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Moafinejad SN, de Aquino BRH, Boniecki M, Pandaranadar Jeyeram IN, Nikolaev G, Magnus M, Farsani M, Badepally N, Wirecki T, Stefaniak F, Bujnicki J. SimRNAweb v2.0: a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories. Nucleic Acids Res 2024; 52:W368-W373. [PMID: 38738621 PMCID: PMC11223799 DOI: 10.1093/nar/gkae356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/07/2024] [Accepted: 04/29/2024] [Indexed: 05/14/2024] Open
Abstract
Research on ribonucleic acid (RNA) structures and functions benefits from easy-to-use tools for computational prediction and analyses of RNA three-dimensional (3D) structure. The SimRNAweb server version 2.0 offers an enhanced, user-friendly platform for RNA 3D structure prediction and analysis of RNA folding trajectories based on the SimRNA method. SimRNA employs a coarse-grained model, Monte Carlo sampling and statistical potentials to explore RNA conformational space, optionally guided by spatial restraints. Recognized for its accuracy in RNA 3D structure prediction in RNA-Puzzles and CASP competitions, SimRNA is particularly useful for incorporating restraints based on experimental data. The new server version introduces performance optimizations and extends user control over simulations and the processing of results. It allows the application of various hard and soft restraints, accommodating alternative structures involving canonical and noncanonical base pairs and unpaired residues, while also integrating data from chemical probing methods. Enhanced features include an improved analysis of folding trajectories, offering advanced clustering options and multiple analyses of the generated trajectories. These updates provide comprehensive tools for detailed RNA structure analysis. SimRNAweb v2.0 significantly broadens the scope of RNA modeling, emphasizing flexibility and user-defined parameter control. The web server is available at https://genesilico.pl/SimRNAweb.
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Affiliation(s)
- S Naeim Moafinejad
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Belisa R H de Aquino
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Michał J Boniecki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Iswarya P N Pandaranadar Jeyeram
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Grigory Nikolaev
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Marcin Magnus
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford St, Cambridge, MA 02138, USA
| | - Masoud Amiri Farsani
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Nagendar Goud Badepally
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Tomasz K Wirecki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Filip Stefaniak
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
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2
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Bernard C, Postic G, Ghannay S, Tahi F. State-of-the-RNArt: benchmarking current methods for RNA 3D structure prediction. NAR Genom Bioinform 2024; 6:lqae048. [PMID: 38745991 PMCID: PMC11091930 DOI: 10.1093/nargab/lqae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/05/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024] Open
Abstract
RNAs are essential molecules involved in numerous biological functions. Understanding RNA functions requires the knowledge of their 3D structures. Computational methods have been developed for over two decades to predict the 3D conformations from RNA sequences. These computational methods have been widely used and are usually categorised as either ab initio or template-based. The performances remain to be improved. Recently, the rise of deep learning has changed the sight of novel approaches. Deep learning methods are promising, but their adaptation to RNA 3D structure prediction remains difficult. In this paper, we give a brief review of the ab initio, template-based and novel deep learning approaches. We highlight the different available tools and provide a benchmark on nine methods using the RNA-Puzzles dataset. We provide an online dashboard that shows the predictions made by benchmarked methods, freely available on the EvryRNA platform: https://evryrna.ibisc.univ-evry.fr/evryrna/state_of_the_rnart/.
