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Crespo-García E, Bueno-Costa A, Esteller M. Single-cell analysis of the epitranscriptome: RNA modifications under the microscope. RNA Biol 2024; 21:1-8. [PMID: 38368619 PMCID: PMC10877985 DOI: 10.1080/15476286.2024.2315385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2024] [Indexed: 02/20/2024] Open
Abstract
The identification of mechanisms capable of modifying genetic information by the addition of covalent RNA modifications distinguishes a level of complexity in gene expression which challenges key long-standing concepts of RNA biology. One of the current challenges of molecular biology is to properly understand the molecular functions of these RNA modifications, with more than 170 different ones having been identified so far. However, it has not been possible to map specific RNA modifications at a single-cell resolution until very recently. This review will highlight the technological advances in single-cell methodologies aimed at assessing and testing the biological function of certain RNA modifications, focusing on m6A. These advances have allowed for the development of novel strategies that enable the study of the 'epitranscriptome'. Nevertheless, despite all these improvements, many challenges and difficulties still need fixing for these techniques to work efficiently.
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Affiliation(s)
- Eva Crespo-García
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Alberto Bueno-Costa
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
- Centro de Investigación Biomédica en Red Cancer (CIBERONC), Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain
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2
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Deng L, Kumar J, Rose R, McIntyre W, Fabris D. Analyzing RNA posttranscriptional modifications to decipher the epitranscriptomic code. MASS SPECTROMETRY REVIEWS 2024; 43:5-38. [PMID: 36052666 DOI: 10.1002/mas.21798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
The discovery of RNA silencing has revealed that non-protein-coding sequences (ncRNAs) can cover essential roles in regulatory networks and their malfunction may result in severe consequences on human health. These findings have prompted a general reassessment of the significance of RNA as a key player in cellular processes. This reassessment, however, will not be complete without a greater understanding of the distribution and function of the over 170 variants of the canonical ribonucleotides, which contribute to the breathtaking structural diversity of natural RNA. This review surveys the analytical approaches employed for the identification, characterization, and detection of RNA posttranscriptional modifications (rPTMs). The merits of analyzing individual units after exhaustive hydrolysis of the initial biopolymer are outlined together with those of identifying their position in the sequence of parent strands. Approaches based on next generation sequencing and mass spectrometry technologies are covered in depth to provide a comprehensive view of their respective merits. Deciphering the epitranscriptomic code will require not only mapping the location of rPTMs in the various classes of RNAs, but also assessing the variations of expression levels under different experimental conditions. The fact that no individual platform is currently capable of meeting all such demands implies that it will be essential to capitalize on complementary approaches to obtain the desired information. For this reason, the review strived to cover the broadest possible range of techniques to provide readers with the fundamental elements necessary to make informed choices and design the most effective possible strategy to accomplish the task at hand.
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Affiliation(s)
- L Deng
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - J Kumar
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - R Rose
- Department of Advanced Research Technologies, New York University Langone Health Center, New York, USA
| | - W McIntyre
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Daniele Fabris
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
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3
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Wang Y, Liu Y, Wang R, Cao F, Guan Y, Chen Y, An B, Qin S, Yao S. Establishment of a prognostic model toward lung squamous cell carcinoma based on m 7G-related genes in the cancer genome atlas. Physiol Genomics 2023; 55:427-439. [PMID: 37575065 PMCID: PMC10642926 DOI: 10.1152/physiolgenomics.00149.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 07/26/2023] [Accepted: 08/07/2023] [Indexed: 08/15/2023] Open
Abstract
Lung squamous cell carcinoma (LUSC) is a non-small cell lung cancer with a poor prognosis owing to late diagnosis. New molecular markers are urgently needed to improve the diagnosis and prognosis of LUSC. 7-Methylguanosine (m7G) modifications, a tRNA modification, are common in eubacteria, eukaryotes, and a few archaea. These modifications promote the turnover and stability of some mRNAs to prevent mRNA decay, improve translation efficiency, and reduce ribosomal pausing but are associated with poor survival in human cancer cells. However, expression of m7G-related genes in LUSC and their association with prognosis remain unclear. In the present study, we identified nine differentially expressed genes related to prognosis by comparing the expression profiles of tumor tissues (502 LUSC reports) with normal tissues (49 adjacent nontumor lung tissue reports). The genes included six upregulated genes (KLK7, LCE3E, AREG, KLK6, ZBED2, and MAPK4) and three downregulated genes (ADH1C, NTS, and ERLIN2). Based on these nine genes, patients with LUSC were classified into low- and high-risk groups to analyze the trends in prognosis. We found that the nine m7G-related genes play important roles in immune regulation, hormone regulation, and drug sensitivity through pathways including antigen processing and presentation, adherent plaques, extracellular matrix receptor interactions, drug metabolism of cytochrome P-450, and metabolism of cytochrome P-450 to xenobiotics; the functions of these genes are likely accomplished in part by m6A modifications. The effect of m7G-related genes on the diagnosis and prognosis of LUSC was further indicated by population analysis.NEW & NOTEWORTHY Based on the differential expression of 7-methylguanosine (m7G) modification-associated genes between normal and lung squamous cell carcinoma (LUSC) tissues, and considering the performance of our m7G-related gene risk profiles as independent risk factors in predicting overall survival, we conclude that m7G modification is closely linked to the development of LUSC. In addition, this study offers a new genetic marker for predicting the prognosis of patients with LUSC and presents a crucial theoretical foundation for future investigations on the relationship between m7G modification-related genes, immunity, and drug sensitivity in LUSC.
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Affiliation(s)
- Yongheng Wang
- School of Public Health, North China University of Science and Technology, Tangshan, People's Republic of China
| | - Yimin Liu
- School of Public Health, North China University of Science and Technology, Tangshan, People's Republic of China
| | - Rui Wang
- School of Public Health, North China University of Science and Technology, Tangshan, People's Republic of China
| | - Fuyuan Cao
- School of Public Health, North China University of Science and Technology, Tangshan, People's Republic of China
| | - Yi Guan
- School of Public Health, North China University of Science and Technology, Tangshan, People's Republic of China
| | - Yulu Chen
- School of Public Health, North China University of Science and Technology, Tangshan, People's Republic of China
| | - Binbin An
- School of Public Health, North China University of Science and Technology, Tangshan, People's Republic of China
| | - Sisi Qin
- School of Public Health, North China University of Science and Technology, Tangshan, People's Republic of China
| | - Sanqiao Yao
- School of Public Health, North China University of Science and Technology, Tangshan, People's Republic of China
- School of Public Health, Xinxiang Medical University, Xinxiang, People's Republic of China
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4
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Zhao Y, Rai J, Li H. Regulation of translation by ribosomal RNA pseudouridylation. SCIENCE ADVANCES 2023; 9:eadg8190. [PMID: 37595043 PMCID: PMC10438446 DOI: 10.1126/sciadv.adg8190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 07/18/2023] [Indexed: 08/20/2023]
Abstract
Pseudouridine is enriched in ribosomal, spliceosomal, transfer, and messenger RNA and thus integral to the central dogma. The chemical basis for how pseudouridine affects the molecular apparatus such as ribosome, however, remains elusive owing to the lack of structures without this natural modification. Here, we studied the translation of a hypopseudouridylated ribosome initiated by the internal ribosome entry site (IRES) elements. We analyzed eight cryo-electron microscopy structures of the ribosome bound with the Taura syndrome virus IRES in multiple functional states. We found widespread loss of pseudouridine-mediated interactions through water and long-range base pairings. In the presence of the translocase, eukaryotic elongation factor 2, and guanosine 5'-triphosphate hydrolysis, the hypopseudouridylated ribosome favors a rare unconducive conformation for decoding that is partially recouped in the ribosome population that remains modified at the P-site uridine. The structural principles learned establish the link between functional defects and modification loss and are likely applicable to other pseudouridine-associated processes.
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Affiliation(s)
- Yu Zhao
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Jay Rai
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Hong Li
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
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5
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Mohl DA, Lagies S, Zodel K, Zumkeller M, Peighambari A, Ganner A, Plattner DA, Neumann-Haefelin E, Adlesic M, Frew IJ, Kammerer B. Integrated Metabolomic and Transcriptomic Analysis of Modified Nucleosides for Biomarker Discovery in Clear Cell Renal Cell Carcinoma. Cells 2023; 12:cells12081102. [PMID: 37190010 DOI: 10.3390/cells12081102] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 03/30/2023] [Accepted: 04/05/2023] [Indexed: 05/17/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) accounts for ~75% of kidney cancers. The biallelic inactivation of the von Hippel-Lindau tumor suppressor gene (VHL) is the truncal driver mutation of most cases of ccRCC. Cancer cells are metabolically reprogrammed and excrete modified nucleosides in larger amounts due to their increased RNA turnover. Modified nucleosides occur in RNAs and cannot be recycled by salvage pathways. Their potential as biomarkers has been demonstrated for breast or pancreatic cancer. To assess their suitability as biomarkers in ccRCC, we used an established murine ccRCC model, harboring Vhl, Trp53 and Rb1 (VPR) knockouts. Cell culture media of this ccRCC model and primary murine proximal tubular epithelial cells (PECs) were investigated by HPLC coupled to triple-quadrupole mass spectrometry using multiple-reaction monitoring. VPR cell lines were significantly distinguishable from PEC cell lines and excreted higher amounts of modified nucleosides such as pseudouridine, 5-methylcytidine or 2'-O-methylcytidine. The method's reliability was confirmed in serum-starved VPR cells. RNA-sequencing revealed the upregulation of specific enzymes responsible for the formation of those modified nucleosides in the ccRCC model. These enzymes included Nsun2, Nsun5, Pus1, Pus7, Naf1 and Fbl. In this study, we identified potential biomarkers for ccRCC for validation in clinical trials.
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Affiliation(s)
- Daniel A Mohl
- Core Competence Metabolomics, Hilde-Mangold-Haus, University of Freiburg, 79104 Freiburg, Germany
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Simon Lagies
- Core Competence Metabolomics, Hilde-Mangold-Haus, University of Freiburg, 79104 Freiburg, Germany
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, Medical Center-University of Freiburg, 79104 Freiburg, Germany
| | - Kyra Zodel
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Centre-University of Freiburg, 79106 Freiburg, Germany
| | - Matthias Zumkeller
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Centre-University of Freiburg, 79106 Freiburg, Germany
| | - Asin Peighambari
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Centre-University of Freiburg, 79106 Freiburg, Germany
| | - Athina Ganner
- Renal Division, Department of Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Dietmar A Plattner
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Elke Neumann-Haefelin
- Renal Division, Department of Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Mojca Adlesic
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Centre-University of Freiburg, 79106 Freiburg, Germany
| | - Ian J Frew
- Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, Medical Centre-University of Freiburg, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Signalling Research Centre BIOSS, University of Freiburg, 79104 Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Faculty of Medicine and Medical Center-University of Freiburg, 79106 Freiburg, Germany
| | - Bernd Kammerer
- Core Competence Metabolomics, Hilde-Mangold-Haus, University of Freiburg, 79104 Freiburg, Germany
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany
- Signalling Research Centre BIOSS, University of Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
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Zhang Q, Zhang W, Cui R, Zhang Y, Niu D. Synthesis of 2,4-diarylated pyrimidines enabled by Ni-catalyzed C–sulfone bond activation. Org Chem Front 2023. [DOI: 10.1039/d2qo01935c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The readily available pyrimidinyl sulfones, in which the C–S bond is cleaved selectively, could serve as electrophiles in the Ni-catalyzed cross-coupling reactions to prepare 2,4-diarylated pyrimidines under mild conditions with a broad scope.
