, z˙ or c˙, z fragments. Our findings seriously challenge the hypothesis that the positive charge responsible for ECD into c, z˙ or c˙, z fragments can generally be a sodium or other metal ion instead of a proton.
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Affiliation(s)
- Eva-Maria Schneeberger
- Institute of Organic Chemistry , Center for Molecular Biosciences Innsbruck (CMBI) , University of Innsbruck , Innrain 80/82 , 6020 Innsbruck , Austria . ; http://www.bioms-breuker.at/
| | - Kathrin Breuker
- Institute of Organic Chemistry , Center for Molecular Biosciences Innsbruck (CMBI) , University of Innsbruck , Innrain 80/82 , 6020 Innsbruck , Austria . ; http://www.bioms-breuker.at/
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35
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Affiliation(s)
- Bei Chen
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
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36
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Ovcharenko A, Rentmeister A. Emerging approaches for detection of methylation sites in RNA. Open Biol 2018; 8:180121. [PMID: 30185602 PMCID: PMC6170510 DOI: 10.1098/rsob.180121] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 08/15/2018] [Indexed: 01/08/2023] Open
Abstract
RNA methylations play a significant regulatory role in diverse biological processes. Although the transcriptome-wide discovery of unknown RNA methylation sites is essential to elucidate their function, the development of a bigger variety of detection approaches is desirable for multiple reasons. Many established detection methods for RNA modifications heavily rely on the specificity of the respective antibodies. Thus, the development of antibody-independent transcriptome-wide methods is beneficial. Even the antibody-independent high-throughput sequencing-based methods are liable to produce false-positive or false-negative results. The development of an independent method for each modification could help validate the detected modification sites. Apart from the transcriptome-wide methods for methylation detection de novo, methods for monitoring the presence of a single methylation at a determined site are also needed. In contrast to the transcriptome-wide detection methods, the techniques used for monitoring purposes need to be cheap, fast and easy to perform. This review considers modern approaches for site-specific detection of methylated nucleotides in RNA. We also discuss the potential of third-generation sequencing methods for direct detection of RNA methylations.
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Affiliation(s)
- Anna Ovcharenko
- Institute of Biochemistry, Department of Chemistry, University of Münster, Wilhelm-Klemm-Straße 2, D-48149 Münster, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, Department of Chemistry, University of Münster, Wilhelm-Klemm-Straße 2, D-48149 Münster, Germany
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37
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Kremser J, Strebitzer E, Plangger R, Juen MA, Nußbaumer F, Glasner H, Breuker K, Kreutz C. Chemical synthesis and NMR spectroscopy of long stable isotope labelled RNA. Chem Commun (Camb) 2018; 53:12938-12941. [PMID: 29155431 DOI: 10.1039/c7cc06747j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We showcase the high potential of the 2'-cyanoethoxymethyl (CEM) methodology to synthesize RNAs with naturally occurring modified residues carrying stable isotope (SI) labels for NMR spectroscopic applications. The method was applied to synthesize RNAs with sizes ranging between 60 to 80 nucleotides. The presented approach gives the possibility to selectively modify larger RNAs (>60 nucleotides) with atom-specifically 13C/15N-labelled building blocks. The method harbors the unique potential to address structural as well as dynamic features of these RNAs with NMR spectroscopy but also using other biophysical methods, such as mass spectrometry (MS), or small angle neutron/X-ray scattering (SANS, SAXS).
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Affiliation(s)
- J Kremser
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria.
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38
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Vušurović J, Schneeberger E, Breuker K. Interactions of Protonated Guanidine and Guanidine Derivatives with Multiply Deprotonated RNA Probed by Electrospray Ionization and Collisionally Activated Dissociation. ChemistryOpen 2017; 6:739-750. [PMID: 29226062 PMCID: PMC5715244 DOI: 10.1002/open.201700143] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/06/2017] [Indexed: 11/25/2022] Open
Abstract
Interactions of ribonucleic acid (RNA) with guanidine and guanidine derivatives are important features in RNA-protein and RNA-drug binding. Here we have investigated noncovalently bound complexes of an 8-nucleotide RNA and six different ligands, all of which have a guanidinium moiety, by using electrospray ionization (ESI) and collisionally activated dissociation (CAD) mass spectrometry (MS). The order of complex stability correlated almost linearly with the number of ligand atoms that can potentially be involved in hydrogen-bond or salt-bridge interactions with the RNA, but not with the proton affinity of the ligands. However, ligand dissociation of the complex ions in CAD was generally accompanied by proton transfer from ligand to RNA, which indicated conversion of salt-bridge into hydrogen-bond interactions. The relative stabilities and dissociation pathways of [RNA+m L-n H] n- complexes with different stoichiometries (m=1-5) and net charge (n= 2-5) revealed both specific and unspecific ligand binding to the RNA.
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Affiliation(s)
- Jovana Vušurović
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Eva‐Maria Schneeberger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
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Jacob R, Zander S, Gutschner T. The Dark Side of the Epitranscriptome: Chemical Modifications in Long Non-Coding RNAs. Int J Mol Sci 2017; 18:ijms18112387. [PMID: 29125541 PMCID: PMC5713356 DOI: 10.3390/ijms18112387] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 11/05/2017] [Accepted: 11/06/2017] [Indexed: 12/20/2022] Open
Abstract
The broad application of next-generation sequencing technologies in conjunction with improved bioinformatics has helped to illuminate the complexity of the transcriptome, both in terms of quantity and variety. In humans, 70–90% of the genome is transcribed, but only ~2% carries the blueprint for proteins. Hence, there is a huge class of non-translated transcripts, called long non-coding RNAs (lncRNAs), which have received much attention in the past decade. Several studies have shown that lncRNAs are involved in a plethora of cellular signaling pathways and actively regulate gene expression via a broad selection of molecular mechanisms. Only recently, sequencing-based, transcriptome-wide studies have characterized different types of post-transcriptional chemical modifications of RNAs. These modifications have been shown to affect the fate of RNA and further expand the variety of the transcriptome. However, our understanding of their biological function, especially in the context of lncRNAs, is still in its infancy. In this review, we will focus on three epitranscriptomic marks, namely pseudouridine (Ψ), N6-methyladenosine (m6A) and 5-methylcytosine (m5C). We will introduce writers, readers, and erasers of these modifications, and we will present methods for their detection. Finally, we will provide insights into the distribution and function of these chemical modifications in selected, cancer-related lncRNAs.
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Affiliation(s)
- Roland Jacob
- Faculty of Medicine, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany.
| | - Sindy Zander
- Faculty of Medicine, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany.
| | - Tony Gutschner
- Faculty of Medicine, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany.
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