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Allouche D, De Bisschop G, Saaidi A, Hardouin P, du Moutier FXL, Ponty Y, Bruno S. RNA Secondary Structure Modeling Following the IPANEMAP Workflow. Methods Mol Biol 2024; 2726:85-104. [PMID: 38780728 DOI: 10.1007/978-1-0716-3519-3_4] [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] [Indexed: 05/25/2024]
Abstract
The structure of RNA molecules and their complexes are crucial for understanding biology at the molecular level. Resolving these structures holds the key to understanding their manifold structure-mediated functions ranging from regulating gene expression to catalyzing biochemical processes. Predicting RNA secondary structure is a prerequisite and a key step to accurately model their three dimensional structure. Although dedicated modelling software are making fast and significant progresses, predicting an accurate secondary structure from the sequence remains a challenge. Their performance can be significantly improved by the incorporation of experimental RNA structure probing data. Many different chemical and enzymatic probes have been developed; however, only one set of quantitative data can be incorporated as constraints for computer-assisted modelling. IPANEMAP is a recent workflow based on RNAfold that can take into account several quantitative or qualitative data sets to model RNA secondary structure. This chapter details the methods for popular chemical probing (DMS, CMCT, SHAPE-CE, and SHAPE-Map) and the subsequent analysis and structure prediction using IPANEMAP.
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Affiliation(s)
- Delphine Allouche
- CiTCOM, Cibles Thérapeutiques et conception de médicaments, UMR8038 CNRS, Université de PARIS, Paris, France
- Sanofi mRNA center of excellence 1541, Marcy-l'Etoile, France
| | - Grégoire De Bisschop
- CiTCOM, Cibles Thérapeutiques et conception de médicaments, UMR8038 CNRS, Université de PARIS, Paris, France
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Afaf Saaidi
- Georgia Institute of Technology, School of Mathematics, Atlanta, GA, USA
| | - Pierre Hardouin
- CiTCOM, Cibles Thérapeutiques et conception de médicaments, UMR8038 CNRS, Université de PARIS, Paris, France
| | | | - Yann Ponty
- CNRS UMR 7161, LIX, Ecole Polytechnique, Palaiseau, France.
| | - Sargueil Bruno
- CiTCOM, Cibles Thérapeutiques et conception de médicaments, UMR8038 CNRS, Université de PARIS, Paris, France.
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2
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Programmable antivirals targeting critical conserved viral RNA secondary structures from influenza A virus and SARS-CoV-2. Nat Med 2022; 28:1944-1955. [PMID: 35982307 PMCID: PMC10132811 DOI: 10.1038/s41591-022-01908-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 06/20/2022] [Indexed: 12/18/2022]
Abstract
Influenza A virus's (IAV's) frequent genetic changes challenge vaccine strategies and engender resistance to current drugs. We sought to identify conserved and essential RNA secondary structures within IAV's genome that are predicted to have greater constraints on mutation in response to therapeutic targeting. We identified and genetically validated an RNA structure (packaging stem-loop 2 (PSL2)) that mediates in vitro packaging and in vivo disease and is conserved across all known IAV isolates. A PSL2-targeting locked nucleic acid (LNA), administered 3 d after, or 14 d before, a lethal IAV inoculum provided 100% survival in mice, led to the development of strong immunity to rechallenge with a tenfold lethal inoculum, evaded attempts to select for resistance and retained full potency against neuraminidase inhibitor-resistant virus. Use of an analogous approach to target SARS-CoV-2, prophylactic administration of LNAs specific for highly conserved RNA structures in the viral genome, protected hamsters from efficient transmission of the SARS-CoV-2 USA_WA1/2020 variant. These findings highlight the potential applicability of this approach to any virus of interest via a process we term 'programmable antivirals', with implications for antiviral prophylaxis and post-exposure therapy.
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Gilmer O, Quignon E, Jousset AC, Paillart JC, Marquet R, Vivet-Boudou V. Chemical and Enzymatic Probing of Viral RNAs: From Infancy to Maturity and Beyond. Viruses 2021; 13:1894. [PMID: 34696322 PMCID: PMC8537439 DOI: 10.3390/v13101894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022] Open
Abstract
RNA molecules are key players in a variety of biological events, and this is particularly true for viral RNAs. To better understand the replication of those pathogens and try to block them, special attention has been paid to the structure of their RNAs. Methods to probe RNA structures have been developed since the 1960s; even if they have evolved over the years, they are still in use today and provide useful information on the folding of RNA molecules, including viral RNAs. The aim of this review is to offer a historical perspective on the structural probing methods used to decipher RNA structures before the development of the selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) methodology and to show how they have influenced the current probing techniques. Actually, these technological breakthroughs, which involved advanced detection methods, were made possible thanks to the development of next-generation sequencing (NGS) but also to the previous works accumulated in the field of structural RNA biology. Finally, we will also discuss how high-throughput SHAPE (hSHAPE) paved the way for the development of sophisticated RNA structural techniques.
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Affiliation(s)
| | | | | | | | - Roland Marquet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR9002, F-67000 Strasbourg, France; (O.G.); (E.Q.); (A.-C.J.); (J.-C.P.)
| | - Valérie Vivet-Boudou
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR9002, F-67000 Strasbourg, France; (O.G.); (E.Q.); (A.-C.J.); (J.-C.P.)
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Abstract
RNA is a pivotal element of the cell which is most of the time found in complex with protein(s) in a cellular environment. RNA can adopt three-dimensional structures that may form specific binding sites not only for proteins but for all sorts of molecules. Since the early days of molecular biology, strategies to probe RNA structure have been developed. Such probes are small molecules or RNases that most of the time specifically react with single strand nucleotides. The precise reaction or cleavage site can be mapped by reverse transcription. It appears that nucleotides in close contact or in proximity of a ligand are no longer reactive to these probes. Carrying the RNA probing experiment in parallel in presence and absence of a ligand yield differences that are known as the ligand "footprint." Such footprints allow for the identification of the precise site of the ligand interaction, but also reveals RNA structural rearrangement upon ligand binding. Here we provide an experimental and analytical workflow to carry RNA footprinting experiments.
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Affiliation(s)
- Grégoire De Bisschop
- CiTCOM, Cibles Thérapeutiques et conception de médicaments, CNRS, Université de Paris, Paris, France.,Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Bruno Sargueil
- CiTCOM, Cibles Thérapeutiques et conception de médicaments, CNRS, Université de Paris, Paris, France.
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5
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Gumna J, Zok T, Figurski K, Pachulska-Wieczorek K, Szachniuk M. RNAthor - fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis. PLoS One 2020; 15:e0239287. [PMID: 33002005 PMCID: PMC7529196 DOI: 10.1371/journal.pone.0239287] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/03/2020] [Indexed: 12/18/2022] Open
Abstract
RNAs adopt specific structures to perform their functions, which are critical to fundamental cellular processes. For decades, these structures have been determined and modeled with strong support from computational methods. Still, the accuracy of the latter ones depends on the availability of experimental data, for example, chemical probing information that can define pseudo-energy constraints for RNA folding algorithms. At the same time, diverse computational tools have been developed to facilitate analysis and visualization of data from RNA structure probing experiments followed by capillary electrophoresis or next-generation sequencing. RNAthor, a new software tool for the fully automated normalization of SHAPE and DMS probing data resolved by capillary electrophoresis, has recently joined this collection. RNAthor automatically identifies unreliable probing data. It normalizes the reactivity information to a uniform scale and uses it in the RNA secondary structure prediction. Our web server also provides tools for fast and easy RNA probing data visualization and statistical analysis that facilitates the comparison of multiple data sets. RNAthor is freely available at http://rnathor.cs.put.poznan.pl/.