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Affiliation(s)
- Qian Zhang
- Department of Emergency, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and School of Chemical Engineering, Sichuan University, Chengdu, China
- Sichuan Institute of Edible Fungi, Shizishan Road No. 4, Jinjiang district, Chengdu, China
| | - Wei Zhang
- Department of Emergency, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Ruoyan Cui
- Department of Emergency, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Yang Zhang
- Department of Emergency, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Dawen Niu
- Department of Emergency, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and School of Chemical Engineering, Sichuan University, Chengdu, China
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7
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Ma L, He LN, Kang S, Gu B, Gao S, Zuo Z. Advances in detecting N6-methyladenosine modification in circRNAs. Methods 2022; 205:234-246. [PMID: 35878749 DOI: 10.1016/j.ymeth.2022.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of noncoding RNAs with covalently single-stranded closed loop structures derived from back-splicing event of linear precursor mRNAs (pre-mRNAs). N6-methyladenosine (m6A), the most abundant epigenetic modification in eukaryotic RNAs, has been shown to play a crucial role in regulating the fate and biological function of circRNAs, and thus affecting various physiological and pathological processes. Accurate identification of m6A modification in circRNAs is an essential step to fully elucidate the crosstalk between m6A and circRNAs. In recent years, the rapid development of high-throughput sequencing technology and bioinformatic methodology has propelled the establishment of a multitude of approaches to detect circRNAs and m6A modification, including in vitro-based and in silico methods. Based on this, the research community has started on a new journey to develop methods for identification of m6A modification in circRNAs. In this review, we provide a comprehensive review and evaluation of the existing methods responsible for detecting circRNAs, m6A modification, and especially, m6A modification in circRNAs, which mainly focused on those developed based on high-throughput technologies and methodology of bioinformatics. This handy reference can help researchers figure out towards which direction this field will go.
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Affiliation(s)
- Lixia Ma
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Henan Key Laboratory of Microbiome and Esophageal Cancer Prevention and Treatment, Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital (College of Clinical Medical) of Henan University of Science and Technology, Luoyang, China
| | - Li-Na He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Shiyang Kang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Bianli Gu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Henan Key Laboratory of Microbiome and Esophageal Cancer Prevention and Treatment, Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital (College of Clinical Medical) of Henan University of Science and Technology, Luoyang, China
| | - Shegan Gao
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Henan Key Laboratory of Microbiome and Esophageal Cancer Prevention and Treatment, Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital (College of Clinical Medical) of Henan University of Science and Technology, Luoyang, China.
| | - Zhixiang Zuo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
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Yang X, Patil S, Joshi S, Jamla M, Kumar V. Exploring epitranscriptomics for crop improvement and environmental stress tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 183:56-71. [PMID: 35567875 DOI: 10.1016/j.plaphy.2022.04.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/27/2022] [Accepted: 04/30/2022] [Indexed: 06/15/2023]
Abstract
Climate change and stressful environmental conditions severely hamper crop growth, development and yield. Plants respond to environmental perturbations, through their plasticity provided by key-genes, governed at post-/transcriptional levels. Gene-regulation in plants is a multilevel process controlled by diverse cellular entities that includes transcription factors (TF), epigenetic regulators and non-coding RNAs beside others. There are successful studies confirming the role of epigenetic modifications (DNA-methylation/histone-modifications) in gene expression. Recent years have witnessed emergence of a highly specialized field the "Epitranscriptomics". Epitranscriptomics deals with investigating post-transcriptional RNA chemical-modifications present across the life forms that change structural, functional and biological characters of RNA. However, deeper insights on of epitranscriptomic modifications, with >140 types known so far, are to be understood fully. Researchers have identified epitranscriptome marks (writers, erasers and readers) and mapped the site-specific RNA modifications (m6A, m5C, 3' uridylation, etc.) responsible for fine-tuning gene expression in plants. Simultaneous advancement in sequencing platforms, upgraded bioinformatic tools and pipelines along with conventional labelled techniques have further given a statistical picture of these epitranscriptomic modifications leading to their potential applicability in crop improvement and developing climate-smart crops. We present herein the insights on epitranscriptomic machinery in plants and how epitranscriptome and epitranscriptomic modifications underlying plant growth, development and environmental stress responses/adaptations. Third-generation sequencing technology, advanced bioinformatics tools and databases being used in plant epitranscriptomics are also discussed. Emphasis is given on potential exploration of epitranscriptome engineering for crop-improvement and developing environmental stress tolerant plants covering current status, challenges and future directions.
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Affiliation(s)
- Xiangbo Yang
- College of Agriculture, Jilin Agricultural Science and Technology University, Jilin, 132101, PR China.
| | - Suraj Patil
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Shrushti Joshi
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Monica Jamla
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India.
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Janowski M, Andrzejewska A. The legacy of mRNA engineering: A lineup of pioneers for the Nobel Prize. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 29:272-284. [PMID: 35855896 PMCID: PMC9278038 DOI: 10.1016/j.omtn.2022.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
mRNA is like Hermes, delivering the genetic code to cellular construction sites, so it has long been of interest, but only to a small group of scientists, and only demonstrating its remarkable efficacy in coronavirus disease 2019 (COVID-19) vaccines allowed it to go out into the open. Therefore, now is the right timing to delve into the stepping stones that underpin this success and pay tribute to the underlying scientists. From this perspective, advances in mRNA engineering have proven crucial to the rapidly growing role of this molecule in healthcare. Development of consecutive generations of cap analogs, including anti-reverse cap analogs (ARCAs), has significantly boosted translation efficacy and maintained an enthusiasm for mRNA research. Nucleotide modification to protect mRNA molecules from the host's immune system, followed by finding appropriate purification and packaging methods, were other links in the chain enabling medical breakthroughs. Currently, vaccines are the central area of mRNA research, but it will reach far beyond COVID-19. Supplementation of missing or abnormal proteins is another large field of mRNA research. Ex vivo cell engineering and genome editing have been expanding recently. Thus, it is time to recognize mRNA pioneers while building upon their legacy.
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Affiliation(s)
- Miroslaw Janowski
- Program in Image Guided Neurointerventions, Center for Advanced Imaging Research, Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD 21201, USA,Tumor Immunology and Immunotherapy Program, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD 21201, USA
| | - Anna Andrzejewska
- NeuroRepair Department, Mossakowski Medical Research Institute, PAS, 5 Pawinskiego Street, 02-106 Warsaw, Poland,Corresponding author Anna Andrzejewska, NeuroRepair Department, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawinskiego Street, 02-106 Warsaw, Poland.
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10
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Wu X, Li C, Wang Z, Zhang Y, Liu S, Chen S, Chen S, Liu W, Liu X. A bioinformatic analysis study of m 7G regulator-mediated methylation modification patterns and tumor microenvironment infiltration in glioblastoma. BMC Cancer 2022; 22:729. [PMID: 35788194 PMCID: PMC9251941 DOI: 10.1186/s12885-022-09791-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 06/16/2022] [Indexed: 11/25/2022] Open
Abstract
Background Glioblastoma is one of the most common brain cancers in adults, and is characterized by recurrence and little curative effect. An effective treatment for glioblastoma patients remains elusive worldwide. 7-methylguanosine (m7G) is a common RNA modification, and its role in tumors has become a research hotspot. Methods By searching for differentially expressed genes related to m7G, we generated a prognostic signature via cluster analysis and established classification criteria of high and low risk scores. The effectiveness of classification was validated using the Non-negative matrix factorization (NMF) algorithm, and repeatedly verified using training and test groups. The dimension reduction method was used to clearly show the difference and clinical significance of the data. All analyses were performed via R (version 4.1.2). Results According to the signature that included four genes (TMOD2, CACNG2, PLOD3, and TMSB10), glioblastoma patients were divided into high and low risk score groups. The survival rates between the two groups were significantly different, and the predictive abilities for 1-, 3-, and 5-year survivals were effective. We further established a Nomogram model to further examine the signature,as well as other clinical factors, with remaining significant results. Our signature can act as an independent prognostic factor related to immune-related processes in glioblastoma. Conclusions Our research addresses the gap in knowledge in the m7G and glioblastoma research fields. The establishment of a prognostic signature and the extended analysis of the tumor microenvironment, immune correlation, and tumor mutation burden further suggest the important role of m7G in the development and development of this disease. This work will provide support for future research. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09791-y.
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Affiliation(s)
- Xinrui Wu
- Department of oncology and chemotherapy, Affiliated Hospital of Nantong University, Nantong, China.,Department of Clinical Medicine, Medical School of Nantong University, Nantong, China
| | - Chuanyu Li
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Zhisu Wang
- Department of Clinical Medicine, Medical School of Nantong University, Nantong, China
| | - Yundi Zhang
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shifan Liu
- Department of Medical imaging, Medical School of Nantong University, Nantong, China
| | - Siqi Chen
- Department of Medical imaging, Medical School of Nantong University, Nantong, China
| | - Shuai Chen
- Department of measurement and control technology and instruments, School of mechanical engineering, Nantong University, Nantong, China
| | - Wangrui Liu
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China. .,Department of Interventional Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Xiaoman Liu
- Department of oncology and chemotherapy, Affiliated Hospital of Nantong University, Nantong, China. .,Department of Clinical Medicine, Medical School of Nantong University, Nantong, China.
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11
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Clark KD. Sample Preparation Strategies for Characterizing RNA Modifications in Small-Volume Samples and Single Cells. LCGC NORTH AMERICA 2022. [DOI: 10.56530/lcgc.na.xb7674j2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
This article describes challenges and opportunities in separation science in the rapidly emerging field of RNA modifications. Recent advances in sample preparation have permitted the analysis of RNA modifications in single cells by liquid chromatography–mass spectrometry (LC–MS). The sample handling and microextraction methods described here pave the way for new insights into the function of these unusual molecules in the brain and biological systems.