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Affiliation(s)
- Clément Bernard
- Université Paris-Saclay, Univ. Evry, IBISC, 91020 Evry-Courcouronnes, France
- LISN - CNRS/Université Paris-Saclay, 91400 Orsay, France
| | - Guillaume Postic
- Université Paris-Saclay, Univ. Evry, IBISC, 91020 Evry-Courcouronnes, France
| | - Sahar Ghannay
- LISN - CNRS/Université Paris-Saclay, 91400 Orsay, France
| | - Fariza Tahi
- Université Paris-Saclay, Univ. Evry, IBISC, 91020 Evry-Courcouronnes, France
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3
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Trinity L, Stege U, Jabbari H. Tying the knot: Unraveling the intricacies of the coronavirus frameshift pseudoknot. PLoS Comput Biol 2024; 20:e1011787. [PMID: 38713726 PMCID: PMC11108256 DOI: 10.1371/journal.pcbi.1011787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 05/21/2024] [Accepted: 04/27/2024] [Indexed: 05/09/2024] Open
Abstract
Understanding and targeting functional RNA structures towards treatment of coronavirus infection can help us to prepare for novel variants of SARS-CoV-2 (the virus causing COVID-19), and any other coronaviruses that could emerge via human-to-human transmission or potential zoonotic (inter-species) events. Leveraging the fact that all coronaviruses use a mechanism known as -1 programmed ribosomal frameshifting (-1 PRF) to replicate, we apply algorithms to predict the most energetically favourable secondary structures (each nucleotide involved in at most one pairing) that may be involved in regulating the -1 PRF event in coronaviruses, especially SARS-CoV-2. We compute previously unknown most stable structure predictions for the frameshift site of coronaviruses via hierarchical folding, a biologically motivated framework where initial non-crossing structure folds first, followed by subsequent, possibly crossing (pseudoknotted), structures. Using mutual information from 181 coronavirus sequences, in conjunction with the algorithm KnotAli, we compute secondary structure predictions for the frameshift site of different coronaviruses. We then utilize the Shapify algorithm to obtain most stable SARS-CoV-2 secondary structure predictions guided by frameshift sequence-specific and genome-wide experimental data. We build on our previous secondary structure investigation of the singular SARS-CoV-2 68 nt frameshift element sequence, by using Shapify to obtain predictions for 132 extended sequences and including covariation information. Previous investigations have not applied hierarchical folding to extended length SARS-CoV-2 frameshift sequences. By doing so, we simulate the effects of ribosome interaction with the frameshift site, providing insight to biological function. We contribute in-depth discussion to contextualize secondary structure dual-graph motifs for SARS-CoV-2, highlighting the energetic stability of the previously identified 3_8 motif alongside the known dominant 3_3 and 3_6 (native-type) -1 PRF structures. Using a combination of thermodynamic methods and sequence covariation, our novel predictions suggest function of the attenuator hairpin via previously unknown pseudoknotted base pairing. While certain initial RNA folding is consistent, other pseudoknotted base pairs form which indicate potential conformational switching between the two structures.
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Affiliation(s)
- Luke Trinity
- Department of Computer Science, University of Victoria, Victoria, British Columbia, Canada
| | - Ulrike Stege
- Department of Computer Science, University of Victoria, Victoria, British Columbia, Canada
| | - Hosna Jabbari
- Department of Biomedical Engineering, University of Alberta, Edmonton, Alberta, Canada
- Institute on Aging and Lifelong Health, Victoria, British Columbia, Canada
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4
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Irving PS, Weeks KM. RNAvigate: efficient exploration of RNA chemical probing datasets. Nucleic Acids Res 2024; 52:2231-2241. [PMID: 38348910 PMCID: PMC10954457 DOI: 10.1093/nar/gkae089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 02/27/2024] Open
Abstract
Chemical probing technologies enable high-throughput examination of diverse structural features of RNA, including local nucleotide flexibility, RNA secondary structure, protein and ligand binding, through-space interaction networks, and multistate structural ensembles. Deep understanding of RNA structure-function relationships typically requires evaluating a system under structure- and function-altering conditions, linking these data with additional information, and visualizing multilayered relationships. Current platforms lack the broad accessibility, flexibility and efficiency needed to iterate on integrative analyses of these diverse, complex data. Here, we share the RNA visualization and graphical analysis toolset RNAvigate, a straightforward and flexible Python library that automatically parses 21 standard file formats (primary sequence annotations, per- and internucleotide data, and secondary and tertiary structures) and outputs 18 plot types. RNAvigate enables efficient exploration of nuanced relationships between multiple layers of RNA structure information and across multiple experimental conditions. Compatibility with Jupyter notebooks enables nonburdensome, reproducible, transparent and organized sharing of multistep analyses and data visualization strategies. RNAvigate simplifies and accelerates discovery and characterization of RNA-centric functions in biology.
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Affiliation(s)
- Patrick S Irving
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
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5
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Thiel BC, Poblete S, Hofacker IL. The Multiscale Ernwin/SPQR RNA Structure Prediction Pipeline. Methods Mol Biol 2024; 2726:377-399. [PMID: 38780739 DOI: 10.1007/978-1-0716-3519-3_15] [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
Aside from the well-known role in protein synthesis, RNA can perform catalytic, regulatory, and other essential biological functions which are determined by its three-dimensional structure. In this regard, a great effort has been made during the past decade to develop computational tools for the prediction of the structure of RNAs from the knowledge of their sequence, incorporating experimental data to refine or guide the modeling process. Nevertheless, this task can become exceptionally challenging when dealing with long noncoding RNAs, constituted by more than 200 nucleotides, due to their large size and the specific interactions involved. In this chapter, we describe a multiscale approach to predict such structures, incorporating SAXS experimental data into a hierarchical procedure which couples two coarse-grained representations: Ernwin, a helix-based approach, which deals with the global arrangement of secondary structure elements, and SPQR, a nucleotide-centered coarse-grained model, which corrects and refines the structures predicted at the coarser level.We describe the methodology through its application on the Braveheart long noncoding RNA, starting from the SAXS and secondary structure data to propose a refined, all-atom structure.