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Affiliation(s)
- Julita Gumna
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Tomasz Zok
- Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Kacper Figurski
- Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | | | - Marta Szachniuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, Poznan, Poland
- * E-mail: (KPW); (MS)
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6
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Hepatitis C Virus Translation Regulation. Int J Mol Sci 2020; 21:ijms21072328. [PMID: 32230899 PMCID: PMC7178104 DOI: 10.3390/ijms21072328] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 12/12/2022] Open
Abstract
Translation of the hepatitis C virus (HCV) RNA genome is regulated by the internal ribosome entry site (IRES), located in the 5’-untranslated region (5′UTR) and part of the core protein coding sequence, and by the 3′UTR. The 5′UTR has some highly conserved structural regions, while others can assume different conformations. The IRES can bind to the ribosomal 40S subunit with high affinity without any other factors. Nevertheless, IRES activity is modulated by additional cis sequences in the viral genome, including the 3′UTR and the cis-acting replication element (CRE). Canonical translation initiation factors (eIFs) are involved in HCV translation initiation, including eIF3, eIF2, eIF1A, eIF5, and eIF5B. Alternatively, under stress conditions and limited eIF2-Met-tRNAiMet availability, alternative initiation factors such as eIF2D, eIF2A, and eIF5B can substitute for eIF2 to allow HCV translation even when cellular mRNA translation is downregulated. In addition, several IRES trans-acting factors (ITAFs) modulate IRES activity by building large networks of RNA-protein and protein–protein interactions, also connecting 5′- and 3′-ends of the viral RNA. Moreover, some ITAFs can act as RNA chaperones that help to position the viral AUG start codon in the ribosomal 40S subunit entry channel. Finally, the liver-specific microRNA-122 (miR-122) stimulates HCV IRES-dependent translation, most likely by stabilizing a certain structure of the IRES that is required for initiation.
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7
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RNApolis: Computational Platform for RNA Structure Analysis. FOUNDATIONS OF COMPUTING AND DECISION SCIENCES 2019. [DOI: 10.2478/fcds-2019-0012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
In the 1970s, computer scientists began to engage in research in the field of structural biology. The first structural databases, as well as models and methods supporting the analysis of biomolecule structures, started to be created. RNA was put at the centre of scientific interest quite late. However, more and more methods dedicated to this molecule are currently being developed. This paper presents RNApolis - a new computing platform, which offers access to seven bioinformatic tools developed to support the RNA structure study. The set of tools include a structural database and systems for predicting, modelling, annotating and evaluating the RNA structure. RNApolis supports research at different structural levels and allows the discovery, establishment, and validation of relationships between the primary, secondary and tertiary structure of RNAs. The platform is freely available at http://rnapolis.pl
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Mailler E, Paillart JC, Marquet R, Smyth RP, Vivet-Boudou V. The evolution of RNA structural probing methods: From gels to next-generation sequencing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1518. [PMID: 30485688 DOI: 10.1002/wrna.1518] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/13/2018] [Accepted: 10/17/2018] [Indexed: 01/09/2023]
Abstract
RNA molecules are important players in all domains of life and the study of the relationship between their multiple flexible states and the associated biological roles has increased in recent years. For several decades, chemical and enzymatic structural probing experiments have been used to determine RNA structure. During this time, there has been a steady improvement in probing reagents and experimental methods, and today the structural biologist community has a large range of tools at its disposal to probe the secondary structure of RNAs in vitro and in cells. Early experiments used radioactive labeling and polyacrylamide gel electrophoresis as read-out methods. This was superseded by capillary electrophoresis, and more recently by next-generation sequencing. Today, powerful structural probing methods can characterize RNA structure on a genome-wide scale. In this review, we will provide an overview of RNA structural probing methodologies from a historical and technical perspective. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Methods > RNA Analyses in vitro and In Silico RNA Methods > RNA Analyses in Cells.
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Affiliation(s)
- Elodie Mailler
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Strasbourg, France
| | | | - Roland Marquet
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Strasbourg, France
| | - Redmond P Smyth
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Strasbourg, France
| | - Valerie Vivet-Boudou
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Strasbourg, France
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9
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Jayaraman D, Kenyon JC. New windows into retroviral RNA structures. Retrovirology 2018; 15:11. [PMID: 29368653 PMCID: PMC5784592 DOI: 10.1186/s12977-018-0393-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/12/2018] [Indexed: 12/16/2022] Open
Abstract
Background The multiple roles of both viral and cellular RNAs have become increasingly apparent in recent years, and techniques to model them have become significantly more powerful, enabling faster and more accurate visualization of RNA structures. Main body Techniques such as SHAPE (selective 2’OH acylation analysed by primer extension) have revolutionized the field, and have been used to examine RNAs belonging to many and diverse retroviruses. Secondary structure probing reagents such as these have been aided by the development of faster methods of analysis either via capillary or next-generation sequencing, allowing the analysis of entire genomes, and of retroviral RNA structures within virions. Techniques to model the three-dimensional structures of these large RNAs have also recently developed. Conclusions The flexibility of retroviral RNAs, both structural and functional, is clear from the results of these new experimental techniques. Retroviral RNA structures and structural changes control many stages of the lifecycle, and both the RNA structures themselves and their interactions with ligands are potential new drug targets. In addition, our growing understanding of retroviral RNA structures is aiding our knowledge of cellular RNA form and function.
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Affiliation(s)
- Dhivya Jayaraman
- Department of Medicine, National University of Singapore, 14 Medical Drive, MD 6, Level 15, Singapore, 117599, Singapore
| | - Julia Claire Kenyon
- Department of Medicine, University of Cambridge, Level 5 Addenbrookes Hospital Hills Rd, Cambridge, CB2 0QQ, UK. .,Department of Microbiology and Immunology, National University of Singapore, 5 Science Drive 2 Blk MD4, Level 3, Singapore, 117545, Singapore. .,Homerton College, University of Cambridge, Hills Rd, Cambridge, CB2 8PH, UK.
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10
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Zhu Y, Huang P, Yang N, Liu R, Liu X, Dai H, Zhang L, Song F, Sun C. Establishment and Application of a High Throughput Screening System Targeting the Interaction between HCV Internal Ribosome Entry Site and Human Eukaryotic Translation Initiation Factor 3. Front Microbiol 2017; 8:977. [PMID: 28611766 PMCID: PMC5447080 DOI: 10.3389/fmicb.2017.00977] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 05/15/2017] [Indexed: 01/06/2023] Open
Abstract
Viruses are intracellular obligate parasites and the host cellular machinery is usually recruited for their replication. Human eukaryotic translation initiation factor 3 (eIF3) could be directly recruited by the hepatitis C virus (HCV) internal ribosome entry site (IRES) to promote the translation of viral proteins. In this study, we establish a fluorescence polarization (FP) based high throughput screening (HTS) system targeting the interaction between HCV IRES and eIF3. By screening a total of 894 compounds with this HTS system, two compounds (Mucl39526 and NP39) are found to disturb the interaction between HCV IRES and eIF3. And these two compounds are further demonstrated to inhibit the HCV IRES-dependent translation in vitro. Thus, this HTS system is functional to screen the potential HCV replication inhibitors targeting human eIF3, which is helpful to overcome the problem of viral resistance. Surprisingly, one compound HP-3, a kind of oxytocin antagonist, is discovered to significantly enhance the interaction between HCV IRES and eIF3 by this HTS system. HP-3 is demonstrated to directly interact with HCV IRES and promote the HCV IRES-dependent translation both in vitro and in vivo, which strongly suggests that HP-3 has potentials to promote HCV replication. Therefore, this HTS system is also useful to screen the potential HCV replication enhancers, which is meaningful for understanding the viral replication and screening novel antiviral drugs. To our knowledge, this is the first HTS system targeting the interaction between eIF3 and HCV IRES, which could be applied to screen both potential HCV replication inhibitors and enhancers.