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12
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Accurate quantification of 3'-terminal 2'-O-methylated small RNAs by utilizing oxidative deep sequencing and stem-loop RT-qPCR. Front Med 2022; 16:240-250. [PMID: 35416629 DOI: 10.1007/s11684-021-0909-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/25/2021] [Indexed: 11/04/2022]
Abstract
The continuing discoveries of novel classes of RNA modifications in various organisms have raised the need for improving sensitive, convenient, and reliable methods for quantifying RNA modifications. In particular, a subset of small RNAs, including microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), are modified at their 3'-terminal nucleotides via 2'-O-methylation. However, quantifying the levels of these small RNAs is difficult because 2'-O-methylation at the RNA 3'-terminus inhibits the activity of polyadenylate polymerase and T4 RNA ligase. These two enzymes are indispensable for RNA labeling or ligation in conventional miRNA quantification assays. In this study, we profiled 3'-terminal 2'-O-methyl plant miRNAs in the livers of rice-fed mice by oxidative deep sequencing and detected increasing amounts of plant miRNAs with prolonged oxidation treatment. We further compared the efficiency of stem-loop and poly(A)-tailed RT-qPCR in quantifying plant miRNAs in animal tissues and identified stem-loop RT-qPCR as the only suitable approach. Likewise, stem-loop RT-qPCR was superior to poly(A)-tailed RT-qPCR in quantifying 3'-terminal 2'-O-methyl piRNAs in human seminal plasma. In summary, this study established a standard procedure for quantifying the levels of 3'-terminal 2'-O-methyl miRNAs in plants and piRNAs. Accurate measurement of the 3'-terminal 2'-O-methylation of small RNAs has profound implications for understanding their pathophysiologic roles in biological systems.
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13
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Guo C, Hu Y, Cao X, Wang Y. HILIC-MS/MS for the Determination of Methylated Adenine Nucleosides in Human Urine. Anal Chem 2021; 93:17060-17068. [PMID: 34902250 PMCID: PMC8751233 DOI: 10.1021/acs.analchem.1c03829] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
N6-methyl-2'-deoxyadenosine (m6dA) is a newly discovered DNA epigenetic mark in mammals. N6-methyladenosine (m6A), 2'-O-methyladenosine (Am), N6,2'-O-dimethyladenosine (m6Am), and N6,N6-dimethyladenosine (m62A) are common RNA modifications. Previous studies illustrated the associations between the aberrations of these methylated adenosines in nucleic acids and cancer. Herein, we developed Fe3O4/graphene-based magnetic dispersive solid-phase extraction for the enrichment and hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS/MS) for the measurements of m6dA, m6A, Am, m6Am, and m62A in human urine samples. We found that malic acid could improve the HILIC-based separation of these modified nucleosides and markedly enhance the sensitivity of their MS detection. With this method, we accurately quantified the contents of these modified adenine nucleosides in urine samples collected from gastric and colorectal cancer patients as well as healthy controls. We found that, relative to healthy controls, urinary m6dA and Am levels are significantly lower for gastric and colorectal cancer patients; while gastric cancer patients also exhibited lower levels of urinary m6A, the trend was opposite for colorectal cancer patients. Together, we developed a robust analytical method for simultaneous measurements of five methylated adenine nucleosides in human urine, and our results revealed an association between the levels of urinary methylated adenine nucleosides and the occurrence of gastric as well as colorectal cancers, suggesting the potential applications of these modified nucleosides as biomarkers for the early detection of these cancers.
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Affiliation(s)
- Cheng Guo
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Yiqiu Hu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Xiaoji Cao
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, California 92521, United States
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14
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Circadian and chemotherapy-related changes in urinary modified nucleosides excretion in patients with metastatic colorectal cancer. Sci Rep 2021; 11:24015. [PMID: 34907230 PMCID: PMC8671418 DOI: 10.1038/s41598-021-03247-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 11/01/2021] [Indexed: 11/29/2022] Open
Abstract
Urinary levels of modified nucleosides reflect nucleic acids turnover and can serve as non-invasive biomarkers for monitoring tumour circadian dynamics, and treatment responses in patients with metastatic colorectal cancer. In 39 patients, median overnight urinary excretion of LC-HRMS determinations of pseudouridine, was ~ tenfold as large as those of 1-methylguanosine, 1-methyladenosine, or 4-acetylcytidine, and ~ 100-fold as large as those of adenosine and cytidine. An increase in any nucleoside excretion after chemotherapy anticipated plasma carcinoembryonic antigen progression 1–2 months later and was associated with poor survival. Ten fractionated urines were collected over 2-days in 29 patients. The median value of the rhythm-adjusted mean of urinary nucleoside excretion varied from 64.3 for pseudouridine down to 0.61 for cytidine. The rhythm amplitudes relative to the 24-h mean of 6 nucleoside excretions were associated with rest duration, supporting a tight link between nucleosides turnover and the rest-activity rhythm. Moreover, the amplitude of the 1-methylguanosine rhythm was correlated with the rest-activity dichotomy index, a significant predictor of survival outcome in prior studies. In conclusion, urinary excretion dynamics of modified nucleosides appeared useful for the characterization of the circadian control of cellular proliferation and for tracking early responses to treatments in colorectal cancer patients.
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15
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Ying X, Liu B, Yuan Z, Huang Y, Chen C, Jiang X, Zhang H, Qi D, Yang S, Lin S, Luo J, Ji W. METTL1-m 7 G-EGFR/EFEMP1 axis promotes the bladder cancer development. Clin Transl Med 2021; 11:e675. [PMID: 34936728 PMCID: PMC8694502 DOI: 10.1002/ctm2.675] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/19/2021] [Accepted: 11/25/2021] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The posttranscriptional modifications of transfer RNA (tRNA) are critical for all aspects of the tRNA function and have been implicated in the tumourigenesis and progression of many human cancers. By contrast, the biological functions of methyltransferase-like 1 (METTL1)-regulated m7 G tRNA modification in bladder cancer (BC) remain obscure. RESULTS In this research, we show that METTL1 was highly expressed in BC, and its level was correlated with poor patient prognosis. Silencing METTL1 suppresses the proliferation, migration and invasion of BC cells in vitro and in vivo. Multi-omics analysis reveals that METTL1-mediated m7 G tRNA modification altered expression of certain target genes, including EGFR/EFEMP1. Mechanistically, METTL1 regulates the translation of EGFR/EFEMP1 via modifying certain tRNAs. Furthermore, forced expression of EGFR/EFEMP1 partially rescues the effect of METTL1 deletion on BC cells. CONCLUSIONS Our findings demonstrate the oncogenic role of METTL1 and the pathological significance of the METTL1-m7 G-EGFR/EFEMP1 axis in the BC development, thus providing potential therapeutic targets for the BC treatment.
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Affiliation(s)
- Xiaoling Ying
- Center for Translational MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhou510080China
- Department of UrologyThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhou510080China
| | - Bixia Liu
- Center for Translational MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhou510080China
| | - Zusen Yuan
- Department of UrologyMinimally Invasive Surgery centerGuangdong Key Laboratory of UrologyThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510230China
| | - Yapeng Huang
- Center for Translational MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhou510080China
- Department of UrologyMinimally Invasive Surgery centerGuangdong Key Laboratory of UrologyThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510230China
| | - Cong Chen
- Center for Translational MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhou510080China
| | - Xu Jiang
- Center for Translational MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhou510080China
| | - Haiqing Zhang
- Center for Translational MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhou510080China
| | - Defeng Qi
- Department of UrologyMinimally Invasive Surgery centerGuangdong Key Laboratory of UrologyThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510230China
| | - Shulan Yang
- Center for Translational MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhou510080China
| | - Shuibin Lin
- Center for Translational MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhou510080China
| | - Junhang Luo
- Department of UrologyThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhou510080China
| | - Weidong Ji
- Center for Translational MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhou510080China
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16
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Panda S, Poudel TN, Hegde P, Aldrich CC. Innovative Strategies for the Construction of Diverse 1'-Modified C-Nucleoside Derivatives. J Org Chem 2021; 86:16625-16640. [PMID: 34756029 DOI: 10.1021/acs.joc.1c01920] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Modified C-nucleosides have proven to be enormously successful as chemical probes to understand fundamental biological processes and as small-molecule drugs for cancer and infectious diseases. Historically, the modification of the glycosyl unit has focused on the 2'-, 3'-, and 4'-positions as well as the ribofuranosyl ring oxygen. By contrast, the 1'-position has rarely been studied due to the labile nature of the anomeric position. However, the improved chemical stability of C-nucleosides allows the modification of the 1'-position with substituents not found in conventional N-nucleosides. Herein, we disclose new chemistry for the installation of diverse substituents at the 1'-position of C-nucleosides, including alkyl, alkenyl, difluoromethyl, and fluoromethyl substituents, using the 4-amino-7-(1'-hydroxy-d-ribofuranosyl)pyrrolo[2,1-f][1,2,4]triazine scaffold as a representative purine nucleoside mimetic.
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Affiliation(s)
- Subhankar Panda
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Tej Narayan Poudel
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Pooja Hegde
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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17
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A regulatory role of circRNA-miRNA-mRNA network in osteoblast differentiation. Biochimie 2021; 193:137-147. [PMID: 34742858 DOI: 10.1016/j.biochi.2021.11.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 02/07/2023]
Abstract
Osteoblast differentiation is an important process in skeletal development and bone remodelling. Serious bone diseases occur from any delay, defect, or imbalance in osteoblastic differentiation. Non-coding RNAs (ncRNAs) play a regulatory role in controlling the expression of proteins under physiological and pathological conditions via inhibiting mRNA translation or degrading mRNA. Circular RNAs (circRNAs) and microRNAs (miRNAs) are the long and small ncRNAs, respectively, which have been reported to regulate the expression of osteoblast marker genes directly or indirectly. Also, recent studies identified the regulatory mechanisms involving the crosstalk among circRNAs, miRNAs, and mRNAs during osteoblast differentiation. Understanding these regulatory mechanisms behind osteoblastic differentiation would help to diagnose or treat bone and bone-related disorders. Hence, the current review comprehensively discussed the regulatory relationship of circRNAs, miRNAs and mRNAs, and their functional role as circRNA-miRNA-mRNA axis in osteoblast differentiation.
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18
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Gupta A, Andresen JL, Manan RS, Langer R. Nucleic acid delivery for therapeutic applications. Adv Drug Deliv Rev 2021; 178:113834. [PMID: 34492233 DOI: 10.1016/j.addr.2021.113834] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/25/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023]
Abstract
Recent medical advances have exploited the ability to address a given disease at the underlying level of transcription and translation. These treatment paradigms utilize nucleic acids - including short interfering RNA (siRNA), microRNA (miRNA), antisense oligonucleotides (ASO), and messenger RNA (mRNA) - to achieve a desired outcome ranging from gene knockdown to induced expression of a selected target protein. Towards this end, numerous strategies for encapsulation or stabilization of various nucleic acid structures have been developed in order to achieve intracellular delivery. In this review, we discuss several therapeutic applications of nucleic acids directed towards specific diseases and tissues of interest, in particular highlighting recent technologies which have reached late-stage clinical trials and received FDA approval.