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Affiliation(s)
- Bernhard C Thiel
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Simón Poblete
- Instituto de Ciencias Físicas y Matemáticas, Universidad Austral de Chile, Valdivia, Chile
- Computational Biology Lab, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad SanSebastián, Santiago, Chile
| | - Ivo L Hofacker
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
- Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria.
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6
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Wu P, Yang L. sRNA Structural Modeling Based on NMR Data. Methods Mol Biol 2024; 2741:383-397. [PMID: 38217664 DOI: 10.1007/978-1-0716-3565-0_20] [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: 01/15/2024]
Abstract
Small non-coding RNAs (sRNAs) play vital roles in gene expression regulation and RNA interference. To comprehend their molecular mechanisms and develop therapeutic approaches, determining the accurate three-dimensional structure of sRNAs is crucial. Although nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for structural biology, obtaining high-resolution structures of sRNAs using NMR data alone can be challenging. In such cases, structural modeling can provide additional details about RNA structures. In this context, we present a protocol for the structural modeling of sRNA using the SimRNA method based on sparse NMR constraints. To demonstrate the efficacy of our method, we provide selected examples of NMR spectra and RNA structures, specifically for the second stem-loop of DsrA sRNA.
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Affiliation(s)
- Pengzhi Wu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People's Republic of China.
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland.
| | - Lingna Yang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
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7
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Levintov L, Vashisth H. Structural and computational studies of HIV-1 RNA. RNA Biol 2024; 21:1-32. [PMID: 38100535 PMCID: PMC10730233 DOI: 10.1080/15476286.2023.2289709] [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] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Viruses remain a global threat to animals, plants, and humans. The type 1 human immunodeficiency virus (HIV-1) is a member of the retrovirus family and carries an RNA genome, which is reverse transcribed into viral DNA and further integrated into the host-cell DNA for viral replication and proliferation. The RNA structures from the HIV-1 genome provide valuable insights into the mechanisms underlying the viral replication cycle. Moreover, these structures serve as models for designing novel therapeutic approaches. Here, we review structural data on RNA from the HIV-1 genome as well as computational studies based on these structural data. The review is organized according to the type of structured RNA element which contributes to different steps in the viral replication cycle. This is followed by an overview of the HIV-1 transactivation response element (TAR) RNA as a model system for understanding dynamics and interactions in the viral RNA systems. The review concludes with a description of computational studies, highlighting the impact of biomolecular simulations in elucidating the mechanistic details of various steps in the HIV-1's replication cycle.
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Affiliation(s)
- Lev Levintov
- Department of Chemical Engineering & Bioengineering, University of New Hampshire, Durham, USA
| | - Harish Vashisth
- Department of Chemical Engineering & Bioengineering, University of New Hampshire, Durham, USA
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8
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Irving PS, Weeks KM. RNAvigate: Efficient exploration of RNA chemical probing datasets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.538311. [PMID: 37162917 PMCID: PMC10168276 DOI: 10.1101/2023.04.25.538311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Chemical probing technologies enable high-throughput examination of diverse structural features of RNA including local nucleotide flexibility, RNA secondary structure, protein- and ligand-binding, through-space interaction networks, and multi-state structural ensembles. Performing these experiments, by themselves, does not directly lead to biological insight. Instead, deep understanding of RNA structure-function relationships typically requires evaluating a system under structure- and function-altering conditions, linking these data with additional information, and visualizing multi-layered relationships. Current platforms lack the broad accessibility, flexibility, and efficiency needed to iterate on integrative analyses of these diverse, complex data. Here, we share the RNA visualization and graphical analysis toolset RNAvigate, a straightforward and flexible Python library. RNAvigate currently automatically parses twenty-one standard file formats (primary sequence annotations, per- and internucleotide data, and secondary and tertiary structures) and outputs eighteen plot types. These features enable efficient exploration of nuanced relationships between chemical probing data, RNA structure, and motif annotations across multiple experimental samples. Compatibility with Jupyter Notebooks enables non-burdensome, reproducible, transparent and organized sharing of multi-step analyses and data visualization strategies. RNAvigate simplifies examination of multi-layered RNA structure information and accelerates discovery and characterization of RNA-centric functions in biology.