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Affiliation(s)
- Yuying Zhu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of SciencesQingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China.,College of Earth Science, University of Chinese Academy of SciencesBeijing, China
| | - Pei Huang
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
| | - Na Yang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of SciencesQingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
| | - Rui Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of SciencesQingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
| | - Xueting Liu
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
| | - Huanqin Dai
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
| | - Lixin Zhang
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of SciencesBeijing, China.,State Key Laboratory of Bioreactor Engineering, East China University of Science and TechnologyShanghai, China
| | - Fuhang Song
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
| | - Chaomin Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of SciencesQingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
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11
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Lian DS, Zhao SJ. Capillary electrophoresis based on nucleic acid detection for diagnosing human infectious disease. Clin Chem Lab Med 2017; 54:707-38. [PMID: 26352354 DOI: 10.1515/cclm-2015-0096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 06/17/2015] [Indexed: 01/22/2023]
Abstract
Rapid transmission, high morbidity, and mortality are the features of human infectious diseases caused by microorganisms, such as bacteria, fungi, and viruses. These diseases may lead within a short period of time to great personal and property losses, especially in regions where sanitation is poor. Thus, rapid diagnoses are vital for the prevention and therapeutic intervention of human infectious diseases. Several conventional methods are often used to diagnose infectious diseases, e.g. methods based on cultures or morphology, or biochemical tests based on metabonomics. Although traditional methods are considered gold standards and are used most frequently, they are laborious, time consuming, and tedious and cannot meet the demand for rapid diagnoses. Disease diagnosis using capillary electrophoresis methods has the advantages of high efficiency, high throughput, and high speed, and coupled with the different nucleic acid detection strategies overcomes the drawbacks of traditional identification methods, precluding many types of false positive and negative results. Therefore, this review focuses on the application of capillary electrophoresis based on nucleic detection to the diagnosis of human infectious diseases, and offers an introduction to the limitations, advantages, and future developments of this approach.
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12
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Cantara WA, Hatterschide J, Wu W, Musier-Forsyth K. RiboCAT: a new capillary electrophoresis data analysis tool for nucleic acid probing. RNA (NEW YORK, N.Y.) 2017; 23:240-249. [PMID: 27821510 PMCID: PMC5238798 DOI: 10.1261/rna.058404.116] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/02/2016] [Indexed: 06/06/2023]
Abstract
Chemical and enzymatic probing of RNA secondary structure and RNA/protein interactions provides the basis for understanding the functions of structured RNAs. However, the ability to rapidly perform such experiments using capillary electrophoresis has been hampered by relatively labor-intensive data analysis software. While these computationally robust programs have been shown to calculate residue-specific reactivities to a high degree of accuracy, they often require time-consuming manual intervention and lack the ability to be easily modified by users. To alleviate these issues, RiboCAT (Ribonucleic acid capillary-electrophoresis analysis tool) was developed as a user-friendly, Microsoft Excel-based tool that reduces the need for manual intervention, thereby significantly shortening the time required for data analysis. Features of this tool include (i) the use of an Excel platform, (ii) a method of intercapillary signal alignment using internal size standards, (iii) a peak-sharpening algorithm to more accurately identify peaks, and (iv) an open architecture allowing for simple user intervention. Furthermore, a complementary tool, RiboDOG (RiboCAT data output generator) was designed to facilitate the comparison of multiple data sets, highlighting potential inconsistencies and inaccuracies that may have occurred during analysis. Using these new tools, the secondary structure of the HIV-1 5' untranslated region (5'UTR) was determined using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE), matching the results of previous work.
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Affiliation(s)
- William A Cantara
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Joshua Hatterschide
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Weixin Wu
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
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13
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Pérez PS, Di Lello FA, Mullen EG, Galdame OA, Livellara BI, Gadano AC, Campos RH, Flichman DM. Compartmentalization of hepatitis C virus variants in patients with hepatocellular carcinoma. Mol Carcinog 2016; 56:371-380. [PMID: 27163636 DOI: 10.1002/mc.22500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 04/03/2016] [Accepted: 05/02/2016] [Indexed: 12/24/2022]
Abstract
Chronic Hepatitis C Virus (HCV) infection is a major risk for hepatocellular carcinoma (HCC) development. HCV Core protein has been associated with the modulation of potentially oncogenic cellular processes and E2 protein has been useful in evolutive studies to analyze the diversity of HCV. Thus, the aim of this study was to evaluate HCV compartmentalization in tumoral, non-tumoral liver tissue and serum and to identify viral mutations potentially involved in carcinogenesis. Samples were obtained from four patients with HCC who underwent liver transplantation. Core and E2 were amplified, cloned and sequenced. Phylogenies and BaTS Test were performed to analyze viral compartmentalization and a signature sequence analysis was conducted by VESPA. The likelihood and Bayesian phylogenies showed a wide degree of compartmentalization in the different patients, ranging from total clustering to a more scattered pattern with small groups. Nevertheless, the association test showed compartmentalization for the three compartments and both viral regions tested in all the patients. Signature amino acid pattern supported the compartmentalization in three of the cases for E2 protein and in two of them for Core. Changes observed in Core included polymorphism R70Q/H previously associated with HCC. In conclusion, evidence of HCV compartmentalization in the liver of HCC patients was provided and further biological characterization of these variants may contribute to the understanding of carcinogenesis mediated by HCV infection. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Paula S Pérez
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Federico A Di Lello
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | | | - Omar A Galdame
- Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | | | | | - Rodolfo H Campos
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Diego M Flichman
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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14
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Lozano G, Jimenez-Aparicio R, Herrero S, Martinez-Salas E. Fingerprinting the junctions of RNA structure by an open-paddlewheel diruthenium compound. RNA (NEW YORK, N.Y.) 2016; 22:330-8. [PMID: 26759454 PMCID: PMC4748811 DOI: 10.1261/rna.054353.115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/05/2015] [Indexed: 05/17/2023]
Abstract
RNA function is determined by its structural organization. The RNA structure consists of the combination of distinct secondary structure motifs connected by junctions that play an essential role in RNA folding. Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) probing is an established methodology to analyze the secondary structure of long RNA molecules in solution, which provides accurate data about unpaired nucleotides. However, the residues located at the junctions of RNA structures usually remain undetected. Here we report an RNA probing method based on the use of a novel open-paddlewheel diruthenium (OPW-Ru) compound [Ru2Cl2(µ-DPhF)3(DMSO)] (DPhF = N,N'-diphenylformamidinate). This compound has four potential coordination sites in a singular disposition to establish covalent bonds with substrates. As a proof of concept, we have analyzed the reactivity of OPW-Ru toward RNA using two viral internal ribosome entry site (IRES) elements whose function depends on the structural organization of the molecule. Our study suggests that the compound OPW-Ru preferentially attacks at positions located one or two nucleotides away from junctions or bulges of the RNA structure. The OPW-Ru fingerprinting data differ from that obtained by other chemical reagents and provides new information about RNA structure features.