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Affiliation(s)
- Akash Gupta
- David H Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02139, USA
| | - Jason L Andresen
- David H Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rajith S Manan
- David H Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert Langer
- David H Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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19
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Aggile K, Napoleon AA. Synthesis of Novel Substituted Piperazin-1- yl-7H-Pyrrolo[2,3-d] Pyrimidines for C-N Bond Formation via Buchwald Hartwig Coupling Reaction. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1991394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Kadirappa Aggile
- School of Advanced Sciences, Department of Chemistry, VIT University, Vellore, India
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20
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Methylation of viral mRNA cap structures by PCIF1 attenuates the antiviral activity of interferon-β. Proc Natl Acad Sci U S A 2021; 118:2025769118. [PMID: 34266951 DOI: 10.1073/pnas.2025769118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Interferons induce cell-intrinsic responses associated with resistance to viral infection. To overcome the suppressive action of interferons and their effectors, viruses have evolved diverse mechanisms. Using vesicular stomatitis virus (VSV), we report that the host cell N6-adenosine messenger RNA (mRNA) cap methylase, phosphorylated C-terminal domain interacting factor 1 (PCIF1), attenuates the antiviral response. We employed cell-based and in vitro biochemical assays to demonstrate that PCIF1 efficiently modifies VSV mRNA cap structures to m7Gpppm6Am and define the substrate requirements for this modification. Functional assays revealed that the PCIF1-dependent modification of VSV mRNA cap structures is inert with regard to mRNA stability, translation, and viral infectivity but attenuates the antiviral effects of the treatment of cells with interferon-β. Cells lacking PCIF1 or expressing a catalytically inactive PCIF1 exhibit an augmented inhibition of viral replication and gene expression following interferon-β treatment. We further demonstrate that the mRNA cap structures of rabies and measles viruses are also modified by PCIF1 to m7Gpppm6Am This work identifies a function of PCIF1 and cap-proximal m6Am in attenuation of the host response to VSV infection that likely extends to other viruses.
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21
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Safaric Tepes P, Pal D, Lindsted T, Ibarra I, Lujambio A, Jimenez Sabinina V, Senturk S, Miller M, Korimerla N, Huang J, Glassman L, Lee P, Zeltsman D, Hyman K, Esposito M, Hannon GJ, Sordella R. An epigenetic switch regulates the ontogeny of AXL-positive/EGFR-TKi-resistant cells by modulating miR-335 expression. eLife 2021; 10:e66109. [PMID: 34254585 PMCID: PMC8285107 DOI: 10.7554/elife.66109] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 06/10/2021] [Indexed: 01/15/2023] Open
Abstract
Despite current advancements in research and therapeutics, lung cancer remains the leading cause of cancer-related mortality worldwide. This is mainly due to the resistance that patients develop against chemotherapeutic agents over the course of treatment. In the context of non-small cell lung cancers (NSCLC) harboring EGFR-oncogenic mutations, augmented levels of AXL and GAS6 have been found to drive resistance to EGFR tyrosine kinase inhibitors such as Erlotinib and Osimertinib in certain tumors with mesenchymal-like features. By studying the ontogeny of AXL-positive cells, we have identified a novel non-genetic mechanism of drug resistance based on cell-state transition. We demonstrate that AXL-positive cells are already present as a subpopulation of cancer cells in Erlotinib-naïve tumors and tumor-derived cell lines and that the expression of AXL is regulated through a stochastic mechanism centered on the epigenetic regulation of miR-335. The existence of a cell-intrinsic program through which AXL-positive/Erlotinib-resistant cells emerge infers the need of treating tumors harboring EGFR-oncogenic mutations upfront with combinatorial treatments targeting both AXL-negative and AXL-positive cancer cells.
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Affiliation(s)
- Polona Safaric Tepes
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
- Faculty of Pharmacy University of LjubljanaLjubljanaSlovenia
| | - Debjani Pal
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
- Graduate Program in Molecular and Cellular Biology, Stony Brook UniversityStony Brook, New YorkUnited States
| | - Trine Lindsted
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Ingrid Ibarra
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Amaia Lujambio
- Icahn School of Medicine at Mount Sinai, Hess Center for Science and MedicineNew YorkUnited States
| | | | - Serif Senturk
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Madison Miller
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Navya Korimerla
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
- Graduate Program in Biomedical Engineering, Stony Brook UniversityNew YorkUnited States
| | - Jiahao Huang
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Lawrence Glassman
- Northwell Health Long Island, Jewish Medical CenterNew YorkUnited States
| | - Paul Lee
- Northwell Health Long Island, Jewish Medical CenterNew YorkUnited States
| | - David Zeltsman
- Northwell Health Long Island, Jewish Medical CenterNew YorkUnited States
| | - Kevin Hyman
- Northwell Health Long Island, Jewish Medical CenterNew YorkUnited States
| | - Michael Esposito
- Northwell Health Long Island, Jewish Medical CenterNew YorkUnited States
| | - Gregory J Hannon
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
- Cancer Research UK – Cambridge Institute, University of CambridgeCambridgeUnited Kingdom
| | - Raffaella Sordella
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
- Watson School of Biological Sciences, Cold Spring Harbor LaboratoryCold Spring HarborUnited States
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22
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Ao C, Zou Q, Yu L. RFhy-m2G: Identification of RNA N2-methylguanosine modification sites based on random forest and hybrid features. Methods 2021; 203:32-39. [PMID: 34033879 DOI: 10.1016/j.ymeth.2021.05.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/04/2021] [Accepted: 05/20/2021] [Indexed: 12/31/2022] Open
Abstract
N2-methylguanosine is a post-transcriptional modification of RNA that is found in eukaryotes and archaea. The biological function of m2G modification discovered so far is to control and stabilize the three-dimensional structure of tRNA and the dynamic barrier of reverse transcription. To discover additional biological functions of m2G, it is necessary to develop time-saving and labor-saving calculation tools to identify m2G. In this paper, based on hybrid features and a random forest, a novel predictor, RFhy-m2G, was developed to identify the m2G modification sites for three species. The hybrid feature used by the predictor is used to fuse the three features of ENAC, PseDNC, and NPPS. These three features include primary sequence derivation properties, physicochemical properties, and position-specific properties. Since there are redundant features in hybrid features, MRMD2.0 is used for optimal feature selection. Through feature analysis, it is found that the optimal hybrid features obtained still contain three kinds of properties, and the hybrid features can more accurately identify m2G modification sites and improve prediction performance. Based on five-fold cross-validation and independent testing to evaluate the prediction model, the accuracies obtained were 0.9982 and 0.9417, respectively. The robustness of the predictor is demonstrated by comparisons with other predictors.
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Affiliation(s)
- Chunyan Ao
- School of Computer Science and Technology, Xidian University, Xi'an, China; Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Liang Yu
- School of Computer Science and Technology, Xidian University, Xi'an, China.
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23
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Berg MD, Brandl CJ. Transfer RNAs: diversity in form and function. RNA Biol 2021; 18:316-339. [PMID: 32900285 PMCID: PMC7954030 DOI: 10.1080/15476286.2020.1809197] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/31/2020] [Accepted: 08/08/2020] [Indexed: 12/11/2022] Open
Abstract
As the adaptor that decodes mRNA sequence into protein, the basic aspects of tRNA structure and function are central to all studies of biology. Yet the complexities of their properties and cellular roles go beyond the view of tRNAs as static participants in protein synthesis. Detailed analyses through more than 60 years of study have revealed tRNAs to be a fascinatingly diverse group of molecules in form and function, impacting cell biology, physiology, disease and synthetic biology. This review analyzes tRNA structure, biosynthesis and function, and includes topics that demonstrate their diversity and growing importance.
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Affiliation(s)
- Matthew D. Berg
- Department of Biochemistry, The University of Western Ontario, London, Canada
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24
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Chai Y, Kondhare D, Zhang A, Leonard P, Seela F. The 2-Amino Group of 8-Aza-7-deaza-7-bromopurine-2,6-diamine and Purine-2,6-diamine as Stabilizer for the Adenine-Thymine Base Pair in Heterochiral DNA with Strands in Anomeric Configuration. Chemistry 2021; 27:2093-2103. [PMID: 33090562 PMCID: PMC7898646 DOI: 10.1002/chem.202004221] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Indexed: 02/05/2023]
Abstract
Stabilization of DNA is beneficial for many applications in the fields of DNA therapeutics, diagnostics, and materials science. Now, this phenomenon is studied on heterochiral DNA, an autonomous DNA recognition system with complementary strands in α-D and β-D configuration showing parallel strand orientation. The 12-mer heterochiral duplexes were constructed from anomeric (α/β-D) oligonucleotide single-strands. Purine-2,6-diamine and 8-aza-7-deaza-7-bromopurine-2,6-diamine 2'-deoxyribonucleosides having the capability to form tridentate base pairs with dT were used to strengthen the stability of the dA-dT base pair. Tm data and thermodynamic values obtained from UV melting profiles indicated that the 8-aza-7-deaza 2'-deoxyribonucleoside decorated with a bromo substituent is so far the most efficient stabilizer for heterochiral DNA. Compared with that, the stabilizing effect of the purine-2,6-diamine 2'-deoxyribonucleoside is low. Global changes of helix structures were identified by circular dichroism (CD) spectra during melting.