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Affiliation(s)
- Patrick S. Irving
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290
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9
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Tieng FYF, Abdullah-Zawawi MR, Md Shahri NAA, Mohamed-Hussein ZA, Lee LH, Mutalib NSA. A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools. Brief Bioinform 2023; 25:bbad421. [PMID: 38040490 PMCID: PMC10753535 DOI: 10.1093/bib/bbad421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 12/03/2023] Open
Abstract
RNA biology has risen to prominence after a remarkable discovery of diverse functions of noncoding RNA (ncRNA). Most untranslated transcripts often exert their regulatory functions into RNA-RNA complexes via base pairing with complementary sequences in other RNAs. An interplay between RNAs is essential, as it possesses various functional roles in human cells, including genetic translation, RNA splicing, editing, ribosomal RNA maturation, RNA degradation and the regulation of metabolic pathways/riboswitches. Moreover, the pervasive transcription of the human genome allows for the discovery of novel genomic functions via RNA interactome investigation. The advancement of experimental procedures has resulted in an explosion of documented data, necessitating the development of efficient and precise computational tools and algorithms. This review provides an extensive update on RNA-RNA interaction (RRI) analysis via thermodynamic- and comparative-based RNA secondary structure prediction (RSP) and RNA-RNA interaction prediction (RIP) tools and their general functions. We also highlighted the current knowledge of RRIs and the limitations of RNA interactome mapping via experimental data. Then, the gap between RSP and RIP, the importance of RNA homologues, the relationship between pseudoknots, and RNA folding thermodynamics are discussed. It is hoped that these emerging prediction tools will deepen the understanding of RNA-associated interactions in human diseases and hasten treatment processes.
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Affiliation(s)
- Francis Yew Fu Tieng
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur 56000, Malaysia
| | | | - Nur Alyaa Afifah Md Shahri
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur 56000, Malaysia
| | - Zeti-Azura Mohamed-Hussein
- Institute of Systems Biology (INBIOSIS), UKM, Selangor 43600, Malaysia
- Department of Applied Physics, Faculty of Science and Technology, UKM, Selangor 43600, Malaysia
| | - Learn-Han Lee
- Sunway Microbiomics Centre, School of Medical and Life Sciences, Sunway University, Sunway City 47500, Malaysia
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University of Malaysia, Selangor 47500, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur 56000, Malaysia
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University of Malaysia, Selangor 47500, Malaysia
- Faculty of Health Sciences, UKM, Kuala Lumpur 50300, Malaysia
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10
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Kuhle B, Chen Q, Schimmel P. tRNA renovatio: Rebirth through fragmentation. Mol Cell 2023; 83:3953-3971. [PMID: 37802077 PMCID: PMC10841463 DOI: 10.1016/j.molcel.2023.09.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/15/2023] [Accepted: 09/12/2023] [Indexed: 10/08/2023]
Abstract
tRNA function is based on unique structures that enable mRNA decoding using anticodon trinucleotides. These structures interact with specific aminoacyl-tRNA synthetases and ribosomes using 3D shape and sequence signatures. Beyond translation, tRNAs serve as versatile signaling molecules interacting with other RNAs and proteins. Through evolutionary processes, tRNA fragmentation emerges as not merely random degradation but an act of recreation, generating specific shorter molecules called tRNA-derived small RNAs (tsRNAs). These tsRNAs exploit their linear sequences and newly arranged 3D structures for unexpected biological functions, epitomizing the tRNA "renovatio" (from Latin, meaning renewal, renovation, and rebirth). Emerging methods to uncover full tRNA/tsRNA sequences and modifications, combined with techniques to study RNA structures and to integrate AI-powered predictions, will enable comprehensive investigations of tRNA fragmentation products and new interaction potentials in relation to their biological functions. We anticipate that these directions will herald a new era for understanding biological complexity and advancing pharmaceutical engineering.