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Affiliation(s)
- Gloria Lozano
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid 28049, Spain
| | - Reyes Jimenez-Aparicio
- Departamento de Química Inorgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Santiago Herrero
- Departamento de Química Inorgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid 28040, Spain
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15
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Fricke M, Dünnes N, Zayas M, Bartenschlager R, Niepmann M, Marz M. Conserved RNA secondary structures and long-range interactions in hepatitis C viruses. RNA (NEW YORK, N.Y.) 2015; 21:1219-32. [PMID: 25964384 PMCID: PMC4478341 DOI: 10.1261/rna.049338.114] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 03/07/2015] [Indexed: 05/02/2023]
Abstract
Hepatitis C virus (HCV) is a hepatotropic virus with a plus-strand RNA genome of ∼9.600 nt. Due to error-prone replication by its RNA-dependent RNA polymerase (RdRp) residing in nonstructural protein 5B (NS5B), HCV isolates are grouped into seven genotypes with several subtypes. By using whole-genome sequences of 106 HCV isolates and secondary structure alignments of the plus-strand genome and its minus-strand replication intermediate, we established refined secondary structures of the 5' untranslated region (UTR), the cis-acting replication element (CRE) in NS5B, and the 3' UTR. We propose an alternative structure in the 5' UTR, conserved secondary structures of 5B stem-loop (SL)1 and 5BSL2, and four possible structures of the X-tail at the very 3' end of the HCV genome. We predict several previously unknown long-range interactions, most importantly a possible circularization interaction between distinct elements in the 5' and 3' UTR, reminiscent of the cyclization elements of the related flaviviruses. Based on analogy to these viruses, we propose that the 5'-3' UTR base-pairing in the HCV genome might play an important role in viral RNA replication. These results may have important implications for our understanding of the nature of the cis-acting RNA elements in the HCV genome and their possible role in regulating the mutually exclusive processes of viral RNA translation and replication.
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Affiliation(s)
- Markus Fricke
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Nadia Dünnes
- Institute of Biochemistry, Medical Faculty, Justus-Liebig-University, 35392 Giessen, Germany
| | - Margarita Zayas
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Michael Niepmann
- Institute of Biochemistry, Medical Faculty, Justus-Liebig-University, 35392 Giessen, Germany
| | - Manja Marz
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany FLI Leibniz Institute for Age Research, 07745 Jena, Germany
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16
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Mutso M, Nikonov A, Pihlak A, Žusinaite E, Viru L, Selyutina A, Reintamm T, Kelve M, Saarma M, Karelson M, Merits A. RNA Interference-Guided Targeting of Hepatitis C Virus Replication with Antisense Locked Nucleic Acid-Based Oligonucleotides Containing 8-oxo-dG Modifications. PLoS One 2015; 10:e0128686. [PMID: 26039055 PMCID: PMC4454572 DOI: 10.1371/journal.pone.0128686] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 04/29/2015] [Indexed: 12/23/2022] Open
Abstract
The inhibitory potency of an antisense oligonucleotide depends critically on its design and the accessibility of its target site. Here, we used an RNA interference-guided approach to select antisense oligonucleotide target sites in the coding region of the highly structured hepatitis C virus (HCV) RNA genome. We modified the conventional design of an antisense oligonucleotide containing locked nucleic acid (LNA) residues at its termini (LNA/DNA gapmer) by inserting 8-oxo-2'-deoxyguanosine (8-oxo-dG) residues into the central DNA region. Obtained compounds, designed with the aim to analyze the effects of 8-oxo-dG modifications on the antisense oligonucleotides, displayed a unique set of properties. Compared to conventional LNA/DNA gapmers, the melting temperatures of the duplexes formed by modified LNA/DNA gapmers and DNA or RNA targets were reduced by approximately 1.6-3.3°C per modification. Comparative transfection studies showed that small interfering RNA was the most potent HCV RNA replication inhibitor (effective concentration 50 (EC50): 0.13 nM), whereas isosequential standard and modified LNA/DNA gapmers were approximately 50-fold less efficient (EC50: 5.5 and 7.1 nM, respectively). However, the presence of 8-oxo-dG residues led to a more complete suppression of HCV replication in transfected cells. These modifications did not affect the efficiency of RNase H cleavage of antisense oligonucleotide:RNA duplexes but did alter specificity, triggering the appearance of multiple cleavage products. Moreover, the incorporation of 8-oxo-dG residues increased the stability of antisense oligonucleotides of different configurations in human serum.
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MESH Headings
- 8-Hydroxy-2'-Deoxyguanosine
- Base Pairing
- Cell Line, Tumor
- Deoxyguanosine/analogs & derivatives
- Deoxyguanosine/chemistry
- Genome, Viral
- Hepacivirus/genetics
- Hepacivirus/growth & development
- Hepatocytes/metabolism
- Hepatocytes/virology
- Humans
- Molecular Targeted Therapy
- Oligonucleotides/chemistry
- Oligonucleotides/metabolism
- Oligonucleotides, Antisense/chemical synthesis
- Oligonucleotides, Antisense/genetics
- Oligonucleotides, Antisense/metabolism
- RNA Cleavage
- RNA Interference
- RNA Stability
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Viral/antagonists & inhibitors
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Structure-Activity Relationship
- Virus Replication
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Affiliation(s)
- Margit Mutso
- Institute of Technology, University of Tartu, Tartu, Estonia
- GeneCode, Ltd., Tallinn, Estonia
| | - Andrei Nikonov
- Institute of Technology, University of Tartu, Tartu, Estonia
- GeneCode, Ltd., Tallinn, Estonia
| | | | - Eva Žusinaite
- Institute of Technology, University of Tartu, Tartu, Estonia
- GeneCode, Ltd., Tallinn, Estonia
| | - Liane Viru
- Institute of Technology, University of Tartu, Tartu, Estonia
- GeneCode, Ltd., Tallinn, Estonia
| | | | - Tõnu Reintamm
- GeneCode, Ltd., Tallinn, Estonia
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Merike Kelve
- GeneCode, Ltd., Tallinn, Estonia
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Mart Saarma
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Mati Karelson
- GeneCode, Ltd., Tallinn, Estonia
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu, Estonia
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17
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Seif E, Niu M, Kleiman L. In virio SHAPE analysis of tRNA(Lys3) annealing to HIV-1 genomic RNA in wild type and protease-deficient virus. Retrovirology 2015; 12:40. [PMID: 25981241 PMCID: PMC4445796 DOI: 10.1186/s12977-015-0171-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 05/06/2015] [Indexed: 11/29/2022] Open
Abstract
Background tRNALys3 annealing to the viral RNA of human immunodeficiency virus type-1 (HIV-1) is an essential step in the virus life cycle, because this tRNA serves as the primer for initiating reverse transcription. tRNALys3 annealing to viral RNA occurs in two steps. First, Gag promotes annealing of tRNALys3 to the viral RNA during cytoplasmic HIV-1 assembly. Second, mature nucleocapsid (NCp7), produced from the processing of Gag by viral protease during viral budding from the cell, remodels the annealed complex to form a more stable interaction between the viral RNA and tRNALys3, resulting in a more tightly bound and efficient primer for reverse transcription. Results In this report, we have used in virio SHAPE analysis of both the 5´-untranslated region in HIV-1 RNA and the annealed tRNALys3 to determine structural differences of the annealed complex that occur between protease-negative (Pr-) and wild type viruses. Our results indicate that the weaker binding of tRNALys3 annealed by Gag in Pr- virions reflects both missing interactions of tRNALys3 with viral RNA regions in the upper PBS stem, and a weaker interaction with the internal stem-loop found within the unannealed primer binding site in viral RNA. Conclusions We propose secondary structure models for the tRNALys3/viral RNA annealed complexes in PR- and wild type viruses that support the two-step annealing model by showing that Gag promotes a partial annealing of tRNALys3 to HIV-1 viral RNA, followed by a more complete annealing by NCp7. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0171-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elias Seif
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, QC, H3T 1E2, Canada.
| | - Meijuan Niu
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, QC, H3T 1E2, Canada.
| | - Lawrence Kleiman
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, QC, H3T 1E2, Canada. .,Department of Medicine, McGill University, Montreal, QC, H3A 1A1, Canada.