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Affiliation(s)
- Yingying Chai
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
- Department of RespiratoryCritical Care Medicine Targeted Tracer, Research and Development LaboratoryWest China HospitalSichuan610041P. R. China
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Aigui Zhang
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
- Laboratorium für Organische und Bioorganische ChemieInstitut für Chemie neuer MaterialienUniversität OsnabrückBarbarastrasse 749069OsnabrückGermany
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25
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Yu AM, Choi YH, Tu MJ. RNA Drugs and RNA Targets for Small Molecules: Principles, Progress, and Challenges. Pharmacol Rev 2020; 72:862-898. [PMID: 32929000 PMCID: PMC7495341 DOI: 10.1124/pr.120.019554] [Citation(s) in RCA: 179] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
RNA-based therapies, including RNA molecules as drugs and RNA-targeted small molecules, offer unique opportunities to expand the range of therapeutic targets. Various forms of RNAs may be used to selectively act on proteins, transcripts, and genes that cannot be targeted by conventional small molecules or proteins. Although development of RNA drugs faces unparalleled challenges, many strategies have been developed to improve RNA metabolic stability and intracellular delivery. A number of RNA drugs have been approved for medical use, including aptamers (e.g., pegaptanib) that mechanistically act on protein target and small interfering RNAs (e.g., patisiran and givosiran) and antisense oligonucleotides (e.g., inotersen and golodirsen) that directly interfere with RNA targets. Furthermore, guide RNAs are essential components of novel gene editing modalities, and mRNA therapeutics are under development for protein replacement therapy or vaccination, including those against unprecedented severe acute respiratory syndrome coronavirus pandemic. Moreover, functional RNAs or RNA motifs are highly structured to form binding pockets or clefts that are accessible by small molecules. Many natural, semisynthetic, or synthetic antibiotics (e.g., aminoglycosides, tetracyclines, macrolides, oxazolidinones, and phenicols) can directly bind to ribosomal RNAs to achieve the inhibition of bacterial infections. Therefore, there is growing interest in developing RNA-targeted small-molecule drugs amenable to oral administration, and some (e.g., risdiplam and branaplam) have entered clinical trials. Here, we review the pharmacology of novel RNA drugs and RNA-targeted small-molecule medications, with a focus on recent progresses and strategies. Challenges in the development of novel druggable RNA entities and identification of viable RNA targets and selective small-molecule binders are discussed. SIGNIFICANCE STATEMENT: With the understanding of RNA functions and critical roles in diseases, as well as the development of RNA-related technologies, there is growing interest in developing novel RNA-based therapeutics. This comprehensive review presents pharmacology of both RNA drugs and RNA-targeted small-molecule medications, focusing on novel mechanisms of action, the most recent progress, and existing challenges.
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MESH Headings
- Aptamers, Nucleotide/pharmacology
- Aptamers, Nucleotide/therapeutic use
- Betacoronavirus
- COVID-19
- Chemistry Techniques, Analytical/methods
- Chemistry Techniques, Analytical/standards
- Clustered Regularly Interspaced Short Palindromic Repeats
- Coronavirus Infections/drug therapy
- Drug Delivery Systems/methods
- Drug Development/organization & administration
- Drug Discovery
- Humans
- MicroRNAs/pharmacology
- MicroRNAs/therapeutic use
- Oligonucleotides, Antisense/pharmacology
- Oligonucleotides, Antisense/therapeutic use
- Pandemics
- Pneumonia, Viral/drug therapy
- RNA/adverse effects
- RNA/drug effects
- RNA/pharmacology
- RNA, Antisense/pharmacology
- RNA, Antisense/therapeutic use
- RNA, Messenger/drug effects
- RNA, Messenger/pharmacology
- RNA, Ribosomal/drug effects
- RNA, Ribosomal/pharmacology
- RNA, Small Interfering/pharmacology
- RNA, Small Interfering/therapeutic use
- RNA, Viral/drug effects
- Ribonucleases/metabolism
- Riboswitch/drug effects
- SARS-CoV-2
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Affiliation(s)
- Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
| | - Young Hee Choi
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
| | - Mei-Juan Tu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
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26
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Nechooshtan G, Yunusov D, Chang K, Gingeras TR. Processing by RNase 1 forms tRNA halves and distinct Y RNA fragments in the extracellular environment. Nucleic Acids Res 2020; 48:8035-8049. [PMID: 32609822 PMCID: PMC7430647 DOI: 10.1093/nar/gkaa526] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/07/2020] [Accepted: 06/26/2020] [Indexed: 12/11/2022] Open
Abstract
Extracellular RNAs participate in intercellular communication, and are being studied as promising minimally invasive diagnostic markers. Several studies in recent years showed that tRNA halves and distinct Y RNA fragments are abundant in the extracellular space, including in biofluids. While their regulatory and diagnostic potential has gained a substantial amount of attention, the biogenesis of these extracellular RNA fragments remains largely unexplored. Here, we demonstrate that these fragments are produced by RNase 1, a highly active secreted nuclease. We use RNA sequencing to investigate the effect of a null mutation of RNase 1 on the levels of tRNA halves and Y RNA fragments in the extracellular environment of cultured human cells. We complement and extend our RNA sequencing results with northern blots, showing that tRNAs and Y RNAs in the non-vesicular extracellular compartment are released from cells as full-length precursors and are subsequently cleaved to distinct fragments. In support of these results, formation of tRNA halves is recapitulated by recombinant human RNase 1 in our in vitro assay. These findings assign a novel function for RNase 1, and position it as a strong candidate for generation of tRNA halves and Y RNA fragments in biofluids.
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Affiliation(s)
- Gal Nechooshtan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Dinar Yunusov
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Kenneth Chang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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27
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Abstract
Chemical modifications of viral RNA are an integral part of the viral life cycle and are present in most classes of viruses. To date, more than 170 RNA modifications have been discovered in all types of cellular RNA. Only a few, however, have been found in viral RNA, and the function of most of these has yet to be elucidated. Those few we have discovered and whose functions we understand have a varied effect on each virus. They facilitate RNA export from the nucleus, aid in viral protein synthesis, recruit host enzymes, and even interact with the host immune machinery. The most common methods for their study are mass spectrometry and antibody assays linked to next-generation sequencing. However, given that the actual amount of modified RNA can be very small, it is important to pair meticulous scientific methodology with the appropriate detection methods and to interpret the results with a grain of salt. Once discovered, RNA modifications enhance our understanding of viruses and present a potential target in combating them. This review provides a summary of the currently known chemical modifications of viral RNA, the effects they have on viral machinery, and the methods used to detect them.
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Affiliation(s)
- Jiří František Potužník
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Cahová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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28
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Otsubo Y, Kamada Y, Yamashita A. Novel Links between TORC1 and Traditional Non-Coding RNA, tRNA. Genes (Basel) 2020; 11:E956. [PMID: 32825021 PMCID: PMC7563549 DOI: 10.3390/genes11090956] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 12/19/2022] Open
Abstract
Target of rapamycin (TOR) is a serine/threonine kinase that modulates cell growth and metabolism in response to environmental changes. Transfer RNA (tRNA) is an abundant and ubiquitous small non-coding RNA that is essential in the translation of mRNAs. Beyond its canonical role, it has been revealed that tRNAs have more diverse functions. TOR complex 1 (TORC1), which is one of the two TOR complexes, regulates tRNA synthesis by controlling RNA polymerase III. In addition to tRNA synthesis regulation, recent studies have revealed hidden connections between TORC1 and tRNA, which are both essential players in eukaryotic cellular activities. Here, we review the accumulating findings on the regulatory links between TORC1 and tRNA-particularly those links in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe.
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Affiliation(s)
- Yoko Otsubo
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan; (Y.O.); (Y.K.)
- National Institute for Fusion Science, 322-6 Oroshi, Toki, Gifu 509-5292, Japan
- Center for Novel Science Initiatives, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Yoshiaki Kamada
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan; (Y.O.); (Y.K.)
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Akira Yamashita
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan; (Y.O.); (Y.K.)
- Center for Novel Science Initiatives, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
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29
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McCown PJ, Ruszkowska A, Kunkler CN, Breger K, Hulewicz JP, Wang MC, Springer NA, Brown JA. Naturally occurring modified ribonucleosides. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1595. [PMID: 32301288 PMCID: PMC7694415 DOI: 10.1002/wrna.1595] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 12/18/2022]
Abstract
The chemical identity of RNA molecules beyond the four standard ribonucleosides has fascinated scientists since pseudouridine was characterized as the “fifth” ribonucleotide in 1951. Since then, the ever‐increasing number and complexity of modified ribonucleosides have been found in viruses and throughout all three domains of life. Such modifications can be as simple as methylations, hydroxylations, or thiolations, complex as ring closures, glycosylations, acylations, or aminoacylations, or unusual as the incorporation of selenium. While initially found in transfer and ribosomal RNAs, modifications also exist in messenger RNAs and noncoding RNAs. Modifications have profound cellular outcomes at various levels, such as altering RNA structure or being essential for cell survival or organism viability. The aberrant presence or absence of RNA modifications can lead to human disease, ranging from cancer to various metabolic and developmental illnesses such as Hoyeraal–Hreidarsson syndrome, Bowen–Conradi syndrome, or Williams–Beuren syndrome. In this review article, we summarize the characterization of all 143 currently known modified ribonucleosides by describing their taxonomic distributions, the enzymes that generate the modifications, and any implications in cellular processes, RNA structure, and disease. We also highlight areas of active research, such as specific RNAs that contain a particular type of modification as well as methodologies used to identify novel RNA modifications. This article is categorized under:RNA Processing > RNA Editing and Modification
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Affiliation(s)
- Phillip J McCown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Agnieszka Ruszkowska
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Charlotte N Kunkler
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Kurtis Breger
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jacob P Hulewicz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Matthew C Wang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Noah A Springer
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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30
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Solvent-free synthesis of isoindolo[2,1-c]pyrazolo[1,5-a]quinazoline and pyrazolo[5',1':2,3]pyrimido[6,1-a]isoindol derivatives through a one-pot three-component reaction. Mol Divers 2020; 25:1123-1130. [PMID: 32076910 DOI: 10.1007/s11030-020-10052-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 02/07/2020] [Indexed: 12/24/2022]
Abstract
Some 5-substituted 3-aminopyrazoles were used for the synthesis of isoindolo[2,1-c]pyrazolo[1,5-a]quinazoline and pyrazolo[5',1':2,3]pyrimido[6,1-a]isoindol derivatives via a mild and efficient one-pot three-component reaction with 2-formylbenzoic acid and different CH-acids under solvent-free condition.
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31
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Synthesis of a structure containing three N-fused heterocycles with very high bond-forming through a one-pot reaction. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.130923] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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32
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Kenderdine T, Nemati R, Baker A, Palmer M, Ujma J, FitzGibbon M, Deng L, Royzen M, Langridge J, Fabris D. High-resolution ion mobility spectrometry-mass spectrometry of isomeric/isobaric ribonucleotide variants. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4465. [PMID: 31697854 PMCID: PMC8363168 DOI: 10.1002/jms.4465] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/13/2019] [Accepted: 10/22/2019] [Indexed: 06/01/2023]
Abstract
In this report, we explored the benefits of cyclic ion mobility (cIM) mass spectrometry in the analysis of isomeric post-transcriptional modifications of RNA. Standard methyl-cytidine samples were initially utilized to test the ability to correctly distinguish different structures sharing the same elemental composition and thus molecular mass. Analyzed individually, the analytes displayed characteristic arrival times (tD ) determined by the different positions of the modifying methyl groups onto the common cytidine scaffold. Analyzed in mixture, the widths of the respective signals resulted in significant overlap that initially prevented their resolution on the tD scale. The separation of the four isomers was achieved by increasing the number of passes through the cIM device, which enabled to fully differentiate the characteristic ion mobility behaviors associated with very subtle structural variations. The placement of the cIM device between the mass-selective quadrupole and the time-of-flight analyzer allowed us to perform gas-phase activation of each of these ion populations, which had been first isolated according to a common mass-to-charge ratio and then separated on the basis of different ion mobility behaviors. The observed fragmentation patterns confirmed the structures of the various isomers thus substantiating the benefits of complementing unique tD information with specific fragmentation data to reach more stringent analyte identification. These capabilities were further tested by analyzing natural mono-nucleotide mixtures obtained by exonuclease digestion of total RNA extracts. In particular, the combination of cIM separation and post-mobility dissociation allowed us to establish the composition of methyl-cytidine and methyl-adenine components present in the entire transcriptome of HeLa cells. For this reason, we expect that this technique will benefit not only epitranscriptomic studies requiring the determination of identity and expression levels of RNA modifications, but also metabolomics investigations involving the analysis of natural extracts that may possibly contain subsets of isomeric/isobaric species.