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Affiliation(s)
- Bernhard Kuhle
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA; Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Qi Chen
- Molecular Medicine Program, Department of Human Genetics, and Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Paul Schimmel
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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Rahaman MM, Khan NS, Zhang S. RNAMotifComp: a comprehensive method to analyze and identify structurally similar RNA motif families. Bioinformatics 2023; 39:i337-i346. [PMID: 37387191 DOI: 10.1093/bioinformatics/btad223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Abstract
MOTIVATION The 3D structures of RNA play a critical role in understanding their functionalities. There exist several computational methods to study RNA 3D structures by identifying structural motifs and categorizing them into several motif families based on their structures. Although the number of such motif families is not limited, a few of them are well-studied. Out of these structural motif families, there exist several families that are visually similar or very close in structure, even with different base interactions. Alternatively, some motif families share a set of base interactions but maintain variation in their 3D formations. These similarities among different motif families, if known, can provide a better insight into the RNA 3D structural motifs as well as their characteristic functions in cell biology. RESULTS In this work, we proposed a method, RNAMotifComp, that analyzes the instances of well-known structural motif families and establishes a relational graph among them. We also have designed a method to visualize the relational graph where the families are shown as nodes and their similarity information is represented as edges. We validated our discovered correlations of the motif families using RNAMotifContrast. Additionally, we used a basic Naïve Bayes classifier to show the importance of RNAMotifComp. The relational analysis explains the functional analogies of divergent motif families and illustrates the situations where the motifs of disparate families are predicted to be of the same family. AVAILABILITY AND IMPLEMENTATION Source code publicly available at https://github.com/ucfcbb/RNAMotifFamilySimilarity.
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Affiliation(s)
- Md Mahfuzur Rahaman
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, United States
| | - Nabila Shahnaz Khan
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, United States
| | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, United States
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12
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Quadrini M, Tesei L, Merelli E. Automatic generation of pseudoknotted RNAs taxonomy. BMC Bioinformatics 2023; 23:575. [PMID: 37322429 DOI: 10.1186/s12859-023-05362-5] [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: 02/18/2022] [Accepted: 05/25/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND The ability to compare RNA secondary structures is important in understanding their biological function and for grouping similar organisms into families by looking at evolutionarily conserved sequences such as 16S rRNA. Most comparison methods and benchmarks in the literature focus on pseudoknot-free structures due to the difficulty of mapping pseudoknots in classical tree representations. Some approaches exist that permit to cluster pseudoknotted RNAs but there is not a general framework for evaluating their performance. RESULTS We introduce an evaluation framework based on a similarity/dissimilarity measure obtained by a comparison method and agglomerative clustering. Their combination automatically partition a set of molecules into groups. To illustrate the framework we define and make available a benchmark of pseudoknotted (16S and 23S) and pseudoknot-free (5S) rRNA secondary structures belonging to Archaea, Bacteria and Eukaryota. We also consider five different comparison methods from the literature that are able to manage pseudoknots. For each method we clusterize the molecules in the benchmark to obtain the taxa at the rank phylum according to the European Nucleotide Archive curated taxonomy. We compute appropriate metrics for each method and we compare their suitability to reconstruct the taxa.
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Affiliation(s)
- Michela Quadrini
- School of Sciences and Technology, University of Camerino, Via Madonna delle Carceri 7, 62032, Camerino, MC, Italy
| | - Luca Tesei
- School of Sciences and Technology, University of Camerino, Via Madonna delle Carceri 7, 62032, Camerino, MC, Italy.
| | - Emanuela Merelli
- School of Sciences and Technology, University of Camerino, Via Madonna delle Carceri 7, 62032, Camerino, MC, Italy
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Kamga Youmbi FI, Kengne Tchendji V, Tayou Djamegni C. P-FARFAR2: A multithreaded greedy approach to sampling low-energy RNA structures in Rosetta FARFAR2. Comput Biol Chem 2023; 104:107878. [PMID: 37167861 DOI: 10.1016/j.compbiolchem.2023.107878] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 04/23/2023] [Accepted: 05/01/2023] [Indexed: 05/13/2023]
Abstract
RNA (ribonucleic acid) structure prediction finds many applications in health science and drug discovery due to its importance in several life regulatory processes. But despite significant advances in the close field of protein prediction, RNA 3D structure still poses a tremendous challenge to predict, especially for large sequences. In this regard, the approach unfolded by Rosetta FARFAR2 (Fragment Assembly of RNA with Full-Atom Refinement, version 2) has shown promising results, but the algorithm is non-deterministic by nature. In this paper, we develop P-FARFAR2: a parallel enhancement of FARFAR2 that increases its ability to assemble low-energy structures via multithreaded exploration of random configurations in a greedy manner. This strategy, appearing in the literature under the term "parallel mechanism", is made viable through two measures: first, the synchronization window is coarsened to several Monte Carlo cycles; second, all but one of the threads are differentiated as auxiliary and set to perform a weakened version of the problem. Following empirical analysis on a diverse range of RNA structures, we report achieving statistical significance in lowering the energy levels of ensuing samples. And consequently, despite the moderate-to-weak correlation between energy levels and prediction accuracy, this achievement happens to propagate to accuracy measurements.