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18
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Lee S, Kim H, Tian S, Lee T, Yoon S, Das R. Automated band annotation for RNA structure probing experiments with numerous capillary electrophoresis profiles. Bioinformatics 2015; 31:2808-15. [PMID: 25943472 DOI: 10.1093/bioinformatics/btv282] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 04/29/2015] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Capillary electrophoresis (CE) is a powerful approach for structural analysis of nucleic acids, with recent high-throughput variants enabling three-dimensional RNA modeling and the discovery of new rules for RNA structure design. Among the steps composing CE analysis, the process of finding each band in an electrophoretic trace and mapping it to a position in the nucleic acid sequence has required significant manual inspection and remains the most time-consuming and error-prone step. The few available tools seeking to automate this band annotation have achieved limited accuracy and have not taken advantage of information across dozens of profiles routinely acquired in high-throughput measurements. RESULTS We present a dynamic-programming-based approach to automate band annotation for high-throughput capillary electrophoresis. The approach is uniquely able to define and optimize a robust target function that takes into account multiple CE profiles (sequencing ladders, different chemical probes, different mutants) collected for the RNA. Over a large benchmark of multi-profile datasets for biological RNAs and designed RNAs from the EteRNA project, the method outperforms prior tools (QuSHAPE and FAST) significantly in terms of accuracy compared with gold-standard manual annotations. The amount of computation required is reasonable at a few seconds per dataset. We also introduce an 'E-score' metric to automatically assess the reliability of the band annotation and show it to be practically useful in flagging uncertainties in band annotation for further inspection. AVAILABILITY AND IMPLEMENTATION The implementation of the proposed algorithm is included in the HiTRACE software, freely available as an online server and for download at http://hitrace.stanford.edu. CONTACT sryoon@snu.ac.kr or rhiju@stanford.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Seungmyung Lee
- Department of ECE, Seoul National University, Seoul 151-744, Korea
| | - Hanjoo Kim
- Department of ECE, Seoul National University, Seoul 151-744, Korea
| | - Siqi Tian
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Taehoon Lee
- Department of ECE, Seoul National University, Seoul 151-744, Korea
| | - Sungroh Yoon
- Department of ECE, Seoul National University, Seoul 151-744, Korea, Interdisciplinary Program in Bionformatics, Seoul National University, Seoul 151-744, Korea and
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA, Department of Physics, Stanford University, Stanford, CA 94305, USA
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19
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Ge P, Zhang S. Computational analysis of RNA structures with chemical probing data. Methods 2015; 79-80:60-6. [PMID: 25687190 DOI: 10.1016/j.ymeth.2015.02.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 01/16/2015] [Accepted: 02/09/2015] [Indexed: 11/28/2022] Open
Abstract
RNAs play various roles, not only as the genetic codes to synthesize proteins, but also as the direct participants of biological functions determined by their underlying high-order structures. Although many computational methods have been proposed for analyzing RNA structures, their accuracy and efficiency are limited, especially when applied to the large RNAs and the genome-wide data sets. Recently, advances in parallel sequencing and high-throughput chemical probing technologies have prompted the development of numerous new algorithms, which can incorporate the auxiliary structural information obtained from those experiments. Their potential has been revealed by the secondary structure prediction of ribosomal RNAs and the genome-wide ncRNA function annotation. In this review, the existing probing-directed computational methods for RNA secondary and tertiary structure analysis are discussed.
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Affiliation(s)
- Ping Ge
- Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816-2362, USA
| | - Shaojie Zhang
- Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816-2362, USA.
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20
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Purzycka KJ, Popenda M, Szachniuk M, Antczak M, Lukasiak P, Blazewicz J, Adamiak RW. Automated 3D RNA structure prediction using the RNAComposer method for riboswitches. Methods Enzymol 2015; 553:3-34. [PMID: 25726459 DOI: 10.1016/bs.mie.2014.10.050] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Understanding the numerous functions of RNAs depends critically on the knowledge of their three-dimensional (3D) structure. In contrast to the protein field, a much smaller number of RNA 3D structures have been assessed using X-ray crystallography, NMR spectroscopy, and cryomicroscopy. This has led to a great demand to obtain the RNA 3D structures using prediction methods. The 3D structure prediction, especially of large RNAs, still remains a significant challenge and there is still a great demand for high-resolution structure prediction methods. In this chapter, we describe RNAComposer, a method and server for the automated prediction of RNA 3D structures based on the knowledge of secondary structure. Its applications are supported by other automated servers: RNA FRABASE and RNApdbee, developed to search and analyze secondary and 3D structures. Another method, RNAlyzer, offers new way to analyze and visualize quality of RNA 3D models. Scope and limitations of RNAComposer in application for an automated prediction of riboswitches' 3D structure will be presented and discussed. Analysis of the cyclic di-GMP-II riboswitch from Clostridium acetobutylicum (PDB ID 3Q3Z) as an example allows for 3D structure prediction of related riboswitches from Clostridium difficile 4, Bacillus halodurans 1, and Thermus aquaticus Y5.1 of yet unknown structures.
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Affiliation(s)
- K J Purzycka
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - M Popenda
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - M Szachniuk
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland; European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - M Antczak
- European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - P Lukasiak
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland; European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - J Blazewicz
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland; European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - R W Adamiak
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland; European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland.
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21
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Abstract
It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from evolutionarily related sequences is one important task in RNA bioinformatics; the methods are useful not only to further functional analyses of ncRNAs but also to improve the accuracy of secondary structure predictions and to find novel functional RNAs from the genome. In this review, I focus on common secondary structure prediction from a given aligned RNA sequence, in which one secondary structure whose length is equal to that of the input alignment is predicted. I systematically review and classify existing tools and algorithms for the problem, by utilizing the information employed in the tools and by adopting a unified viewpoint based on maximum expected gain (MEG) estimators. I believe that this classification will allow a deeper understanding of each tool and provide users with useful information for selecting tools for common secondary structure predictions.
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22
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García-Sacristán A, Moreno M, Ariza-Mateos A, López-Camacho E, Jáudenes RM, Vázquez L, Gómez J, Martín-Gago JÁ, Briones C. A magnesium-induced RNA conformational switch at the internal ribosome entry site of hepatitis C virus genome visualized by atomic force microscopy. Nucleic Acids Res 2014; 43:565-80. [PMID: 25510496 PMCID: PMC4288189 DOI: 10.1093/nar/gku1299] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The 5' untranslated region of hepatitis C virus (HCV) genomic RNA contains an internal ribosome entry site (IRES) element, composed of domains II-IV, which is required for cap-independent translation initiation. Little information on the 3D structure of the whole functional HCV IRES is still available. Here, we use atomic force microscopy to visualize the HCV IRES conformation in its natural sequence context, which includes the upstream domain I and the essential, downstream domains V and VI. The 574 nt-long molecule analyzed underwent an unexpected, Mg(2+)-induced switch between two alternative conformations: from 'open', elongated morphologies at 0-2 mM Mg(2+) concentration to a 'closed', comma-shaped conformation at 4-6 mM Mg(2+). This sharp transition, confirmed by gel-shift analysis and partial RNase T1 cleavage, was hindered by the microRNA miR-122. The comma-shaped IRES-574 molecules visualized at 4-6 mM Mg(2+) in the absence of miR-122 showed two arms. Our data support that the first arm would contain domain III, while the second one would be composed of domains (I-II)+(V-VI) thanks to a long-range RNA interaction between the I-II spacer and the basal region of domain VI. This reinforces the previously described structural continuity between the HCV IRES and its flanking domains I, V and VI.