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Affiliation(s)
| | | | - A. Baker
- Waters Corporation, Wilmslow SK9 4AX, UK
| | - M. Palmer
- Waters Corporation, Wilmslow SK9 4AX, UK
| | - J. Ujma
- Waters Corporation, Wilmslow SK9 4AX, UK
| | - M FitzGibbon
- University at Albany, Albany, NY 12222
- University of California San Diego, La Jolla, CA 92093
| | - L. Deng
- University at Albany, Albany, NY 12222
| | - M. Royzen
- University at Albany, Albany, NY 12222
| | | | - D. Fabris
- University at Albany, Albany, NY 12222
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33
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Netzband R, Pager CT. Epitranscriptomic marks: Emerging modulators of RNA virus gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1576. [PMID: 31694072 PMCID: PMC7169815 DOI: 10.1002/wrna.1576] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 12/27/2022]
Abstract
Epitranscriptomics, the study of posttranscriptional chemical moieties placed on RNA, has blossomed in recent years. This is due in part to the emergence of high‐throughput detection methods as well as the burst of discoveries showing biological function of select chemical marks. RNA modifications have been shown to affect RNA structure, localization, and functions such as alternative splicing, stabilizing transcripts, nuclear export, cap‐dependent and cap‐independent translation, microRNA biogenesis and binding, RNA degradation, and immune regulation. As such, the deposition of chemical marks on RNA has the unique capability to spatially and temporally regulate gene expression. The goal of this article is to present the exciting convergence of the epitranscriptomic and virology fields, specifically the deposition and biological impact of N7‐methylguanosine, ribose 2′‐O‐methylation, pseudouridine, inosine, N6‐methyladenosine, and 5‐methylcytosine epitranscriptomic marks on gene expression of RNA viruses. This article is categorized under:RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications
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Affiliation(s)
- Rachel Netzband
- Department of Biological Sciences, The RNA Institute, University at Albany-SUNY, Albany, New York
| | - Cara T Pager
- Department of Biological Sciences, The RNA Institute, University at Albany-SUNY, Albany, New York
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34
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Casella G, Tsitsipatis D, Abdelmohsen K, Gorospe M. mRNA methylation in cell senescence. WILEY INTERDISCIPLINARY REVIEWS. RNA 2019; 10:e1547. [PMID: 31144457 PMCID: PMC8474013 DOI: 10.1002/wrna.1547] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/23/2019] [Accepted: 05/01/2019] [Indexed: 01/06/2023]
Abstract
Cellular senescence, a developmental program central to normal aging and aging pathologies, is robustly regulated at the post-transcriptional level. This regulation involves the interaction of RNA-binding proteins and noncoding RNAs with senescence-associated messenger RNAs (mRNAs). There is increasing evidence that these associations are modulated by chemical modifications of specific mRNA nucleotides which can enhance or reduce the binding of regulatory factors. Recent technological advances in mass spectrometry, next-generation sequencing, and genome mapping have improved markedly the detection of mRNA modifications. Given the rising interest in the epitranscriptomic control of gene expression in aging, we discuss our incipient understanding of the chemical mRNA modifications, specifically m6 A and m5 C, that influence cellular senescence. This article is categorized under: RNA Export and Localization > RNA Localization RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Gabriel Casella
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Dimitrios Tsitsipatis
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
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35
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He CC, Hamlow LA, Zhu Y, Nei YW, Fan L, McNary CP, Maître P, Steinmetz V, Schindler B, Compagnon I, Armentrout PB, Rodgers MT. Structural and Energetic Effects of O2'-Ribose Methylation of Protonated Pyrimidine Nucleosides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2318-2334. [PMID: 31435890 DOI: 10.1007/s13361-019-02300-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/18/2019] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
The 2'-substituents distinguish DNA from RNA nucleosides. 2'-O-methylation occurs naturally in RNA and plays important roles in biological processes. Such 2'-modifications may alter the hydrogen-bonding interactions of the nucleoside and thus may affect the conformations of the nucleoside in an RNA chain. Structures of the protonated 2'-O-methylated pyrimidine nucleosides were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy, assisted by electronic structure calculations. The glycosidic bond stabilities of the protonated 2'-O-methylated pyrimidine nucleosides, [Nuom+H]+, were also examined and compared to their DNA and RNA nucleoside analogues via energy-resolved collision-induced dissociation (ER-CID). The preferred sites of protonation of the 2'-O-methylated pyrimidine nucleosides parallel their canonical DNA and RNA nucleoside analogues, [dNuo+H]+ and [Nuo+H]+, yet their nucleobase orientation and sugar puckering differ. The glycosidic bond stabilities of the protonated pyrimidine nucleosides follow the order: [dNuo+H]+ < [Nuo+H]+ < [Nuom+H]+. The slightly altered structures help explain the stabilization induced by 2'-O-methylation of the pyrimidine nucleosides.
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Affiliation(s)
- C C He
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - L A Hamlow
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - Y Zhu
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - Y-W Nei
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - L Fan
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - C P McNary
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - P Maître
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - V Steinmetz
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - B Schindler
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Villeurbanne, France
| | - I Compagnon
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Villeurbanne, France
| | - P B Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA.
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36
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Matsuzawa S, Wakata Y, Ebi F, Isobe M, Kurosawa N. Development and validation of monoclonal antibodies against N6-methyladenosine for the detection of RNA modifications. PLoS One 2019; 14:e0223197. [PMID: 31577817 PMCID: PMC6774519 DOI: 10.1371/journal.pone.0223197] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/16/2019] [Indexed: 12/21/2022] Open
Abstract
RNA contains various chemical modifications, among which N6-methyladenosine (m6A) is the most prevalent modified nucleotide in eukaryotic mRNA. Emerging evidence suggests that m6A plays an important role in regulating a variety of cellular functions by controlling mRNA processing, translation and degradation. Because m6A is not detectable by standard chemical modification-based approaches, immunological methods, such as ELISA, immunoblotting, immunohistochemistry, m6A RNA immunoprecipitation sequencing and m6A individual-nucleotide resolution cross-linking and immunoprecipitation, have been employed to detect m6A in RNA. Although the most important factor determining the success of these methods is the integrity of highly specific antibodies against m6A, the development of m6A-specific monoclonal antibodies has been challenging. We developed anti-m6A monoclonal antibodies using our recently developed single cell-based monoclonal antibody production system. The binding of one selected antibody, #B1-3, to RNA oligoribonucleotide containing a single m6A had an equilibrium dissociation constant of 6.5 nM, and this antibody exhibited negligible binding to oligoribonucleotides containing a single N1-methyladenosine and unmodified adenosine. The binding was competed by the addition of increasing concentrations of N6-methyl-ATP but not N1-methyl-ATP or ATP. Furthermore, this mAb specifically crosslinked m6A-containing oligoribonucleotide by ultraviolet light, resulting in the induction of cDNA truncation at m6A position. These results show the feasibility of using the validated m6A monoclonal antibody for the specific detection of m6A in RNA.
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Affiliation(s)
- Shun Matsuzawa
- Graduate School of Innovative Life Science, University of Toyama, Toyama-shi, Toyama, Japan
- Medical & Biological Laboratories Co., Ltd., Akaho, Komagane, Nagano, Japan
| | - Yuka Wakata
- Graduate School of Innovative Life Science, University of Toyama, Toyama-shi, Toyama, Japan
| | - Fumiya Ebi
- Graduate School of Science and Engineering for Education, University of Toyama, Gofuku, Toyama-shi, Toyama, Japan
| | - Masaharu Isobe
- Laboratory of Molecular and Cellular Biology, Faculty of Science and Engineering, Graduate School, University of Toyama, Gofuku, Toyama-shi, Toyama, Japan
| | - Nobuyuki Kurosawa
- Laboratory of Molecular and Cellular Biology, Faculty of Science and Engineering, Graduate School, University of Toyama, Gofuku, Toyama-shi, Toyama, Japan
- * E-mail:
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37
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Chen W, Song X, Lv H, Lin H. iRNA-m2G: Identifying N 2-methylguanosine Sites Based on Sequence-Derived Information. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 18:253-258. [PMID: 31581049 PMCID: PMC6796771 DOI: 10.1016/j.omtn.2019.08.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/06/2019] [Accepted: 08/19/2019] [Indexed: 12/11/2022]
Abstract
RNA N2-methylguanosine (m2G) is one kind of posttranscriptional modification and plays crucial roles in the control and stabilization of tRNA. However, our knowledge about the biological functions of m2G is still limited. The key step of revealing its new function is to recognize the m2G sites in the transcriptome. Since there is no effective method for detecting m2G sites, it is desirable to develop new methods to identify m2G sites. In this study, a computational predictor called iRNA-m2G was proposed to identify m2G sites in eukaryotic transcriptomes. In iRNA-m2G, the RNA sequences were encoded by using nucleotide chemical property and accumulated nucleotide frequency. iRNA-m2G was not only validated by the rigorous jackknife test on the benchmark dataset but also examined by performing cross-species validations. In addition, iRNA-m2G was also tested on an independent dataset. It was found that the accuracies obtained by iRNA-m2G were all quite promising in these tests, indicating that the proposed method could become a powerful tool for identifying m2G sites. Finally, a user-friendly web server for iRNA-m2G is freely accessible at http://lin-group.cn/server/iRNA-m2G.php.
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Affiliation(s)
- Wei Chen
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611730, China; Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China.
| | - Xiaoming Song
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China
| | - Hao Lv
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.