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Affiliation(s)
- Ana García-Sacristán
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid 28850, Spain Centro de Investigaciones Biomédicas en Red de Enfermedades Hepáticas y Digestivas, (CIBERehd), Spain
| | - Miguel Moreno
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid 28850, Spain
| | - Ascensión Ariza-Mateos
- Centro de Investigaciones Biomédicas en Red de Enfermedades Hepáticas y Digestivas, (CIBERehd), Spain Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina 'López-Neyra' (CSIC), Parque Tecnológico Ciencias de la Salud, Armilla, Granada 18016, Spain
| | - Elena López-Camacho
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid 28850, Spain Instituto de Ciencia de Materiales de Madrid (CSIC), Cantoblanco, Madrid 28049, Spain
| | - Rosa M Jáudenes
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid 28850, Spain
| | - Luis Vázquez
- Instituto de Ciencia de Materiales de Madrid (CSIC), Cantoblanco, Madrid 28049, Spain
| | - Jordi Gómez
- Centro de Investigaciones Biomédicas en Red de Enfermedades Hepáticas y Digestivas, (CIBERehd), Spain Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina 'López-Neyra' (CSIC), Parque Tecnológico Ciencias de la Salud, Armilla, Granada 18016, Spain
| | - José Ángel Martín-Gago
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid 28850, Spain Instituto de Ciencia de Materiales de Madrid (CSIC), Cantoblanco, Madrid 28049, Spain
| | - Carlos Briones
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid 28850, Spain Centro de Investigaciones Biomédicas en Red de Enfermedades Hepáticas y Digestivas, (CIBERehd), Spain
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23
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Sztuba-Solinska J, Le Grice SFJ. Insights into secondary and tertiary interactions of dengue virus RNA by SHAPE. Methods Mol Biol 2014; 1138:225-39. [PMID: 24696340 DOI: 10.1007/978-1-4939-0348-1_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Dengue virus (DENV) is a single-stranded positive-sense RNA virus belonging to the Flaviviridae family. The DENV RNA genome contains multiple cis-acting elements that continue to unravel their essential role in managing viral molecular processes. Attempts have been made to predict the secondary structure of DENV RNA using a variety of computational tools. Nevertheless, a greater degree of accuracy is achieved when these methods are complemented with structure probing experimentation. This chapter outlines detailed methodology for the structural study of DENV subgenomic minigenome RNA by applying high-throughput selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE). High-throughput SHAPE combines a novel chemical probing technology with reverse transcription, capillary electrophoresis, and secondary structure prediction software to rapidly and reproducibly determine the structure of RNAs from several hundred to several thousand nucleotides at single-nucleotide resolution. This methodology investigates local structure for all positions in a sequence-independent manner and as such it is particularly useful in predicting RNA secondary and tertiary interactions.
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Affiliation(s)
- Joanna Sztuba-Solinska
- RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
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24
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Tian S, Cordero P, Kladwang W, Das R. High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states. RNA (NEW YORK, N.Y.) 2014; 20:1815-26. [PMID: 25183835 PMCID: PMC4201832 DOI: 10.1261/rna.044321.114] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The three-dimensional conformations of noncoding RNAs underpin their biochemical functions but have largely eluded experimental characterization. Here, we report that integrating a classic mutation/rescue strategy with high-throughput chemical mapping enables rapid RNA structure inference with unusually strong validation. We revisit a 16S rRNA domain for which SHAPE (selective 2'-hydroxyl acylation with primer extension) and limited mutational analysis suggested a conformational change between apo- and holo-ribosome conformations. Computational support estimates, data from alternative chemical probes, and mutate-and-map (M(2)) experiments highlight issues of prior methodology and instead give a near-crystallographic secondary structure. Systematic interrogation of single base pairs via a high-throughput mutation/rescue approach then permits incisive validation and refinement of the M(2)-based secondary structure. The data further uncover the functional conformation as an excited state (20 ± 10% population) accessible via a single-nucleotide register shift. These results correct an erroneous SHAPE inference of a ribosomal conformational change, expose critical limitations of conventional structure mapping methods, and illustrate practical steps for more incisively dissecting RNA dynamic structure landscapes.
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Affiliation(s)
- Siqi Tian
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
| | - Pablo Cordero
- Biomedical Informatics Program, Stanford University, Stanford, California 94305, USA
| | - Wipapat Kladwang
- Department of Physics, Stanford University, Stanford, California 94305, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA Biomedical Informatics Program, Stanford University, Stanford, California 94305, USA Department of Physics, Stanford University, Stanford, California 94305, USA
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25
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Hepatitis delta antigen requires a flexible quasi-double-stranded RNA structure to bind and condense hepatitis delta virus RNA in a ribonucleoprotein complex. J Virol 2014; 88:7402-11. [PMID: 24741096 DOI: 10.1128/jvi.00443-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
UNLABELLED The circular genome and antigenome RNAs of hepatitis delta virus (HDV) form characteristic unbranched, quasi-double-stranded RNA secondary structures in which short double-stranded helical segments are interspersed with internal loops and bulges. The ribonucleoprotein complexes (RNPs) formed by these RNAs with the virus-encoded protein hepatitis delta antigen (HDAg) perform essential roles in the viral life cycle, including viral replication and virion formation. Little is understood about the formation and structure of these complexes and how they function in these key processes. Here, the specific RNA features required for HDAg binding and the topology of the complexes formed were investigated. Selective 2'OH acylation analyzed by primer extension (SHAPE) applied to free and HDAg-bound HDV RNAs indicated that the characteristic secondary structure of the RNA is preserved when bound to HDAg. Notably, the analysis indicated that predicted unpaired positions in the RNA remained dynamic in the RNP. Analysis of the in vitro binding activity of RNAs in which internal loops and bulges were mutated and of synthetically designed RNAs demonstrated that the distinctive secondary structure, not the primary RNA sequence, is the major determinant of HDAg RNA binding specificity. Atomic force microscopy analysis of RNPs formed in vitro revealed complexes in which the HDV RNA is substantially condensed by bending or wrapping. Our results support a model in which the internal loops and bulges in HDV RNA contribute flexibility to the quasi-double-stranded structure that allows RNA bending and condensing by HDAg. IMPORTANCE RNA-protein complexes (RNPs) formed by the hepatitis delta virus RNAs and protein, HDAg, perform critical roles in virus replication. Neither the structures of these RNPs nor the RNA features required to form them have been characterized. HDV RNA is unusual in that it forms an unbranched quasi-double-stranded structure in which short base-paired segments are interspersed with internal loops and bulges. We analyzed the role of the HDV RNA sequence and secondary structure in the formation of a minimal RNP and visualized the structure of this RNP using atomic force microscopy. Our results indicate that HDAg does not recognize the primary sequence of the RNA; rather, the principle contribution of unpaired bases in HDV RNA to HDAg binding is to allow flexibility in the unbranched quasi-double-stranded RNA structure. Visualization of RNPs by atomic force microscopy indicated that the RNA is significantly bent or condensed in the complex.
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26
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Abstract
Transcriptomics experiments and computational predictions both enable systematic discovery of new functional RNAs. However, many putative noncoding transcripts arise instead from artifacts and biological noise, and current computational prediction methods have high false positive rates. I discuss prospects for improving computational methods for analyzing and identifying functional RNAs, with a focus on detecting signatures of conserved RNA secondary structure. An interesting new front is the application of chemical and enzymatic experiments that probe RNA structure on a transcriptome-wide scale. I review several proposed approaches for incorporating structure probing data into the computational prediction of RNA secondary structure. Using probabilistic inference formalisms, I show how all these approaches can be unified in a well-principled framework, which in turn allows RNA probing data to be easily integrated into a wide range of analyses that depend on RNA secondary structure inference. Such analyses include homology search and genome-wide detection of new structural RNAs.
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Affiliation(s)
- Sean R Eddy
- Howard Hughes Medical Institute Janelia Farm Research Campus, Ashburn, Virginia 20147;
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27
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Kwok CK, Ding Y, Tang Y, Assmann SM, Bevilacqua PC. Determination of in vivo RNA structure in low-abundance transcripts. Nat Commun 2013; 4:2971. [DOI: 10.1038/ncomms3971] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 11/19/2013] [Indexed: 01/19/2023] Open
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28
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Seif E, Niu M, Kleiman L. Annealing to sequences within the primer binding site loop promotes an HIV-1 RNA conformation favoring RNA dimerization and packaging. RNA (NEW YORK, N.Y.) 2013; 19:1384-1393. [PMID: 23960173 PMCID: PMC3854529 DOI: 10.1261/rna.038497.113] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 07/02/2013] [Indexed: 06/02/2023]
Abstract
The 5' untranslated region (5' UTR) of HIV-1 genomic RNA (gRNA) includes structural elements that regulate reverse transcription, transcription, translation, tRNA(Lys3) annealing to the gRNA, and gRNA dimerization and packaging into viruses. It has been reported that gRNA dimerization and packaging are regulated by changes in the conformation of the 5'-UTR RNA. In this study, we show that annealing of tRNA(Lys3) or a DNA oligomer complementary to sequences within the primer binding site (PBS) loop of the 5' UTR enhances its dimerization in vitro. Structural analysis of the 5'-UTR RNA using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) shows that the annealing promotes a conformational change of the 5' UTR that has been previously reported to favor gRNA dimerization and packaging into virus. The model predicted by SHAPE analysis is supported by antisense experiments designed to test which annealed sequences will promote or inhibit gRNA dimerization. Based on reports showing that the gRNA dimerization favors its incorporation into viruses, we tested the ability of a mutant gRNA unable to anneal to tRNA(Lys3) to be incorporated into virions. We found a ∼60% decrease in mutant gRNA packaging compared with wild-type gRNA. Together, these data further support a model for viral assembly in which the initial annealing of tRNA(Lys3) to gRNA is cytoplasmic, which in turn aids in the promotion of gRNA dimerization and its incorporation into virions.
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Affiliation(s)
- Elias Seif
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Meijuan Niu
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Lawrence Kleiman
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
- Department of Medicine, McGill University, Montreal, Quebec H3A 1A1, Canada
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29
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Kim H, Cordero P, Das R, Yoon S. HiTRACE-Web: an online tool for robust analysis of high-throughput capillary electrophoresis. Nucleic Acids Res 2013; 41:W492-8. [PMID: 23761448 PMCID: PMC3692083 DOI: 10.1093/nar/gkt501] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Revised: 05/08/2013] [Accepted: 05/15/2013] [Indexed: 01/14/2023] Open
Abstract
To facilitate the analysis of large-scale high-throughput capillary electrophoresis data, we previously proposed a suite of efficient analysis software named HiTRACE (High Throughput Robust Analysis of Capillary Electrophoresis). HiTRACE has been used extensively for quantitating data from RNA and DNA structure mapping experiments, including mutate-and-map contact inference, chromatin footprinting, the Eterna RNA design project and other high-throughput applications. However, HiTRACE is based on a suite of command-line MATLAB scripts that requires nontrivial efforts to learn, use and extend. Here, we present HiTRACE-Web, an online version of HiTRACE that includes standard features previously available in the command-line version and additional features such as automated band annotation and flexible adjustment of annotations, all via a user-friendly environment. By making use of parallelization, the on-line workflow is also faster than software implementations available to most users on their local computers. Free access: http://hitrace.org.
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Affiliation(s)
- Hanjoo Kim
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 151-744, Korea, Bioinformatics Institute, Seoul National University, Seoul 151-747, Korea, Program in Biomedical Informatics, School of Medicine, Stanford University, Stanford CA 94305, USA, Department of Biochemistry, Stanford University, Stanford, CA 94305, USA and Department of Physics, Stanford University, Stanford, CA 94305, USA
| | - Pablo Cordero
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 151-744, Korea, Bioinformatics Institute, Seoul National University, Seoul 151-747, Korea, Program in Biomedical Informatics, School of Medicine, Stanford University, Stanford CA 94305, USA, Department of Biochemistry, Stanford University, Stanford, CA 94305, USA and Department of Physics, Stanford University, Stanford, CA 94305, USA
| | - Rhiju Das
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 151-744, Korea, Bioinformatics Institute, Seoul National University, Seoul 151-747, Korea, Program in Biomedical Informatics, School of Medicine, Stanford University, Stanford CA 94305, USA, Department of Biochemistry, Stanford University, Stanford, CA 94305, USA and Department of Physics, Stanford University, Stanford, CA 94305, USA
| | - Sungroh Yoon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 151-744, Korea, Bioinformatics Institute, Seoul National University, Seoul 151-747, Korea, Program in Biomedical Informatics, School of Medicine, Stanford University, Stanford CA 94305, USA, Department of Biochemistry, Stanford University, Stanford, CA 94305, USA and Department of Physics, Stanford University, Stanford, CA 94305, USA
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30
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Lusvarghi S, Sztuba-Solinska J, Purzycka KJ, Rausch JW, Le Grice SFJ. RNA secondary structure prediction using high-throughput SHAPE. J Vis Exp 2013:e50243. [PMID: 23748604 DOI: 10.3791/50243] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Understanding the function of RNA involved in biological processes requires a thorough knowledge of RNA structure. Toward this end, the methodology dubbed "high-throughput selective 2' hydroxyl acylation analyzed by primer extension", or SHAPE, allows prediction of RNA secondary structure with single nucleotide resolution. This approach utilizes chemical probing agents that preferentially acylate single stranded or flexible regions of RNA in aqueous solution. Sites of chemical modification are detected by reverse transcription of the modified RNA, and the products of this reaction are fractionated by automated capillary electrophoresis (CE). Since reverse transcriptase pauses at those RNA nucleotides modified by the SHAPE reagents, the resulting cDNA library indirectly maps those ribonucleotides that are single stranded in the context of the folded RNA. Using ShapeFinder software, the electropherograms produced by automated CE are processed and converted into nucleotide reactivity tables that are themselves converted into pseudo-energy constraints used in the RNAStructure (v5.3) prediction algorithm. The two-dimensional RNA structures obtained by combining SHAPE probing with in silico RNA secondary structure prediction have been found to be far more accurate than structures obtained using either method alone.
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Affiliation(s)
- Sabrina Lusvarghi
- RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory for Cancer Research, USA
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31
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Hamada M. Direct updating of an RNA base-pairing probability matrix with marginal probability constraints. J Comput Biol 2013; 19:1265-76. [PMID: 23210474 DOI: 10.1089/cmb.2012.0215] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A base-pairing probability matrix (BPPM) stores the probabilities for every possible base pair in an RNA sequence and has been used in many algorithms in RNA informatics (e.g., RNA secondary structure prediction and motif search). In this study, we propose a novel algorithm to perform iterative updates of a given BPPM, satisfying marginal probability constraints that are (approximately) given by recently developed biochemical experiments, such as SHAPE, PAR, and FragSeq. The method is easily implemented and is applicable to common models for RNA secondary structures, such as energy-based or machine-learning-based models. In this article, we focus mainly on the details of the algorithms, although preliminary computational experiments will also be presented.
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Affiliation(s)
- Michiaki Hamada
- The University of Tokyo, Graduate School of Frontier Science, Kashiwa, Japan.
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32
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Yonemoto H, Asai K, Hamada M. CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs. Int J Mol Sci 2013; 14:6144-56. [PMID: 23507751 PMCID: PMC3634467 DOI: 10.3390/ijms14036144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 01/28/2013] [Accepted: 02/28/2013] [Indexed: 12/31/2022] Open
Abstract
Due to the recent discovery of non-coding RNAs (ncRNAs), multiple sequence alignment (MSA) of those long RNA sequences is becoming increasingly important for classifying and determining the functional motifs in RNAs. However, not only primary (nucleotide) sequences, but also secondary structures of ncRNAs are closely related to their function and are conserved evolutionarily. Hence, information about secondary structures should be considered in the sequence alignment of ncRNAs. Yet, in general, a huge computational time is required in order to compute MSAs, taking secondary structure information into account. In this paper, we describe a fast and accurate web server, called CentroidAlign-Web, which can handle long RNA sequences. The web server also appropriately incorporates information about known secondary structures into MSAs. Computational experiments indicate that our web server is fast and accurate enough to handle long RNA sequences. CentroidAlign-Web is freely available from http://centroidalign.ncrna.org/.