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38
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Bushkin GG, Pincus D, Morgan JT, Richardson K, Lewis C, Chan SH, Bartel DP, Fink GR. m 6A modification of a 3' UTR site reduces RME1 mRNA levels to promote meiosis. Nat Commun 2019; 10:3414. [PMID: 31363087 PMCID: PMC6667471 DOI: 10.1038/s41467-019-11232-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 06/28/2019] [Indexed: 01/23/2023] Open
Abstract
Despite the vast number of modification sites mapped within mRNAs, known examples of consequential mRNA modifications remain rare. Here, we provide multiple lines of evidence to show that Ime4p, an N6-methyladenosine (m6A) methyltransferase required for meiosis in yeast, acts by methylating a site in the 3′ UTR of the mRNA encoding Rme1p, a transcriptional repressor of meiosis. Consistent with this mechanism, genetic analyses reveal that IME4 functions upstream of RME1. Transcriptome-wide, RME1 is the primary message that displays both increased methylation and reduced expression in an Ime4p-dependent manner. In yeast strains for which IME4 is dispensable for meiosis, a natural polymorphism in the RME1 promoter reduces RME1 transcription, obviating the requirement for methylation. Mutation of a single m6A site in the RME1 3′ UTR increases Rme1p repressor production and reduces meiotic efficiency. These results reveal the molecular and physiological consequences of a modification in the 3′ UTR of an mRNA. Ime4p is a yeast N6-methyladenosine (m6A) methyltransferase with an unknown role in meiosis. Rme1p is a repressor of meiosis. Here the authors show that Ime4p methylates RME1 3′ UTR to reduce its expression and enable meiosis, thus providing an example of an m6A site with a physiological role.
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Affiliation(s)
- G Guy Bushkin
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA. .,Department of Molecular Genetics and Cell Biology and the Center for Physics of Evolving Systems, University of Chicago, Chicago, IL, 60637, USA.
| | - David Pincus
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.,Department of Molecular Genetics and Cell Biology and the Center for Physics of Evolving Systems, University of Chicago, Chicago, IL, 60637, USA
| | - Jeffrey T Morgan
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Howard Hughes Medical Institute, Cambridge, MA, 02142, USA
| | - Kris Richardson
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - Caroline Lewis
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - Sze Ham Chan
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - David P Bartel
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Howard Hughes Medical Institute, Cambridge, MA, 02142, USA
| | - Gerald R Fink
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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39
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McIntyre W, Netzband R, Bonenfant G, Biegel JM, Miller C, Fuchs G, Henderson E, Arra M, Canki M, Fabris D, Pager CT. Positive-sense RNA viruses reveal the complexity and dynamics of the cellular and viral epitranscriptomes during infection. Nucleic Acids Res 2019; 46:5776-5791. [PMID: 29373715 PMCID: PMC6009648 DOI: 10.1093/nar/gky029] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 01/15/2018] [Indexed: 12/26/2022] Open
Abstract
More than 140 post-transcriptional modifications (PTMs) are known to decorate cellular RNAs, but their incidence, identity and significance in viral RNA are still largely unknown. We have developed an agnostic analytical approach to comprehensively survey PTMs on viral and cellular RNAs. Specifically, we used mass spectrometry to analyze PTMs on total RNA isolated from cells infected with Zika virus, Dengue virus, hepatitis C virus (HCV), poliovirus and human immunodeficiency virus type 1. All five RNA viruses significantly altered global PTM landscapes. Examination of PTM profiles of individual viral genomes isolated by affinity capture revealed a plethora of PTMs on viral RNAs, which far exceeds the handful of well-characterized modifications. Direct comparison of viral epitranscriptomes identified common and virus-specific PTMs. In particular, specific dimethylcytosine modifications were only present in total RNA from virus-infected cells, and in intracellular HCV RNA, and viral RNA from Zika and HCV virions. Moreover, dimethylcytosine abundance during viral infection was modulated by the cellular DEAD-box RNA helicase DDX6. By opening the Pandora's box on viral PTMs, this report presents numerous questions and hypotheses on PTM function and strongly supports PTMs as a new tier of regulation by which RNA viruses subvert the host and evade cellular surveillance systems.
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Affiliation(s)
- Will McIntyre
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Rachel Netzband
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Gaston Bonenfant
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Jason M Biegel
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Clare Miller
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Gabriele Fuchs
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Eric Henderson
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Manoj Arra
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208, USA
| | - Mario Canki
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208, USA
| | - Daniele Fabris
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Cara T Pager
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
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40
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Cicada Endosymbionts Have tRNAs That Are Correctly Processed Despite Having Genomes That Do Not Encode All of the tRNA Processing Machinery. mBio 2019; 10:mBio.01950-18. [PMID: 31213566 PMCID: PMC6581868 DOI: 10.1128/mbio.01950-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The smallest bacterial genomes, in the range of about 0.1 to 0.5 million base pairs, are commonly found in the nutritional endosymbionts of insects. These tiny genomes are missing genes that encode proteins and RNAs required for the translation of mRNAs, one of the most highly conserved and important cellular processes. In this study, we found that the bacterial endosymbionts of cicadas have genomes which encode incomplete tRNA sets and lack genes required for tRNA processing. Nevertheless, we found that endosymbiont tRNAs are correctly processed at their 5′ and 3′ ends and, surprisingly, that mostly exist as tRNA halves. We hypothesize that the cicada host must supply its symbionts with these missing tRNA processing activities. Gene loss and genome reduction are defining characteristics of endosymbiotic bacteria. The most highly reduced endosymbiont genomes have lost numerous essential genes related to core cellular processes such as replication, transcription, and translation. Computational gene predictions performed for the genomes of the two bacterial symbionts of the cicada Diceroprocta semicincta, “Candidatus Hodgkinia cicadicola” (Alphaproteobacteria) and “Ca. Sulcia muelleri” (Bacteroidetes), have found only 26 and 16 tRNA genes and 15 and 10 aminoacyl tRNA synthetase genes, respectively. Furthermore, the original “Ca. Hodgkinia cicadicola” genome annotation was missing several essential genes involved in tRNA processing, such as those encoding RNase P and CCA tRNA nucleotidyltransferase as well as several RNA editing enzymes required for tRNA maturation. How these cicada endosymbionts perform basic translation-related processes remains unknown. Here, by sequencing eukaryotic mRNAs and total small RNAs, we show that the limited tRNA set predicted by computational annotation of “Ca. Sulcia muelleri” and “Ca. Hodgkinia cicadicola” is likely correct. Furthermore, we show that despite the absence of genes encoding tRNA processing activities in the symbiont genomes, symbiont tRNAs have correctly processed 5′ and 3′ ends and seem to undergo nucleotide modification. Surprisingly, we found that most “Ca. Hodgkinia cicadicola” and “Ca. Sulcia muelleri” tRNAs exist as tRNA halves. We hypothesize that “Ca. Sulcia muelleri” and “Ca. Hodgkinia cicadicola” tRNAs function in bacterial translation but require host-encoded enzymes to do so.
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41
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Vandivier LE, Anderson ZD, Gregory BD. HAMR: High-Throughput Annotation of Modified Ribonucleotides. Methods Mol Biol 2019; 1870:51-67. [PMID: 30539546 DOI: 10.1007/978-1-4939-8808-2_4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Ribonucleotides can be decorated with over 100 types of covalent chemical modifications. These modifications change the structure, function, and catalytic activity of RNAs, forming a layer of posttranscriptional regulation termed the epitranscriptome. Recent advances in high-throughput mapping have demonstrated these modifications are abundant and mark nearly all classes of RNAs, including messenger RNAs. Here, we outline one such technique called high-throughput annotation of modified ribonucleotides (HAMR). HAMR exploits the tendency of certain modified ribonucleotides to interfere with base pairing, leading to errors in complementary DNA synthesis during RNA sequencing library preparation. In total, we present a computational protocol for in silico identification of modifications with HAMR, which can be retroactively applied to a variety of RNA sequencing techniques.
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Affiliation(s)
- Lee E Vandivier
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.,Cell and Molecular Biology Graduate Program, University of Pennsylvania, Philadelphia, PA, USA
| | - Zachary D Anderson
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA. .,Cell and Molecular Biology Graduate Program, University of Pennsylvania, Philadelphia, PA, USA.
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42
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tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii. J Bacteriol 2019; 201:JB.00690-18. [PMID: 30745370 DOI: 10.1128/jb.00690-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/31/2019] [Indexed: 12/13/2022] Open
Abstract
tRNAs play a critical role in mRNA decoding, and posttranscriptional modifications within tRNAs drive decoding efficiency and accuracy. The types and positions of tRNA modifications in model bacteria have been extensively studied, and tRNA modifications in a few eukaryotic organisms have also been characterized and localized to particular tRNA sequences. However, far less is known regarding tRNA modifications in archaea. While the identities of modifications have been determined for multiple archaeal organisms, Haloferax volcanii is the only organism for which modifications have been extensively localized to specific tRNA sequences. To improve our understanding of archaeal tRNA modification patterns and codon-decoding strategies, we have used liquid chromatography and tandem mass spectrometry to characterize and then map posttranscriptional modifications on 34 of the 35 unique tRNA sequences of Methanocaldococcus jannaschii A new posttranscriptionally modified nucleoside, 5-cyanomethyl-2-thiouridine (cnm5s2U), was discovered and localized to position 34. Moreover, data consistent with wyosine pathway modifications were obtained beyond the canonical tRNAPhe as is typical for eukaryotes. The high-quality mapping of tRNA anticodon loops enriches our understanding of archaeal tRNA modification profiles and decoding strategies.IMPORTANCE While many posttranscriptional modifications in M. jannaschii tRNAs are also found in bacteria and eukaryotes, several that are unique to archaea were identified. By RNA modification mapping, the modification profiles of M. jannaschii tRNA anticodon loops were characterized, allowing a comparative analysis with H. volcanii modification profiles as well as a general comparison with bacterial and eukaryotic decoding strategies. This general comparison reveals that M. jannaschii, like H. volcanii, follows codon-decoding strategies similar to those used by bacteria, although position 37 appears to be modified to a greater extent than seen in H. volcanii.
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43
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Abstract
Small-molecule and protein/antibody drugs mainly act on genome-derived proteins to exert pharmacological effects. RNA based therapies hold the promise to expand the range of druggable targets from proteins to RNAs and the genome, as evidenced by several RNA drugs approved for clinical practice and many others under active trials. While chemo-engineered RNA mimics have found their success in marketed drugs and continue dominating basic research and drug development, these molecules are usually conjugated with extensive and various modifications. This makes them completely different from cellular RNAs transcribed from the genome that usually consist of unmodified ribonucleotides or just contain a few posttranscriptional modifications. The use of synthetic RNA mimics for RNA research and drug development is also in contrast with the ultimate success of protein research and therapy utilizing biologic or recombinant proteins produced and folded in living cells instead of polypeptides or proteins synthesized in vitro. Indeed, efforts have been made recently to develop RNA bioengineering technologies for cost-effective and large-scale production of biologic RNA molecules that may better capture the structures, functions, and safety profiles of natural RNAs. In this article, we provide an overview on RNA therapeutics for the treatment of human diseases via RNA interference mechanisms. By illustrating the structural differences between natural RNAs and chemo-engineered RNA mimics, we focus on discussion of a novel class of bioengineered/biologic RNA agents produced through fermentation and their potential applications to RNA research and drug development.
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Affiliation(s)
- Ai-Ming Yu
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA.
| | - Chao Jian
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Allan H Yu
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Mei-Juan Tu
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
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44
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Devereaux ZJ, Zhu Y, Rodgers MT. Relative glycosidic bond stabilities of naturally occurring methylguanosines: 7-methylation is intrinsically activating. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:16-29. [PMID: 30189754 DOI: 10.1177/1469066718798097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The frequency and diversity of posttranscriptional modifications add an additional layer of chemical complexity beyond canonical nucleic acid sequence. Methylations are particularly frequently occurring and often highly conserved throughout the kingdoms of life. However, the intricate functions of these modified nucleic acid constituents are often not fully understood. Systematic foundational research that reduces systems to their minimum constituents may aid in unraveling the complexities of nucleic acid biochemistry. Here, we examine the relative intrinsic N-glycosidic bond stabilities of guanosine and five naturally occurring methylguanosines (O2'-, 1-, 7-, N2,N2-di-, and N2,N2,O2'-trimethylguanosine) probed by energy-resolved collision-induced dissociation tandem mass spectrometry and complemented with quantum chemical calculations. Apparent glycosidic bond stability is generally found to increase with increasing methyl substitution (canonical < mono- < di- < trimethylated). Many biochemical transformations, including base excision repair mechanisms, involve protonation and/or noncovalent interactions to increase nucleobase leaving-group ability. The protonated gas-phase methylguanosines require less activation energy for glycosidic bond cleavage than their sodium cationized forms. However, methylation at the N7 position intrinsically weakens the glycosidic bond of 7-methylguanosine more significantly than subsequent cationization, and thus 7-methylguanosine is suggested to be under perpetually activated conditions. N7 methylation also alters the nucleoside geometric preferences relative to the other systems, including the nucleobase orientation in the neutral form, sugar puckering in the protonated form, and the preferred protonation and sodium cation binding sites. All of the methylated guanosines examined here are predicted to have proton affinities and gas-phase basicities that exceed that of canonical guanosine. Additionally, the proton affinity and gas-phase basicity trends exhibit a roughly inverse correlation with the apparent glycosidic bond stabilities.
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Affiliation(s)
| | - Y Zhu
- Department of Chemistry, Wayne State University, Detroit, USA
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, USA
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45
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Joshi K, Cao L, Farabaugh PJ. The problem of genetic code misreading during protein synthesis. Yeast 2019; 36:35-42. [DOI: 10.1002/yea.3374] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/11/2018] [Accepted: 12/13/2018] [Indexed: 02/01/2023] Open
Affiliation(s)
- Kartikeya Joshi
- Department of Biological Sciences; University of Maryland Baltimore County; Baltimore Maryland, USA
| | - Ling Cao
- Department of Biological Sciences; University of Maryland Baltimore County; Baltimore Maryland, USA
| | - Philip J. Farabaugh
- Department of Biological Sciences; University of Maryland Baltimore County; Baltimore Maryland, USA
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46
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Okamura H, Becker S, Tiede N, Wiedemann S, Feldmann J, Carell T. A one-pot, water compatible synthesis of pyrimidine nucleobases under plausible prebiotic conditions. Chem Commun (Camb) 2019; 55:1939-1942. [DOI: 10.1039/c8cc09435g] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A prebiotically plausible one-pot formation pathway of 4-substituted pyrimidine nucleobases in water, starting from cyanoacetylene.
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Affiliation(s)
- Hidenori Okamura
- Center for Integrated Protein Science (CiPSM) at the Department of Chemistry
- Ludwig-Maximilians-Universität München
- 81377 München
- Germany
| | - Sidney Becker
- Center for Integrated Protein Science (CiPSM) at the Department of Chemistry
- Ludwig-Maximilians-Universität München
- 81377 München
- Germany
| | - Niklas Tiede
- Center for Integrated Protein Science (CiPSM) at the Department of Chemistry
- Ludwig-Maximilians-Universität München
- 81377 München
- Germany
| | - Stefan Wiedemann
- Center for Integrated Protein Science (CiPSM) at the Department of Chemistry
- Ludwig-Maximilians-Universität München
- 81377 München
- Germany
| | - Jonas Feldmann
- Center for Integrated Protein Science (CiPSM) at the Department of Chemistry
- Ludwig-Maximilians-Universität München
- 81377 München
- Germany
| | - Thomas Carell
- Center for Integrated Protein Science (CiPSM) at the Department of Chemistry
- Ludwig-Maximilians-Universität München
- 81377 München
- Germany
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47
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Abstract
Noncoding RNAs (ncRNAs) have received much attention due to their central role in gene expression and translational regulation as well as due to their involvement in several biological processes and disease development. Small noncoding RNAs (sncRNAs), such as microRNAs and piwiRNAs, have been thoroughly investigated and functionally characterized. Long noncoding RNAs (lncRNAs), known to play an important role in chromatin-interacting transcription regulation, posttranscriptional regulation, cell-to-cell signaling, and protein regulation, are also being investigated to further elucidate their functional roles.Next-generation sequencing (NGS) technologies have greatly aided in characterizing the ncRNAome. Moreover, the coupling of NGS technology together with bioinformatics tools has been essential to the genome-wide detection of RNA modifications in ncRNAs. RNA editing, a common human co-transcriptional and posttranscriptional modification, is a dynamic biological phenomenon able to alter the sequence and the structure of primary transcripts (both coding and noncoding RNAs) during the maturation process, consequently influencing the biogenesis, as well as the function, of ncRNAs. In particular, the dysregulation of the RNA editing machineries have been associated with the onset of human diseases.In this chapter we discuss the potential functions of ncRNA editing and describe the knowledge base and bioinformatics resources available to investigate such phenomenon.
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48
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Guide snoRNAs: Drivers or Passengers in Human Disease? BIOLOGY 2018; 8:biology8010001. [PMID: 30577491 PMCID: PMC6466398 DOI: 10.3390/biology8010001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/16/2018] [Accepted: 12/18/2018] [Indexed: 01/17/2023]
Abstract
In every domain of life, RNA-protein interactions play a significant role in co- and post-transcriptional modifications and mRNA translation. RNA performs diverse roles inside the cell, and therefore any aberrancy in their function can cause various diseases. During maturation from its primary transcript, RNA undergoes several functionally important post-transcriptional modifications including pseudouridylation and ribose 2′-O-methylation. These modifications play a critical role in the stability of the RNA. In the last few decades, small nucleolar RNAs (snoRNAs) were revealed to be one of the main components to guide these modifications. Due to their active links to the nucleoside modification, deregulation in the snoRNA expressions can cause multiple disorders in humans. Additionally, host genes carrying snoRNA-encoding sequences in their introns also show differential expression in disease. Although few reports support a causal link between snoRNA expression and disease manifestation, this emerging field will have an impact on the way we think about biomarkers or identify novel targets for therapy. This review focuses on the intriguing aspect of snoRNAs that function as a guide in post-transcriptional RNA modification, and regulation of their host genes in human disease.
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49
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7-Methylguanosine Modifications in Transfer RNA (tRNA). Int J Mol Sci 2018; 19:ijms19124080. [PMID: 30562954 PMCID: PMC6320965 DOI: 10.3390/ijms19124080] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/05/2018] [Accepted: 12/13/2018] [Indexed: 01/15/2023] Open
Abstract
More than 90 different modified nucleosides have been identified in tRNA. Among the tRNA modifications, the 7-methylguanosine (m7G) modification is found widely in eubacteria, eukaryotes, and a few archaea. In most cases, the m7G modification occurs at position 46 in the variable region and is a product of tRNA (m7G46) methyltransferase. The m7G46 modification forms a tertiary base pair with C13-G22, and stabilizes the tRNA structure. A reaction mechanism for eubacterial tRNA m7G methyltransferase has been proposed based on the results of biochemical, bioinformatic, and structural studies. However, an experimentally determined mechanism of methyl-transfer remains to be ascertained. The physiological functions of m7G46 in tRNA have started to be determined over the past decade. For example, tRNA m7G46 or tRNA (m7G46) methyltransferase controls the amount of other tRNA modifications in thermophilic bacteria, contributes to the pathogenic infectivity, and is also associated with several diseases. In this review, information of tRNA m7G modifications and tRNA m7G methyltransferases is summarized and the differences in reaction mechanism between tRNA m7G methyltransferase and rRNA or mRNA m7G methylation enzyme are discussed.
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50
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Thapar R, Bacolla A, Oyeniran C, Brickner JR, Chinnam NB, Mosammaparast N, Tainer JA. RNA Modifications: Reversal Mechanisms and Cancer. Biochemistry 2018; 58:312-329. [PMID: 30346748 DOI: 10.1021/acs.biochem.8b00949] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
An emerging molecular understanding of RNA alkylation and its removal is transforming our knowledge of RNA biology and its interplay with cancer chemotherapy responses. DNA modifications are known to perform critical functions depending on the genome template, including gene expression, DNA replication timing, and DNA damage protection, yet current results suggest that the chemical diversity of DNA modifications pales in comparison to those on RNA. More than 150 RNA modifications have been identified to date, and their complete functional implications are still being unveiled. These include intrinsic roles such as proper processing and RNA maturation; emerging evidence has furthermore uncovered RNA modification "readers", seemingly analogous to those identified for histone modifications. These modification recognition factors may regulate mRNA stability, localization, and interaction with translation machinery, affecting gene expression. Not surprisingly, tumors differentially modulate factors involved in expressing these marks, contributing to both tumorigenesis and responses to alkylating chemotherapy. Here we describe the current understanding of RNA modifications and their removal, with a focus primarily on methylation and alkylation as functionally relevant changes to the transcriptome. Intriguingly, some of the same RNA modifications elicited by physiological processes are also produced by alkylating agents, thus blurring the lines between what is a physiological mark and a damage-induced modification. Furthermore, we find that a high level of gene expression of enzymes with RNA dealkylation activity is a sensitive readout for poor survival in four different cancer types, underscoring the likely importance of examining RNA dealkylation mechanisms to cancer biology and for cancer treatment and prognosis.
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Affiliation(s)
- Roopa Thapar
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
| | - Clement Oyeniran
- Department of Pathology and Immunology, Siteman Cancer Center , Washington University in St. Louis School of Medicine , St. Louis , Missouri 63110 , United States
| | - Joshua R Brickner
- Department of Pathology and Immunology, Siteman Cancer Center , Washington University in St. Louis School of Medicine , St. Louis , Missouri 63110 , United States
| | - Naga Babu Chinnam
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Siteman Cancer Center , Washington University in St. Louis School of Medicine , St. Louis , Missouri 63110 , United States
| | - John A Tainer
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
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