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Affiliation(s)
- Haruka Yonemoto
- Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8561, Japan; E-Mails: yonemoto (H.Y.); (K.A.)
| | - Kiyoshi Asai
- Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8561, Japan; E-Mails: yonemoto (H.Y.); (K.A.)
- Computational Biology Research Center (CBRC), the National Institute of Advanced Industrial Science and Technology (AIST), Tokyo Waterfront Bio-IT Research Building, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Michiaki Hamada
- Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8561, Japan; E-Mails: yonemoto (H.Y.); (K.A.)
- Computational Biology Research Center (CBRC), the National Institute of Advanced Industrial Science and Technology (AIST), Tokyo Waterfront Bio-IT Research Building, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
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33
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Karabiber F, McGinnis JL, Favorov OV, Weeks KM. QuShape: rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis. RNA (NEW YORK, N.Y.) 2013; 19. [PMID: 23188808 PMCID: PMC3527727 DOI: 10.1261/rna.036327.112] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Chemical probing of RNA and DNA structure is a widely used and highly informative approach for examining nucleic acid structure and for evaluating interactions with protein and small-molecule ligands. Use of capillary electrophoresis to analyze chemical probing experiments yields hundreds of nucleotides of information per experiment and can be performed on automated instruments. Extraction of the information from capillary electrophoresis electropherograms is a computationally intensive multistep analytical process, and no current software provides rapid, automated, and accurate data analysis. To overcome this bottleneck, we developed a platform-independent, user-friendly software package, QuShape, that yields quantitatively accurate nucleotide reactivity information with minimal user supervision. QuShape incorporates newly developed algorithms for signal decay correction, alignment of time-varying signals within and across capillaries and relative to the RNA nucleotide sequence, and signal scaling across channels or experiments. An analysis-by-reference option enables multiple, related experiments to be fully analyzed in minutes. We illustrate the usefulness and robustness of QuShape by analysis of RNA SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) experiments.
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Affiliation(s)
- Fethullah Karabiber
- Department of Computer Engineering, Yildiz Technical University, 34220, Istanbul, Turkey
| | - Jennifer L. McGinnis
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
| | - Oleg V. Favorov
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, North Carolina 27599-7575, USA
- Corresponding authorsE-mail E-mail
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
- Corresponding authorsE-mail E-mail
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34
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Romero-López C, Barroso-Deljesus A, García-Sacristán A, Briones C, Berzal-Herranz A. The folding of the hepatitis C virus internal ribosome entry site depends on the 3'-end of the viral genome. Nucleic Acids Res 2012; 40:11697-713. [PMID: 23066110 PMCID: PMC3526292 DOI: 10.1093/nar/gks927] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Hepatitis C virus (HCV) translation initiation is directed by an internal ribosome entry site (IRES) and regulated by distant regions at the 3′-end of the viral genome. Through a combination of improved RNA chemical probing methods, SHAPE structural analysis and screening of RNA accessibility using antisense oligonucleotide microarrays, here, we show that HCV IRES folding is fine-tuned by the genomic 3′-end. The essential IRES subdomains IIIb and IIId, and domain IV, adopted a different conformation in the presence of the cis-acting replication element and/or the 3′-untranslatable region compared to that taken up in their absence. Importantly, many of the observed changes involved significant decreases in the dimethyl sulfate or N-methyl-isatoic anhydride reactivity profiles at subdomains IIIb and IIId, while domain IV appeared as a more flexible element. These observations were additionally confirmed in a replication-competent RNA molecule. Significantly, protein factors are not required for these conformational differences to be made manifest. Our results suggest that a complex, direct and long-distance RNA–RNA interaction network plays an important role in the regulation of HCV translation and replication, as well as in the switching between different steps of the viral cycle.
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Affiliation(s)
- Cristina Romero-López
- Departamento de Biología Molecular, Instituto de Parasitología y Biomedicina López-Neyra, IPBLN-CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento s/n, Armilla, 18100 Granada, Spain.
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35
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Tuplin A, Struthers M, Simmonds P, Evans DJ. A twist in the tail: SHAPE mapping of long-range interactions and structural rearrangements of RNA elements involved in HCV replication. Nucleic Acids Res 2012; 40:6908-21. [PMID: 22561372 PMCID: PMC3413155 DOI: 10.1093/nar/gks370] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The RNA structure and long-range interactions of the SL9266 cis-acting replication element located within the NS5B coding region of hepatitis C virus (HCV) were determined using selective 2′-hydroxyl acylation analysed by primer extension. Marked differences were found in the long-range interactions of SL9266 when the two widely used genotype 2a JFH-1 (HCVcc) and genotype 1b Con1b sub-genomic replicon systems were compared. In both genomes, there was evidence for interaction of the sub-terminal bulge loop of SL9266 and sequences around nucleotide 9110, though the replication phenotype of genomes bearing mutations that disrupted this interaction was fundamentally different. In contrast, a ‘kissing loop’ interaction between the terminal loop of SL9266 and sequences in the 3′-untranslated X-tail was only detectable in JFH-1-based genomes. In the latter, where both long-range interactions are present, they were independent, implying that SL9266 forms the core of an extended pseudoknot. The presence of the ‘kissing loop’ interaction inhibited the formation of SL9571 in the 3′-X-tail, an RNA structure implicated in genome replication. We propose that, SL9266 may contribute a switch function that modulates the mutually incompatible translation and replication events that must occur for replication of the positive-strand RNA genome of HCV.
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Affiliation(s)
- Andrew Tuplin
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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36
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Popenda M, Szachniuk M, Antczak M, Purzycka KJ, Lukasiak P, Bartol N, Blazewicz J, Adamiak RW. Automated 3D structure composition for large RNAs. Nucleic Acids Res 2012; 40:e112. [PMID: 22539264 PMCID: PMC3413140 DOI: 10.1093/nar/gks339] [Citation(s) in RCA: 478] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues.
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Affiliation(s)
- Mariusz Popenda
- Laboratory of Structural Chemistry of Nucleic Acids, Laboratory of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704 and Institute of Computing Science, Poznan University of Technology, Poznan 60-965, Poland
| | - Marta Szachniuk
- Laboratory of Structural Chemistry of Nucleic Acids, Laboratory of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704 and Institute of Computing Science, Poznan University of Technology, Poznan 60-965, Poland
| | - Maciej Antczak
- Laboratory of Structural Chemistry of Nucleic Acids, Laboratory of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704 and Institute of Computing Science, Poznan University of Technology, Poznan 60-965, Poland
| | - Katarzyna J. Purzycka
- Laboratory of Structural Chemistry of Nucleic Acids, Laboratory of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704 and Institute of Computing Science, Poznan University of Technology, Poznan 60-965, Poland
| | - Piotr Lukasiak
- Laboratory of Structural Chemistry of Nucleic Acids, Laboratory of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704 and Institute of Computing Science, Poznan University of Technology, Poznan 60-965, Poland
| | - Natalia Bartol
- Laboratory of Structural Chemistry of Nucleic Acids, Laboratory of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704 and Institute of Computing Science, Poznan University of Technology, Poznan 60-965, Poland
| | - Jacek Blazewicz
- Laboratory of Structural Chemistry of Nucleic Acids, Laboratory of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704 and Institute of Computing Science, Poznan University of Technology, Poznan 60-965, Poland
| | - Ryszard W. Adamiak
- Laboratory of Structural Chemistry of Nucleic Acids, Laboratory of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704 and Institute of Computing Science, Poznan University of Technology, Poznan 60-965, Poland
- *To whom correspondence should be addressed. Tel: +48 61 8528503; Fax: +48 61 8520532;
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