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Affiliation(s)
| | - Vianney Kengne Tchendji
- Department of Mathematics and Computer Science, University of Dschang, PO Box 67, Dschang, Cameroon.
| | - Clémentin Tayou Djamegni
- Department of Mathematics and Computer Science, University of Dschang, PO Box 67, Dschang, Cameroon; Department of Computer Engineering, University of Dschang, PO Box 134, Bandjoun, Cameroon.
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14
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How does precursor RNA structure influence RNA processing and gene expression? Biosci Rep 2023; 43:232489. [PMID: 36689327 PMCID: PMC9977717 DOI: 10.1042/bsr20220149] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 01/24/2023] Open
Abstract
RNA is a fundamental biomolecule that has many purposes within cells. Due to its single-stranded and flexible nature, RNA naturally folds into complex and dynamic structures. Recent technological and computational advances have produced an explosion of RNA structural data. Many RNA structures have regulatory and functional properties. Studying the structure of nascent RNAs is particularly challenging due to their low abundance and long length, but their structures are important because they can influence RNA processing. Precursor RNA processing is a nexus of pathways that determines mature isoform composition and that controls gene expression. In this review, we examine what is known about human nascent RNA structure and the influence of RNA structure on processing of precursor RNAs. These known structures provide examples of how other nascent RNAs may be structured and show how novel RNA structures may influence RNA processing including splicing and polyadenylation. RNA structures can be targeted therapeutically to treat disease.
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15
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Sabei A, Caldas Baia TG, Saffar R, Martin J, Frezza E. Internal Normal Mode Analysis Applied to RNA Flexibility and Conformational Changes. J Chem Inf Model 2023; 63:2554-2572. [PMID: 36972178 DOI: 10.1021/acs.jcim.2c01509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
We investigated the capability of internal normal modes to reproduce RNA flexibility and predict observed RNA conformational changes and, notably, those induced by the formation of RNA-protein and RNA-ligand complexes. Here, we extended our iNMA approach developed for proteins to study RNA molecules using a simplified representation of the RNA structure and its potential energy. Three data sets were also created to investigate different aspects. Despite all the approximations, our study shows that iNMA is a suitable method to take into account RNA flexibility and describe its conformational changes opening the route to its applicability in any integrative approach where these properties are crucial.
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16
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Trinity L, Wark I, Lansing L, Jabbari H, Stege U. Shapify: Paths to SARS-CoV-2 frameshifting pseudoknot. PLoS Comput Biol 2023; 19:e1010922. [PMID: 36854032 PMCID: PMC10004594 DOI: 10.1371/journal.pcbi.1010922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 03/10/2023] [Accepted: 02/05/2023] [Indexed: 03/02/2023] Open
Abstract
Multiple coronaviruses including MERS-CoV causing Middle East Respiratory Syndrome, SARS-CoV causing SARS, and SARS-CoV-2 causing COVID-19, use a mechanism known as -1 programmed ribosomal frameshifting (-1 PRF) to replicate. SARS-CoV-2 possesses a unique RNA pseudoknotted structure that stimulates -1 PRF. Targeting -1 PRF in SARS-CoV-2 to impair viral replication can improve patients' prognoses. Crucial to developing these therapies is understanding the structure of the SARS-CoV-2 -1 PRF pseudoknot. Our goal is to expand knowledge of -1 PRF structural conformations. Following a structural alignment approach, we identify similarities in -1 PRF pseudoknots of SARS-CoV-2, SARS-CoV, and MERS-CoV. We provide in-depth analysis of the SARS-CoV-2 and MERS-CoV -1 PRF pseudoknots, including reference and noteworthy mutated sequences. To better understand the impact of mutations, we provide insight on -1 PRF pseudoknot sequence mutations and their effect on resulting structures. We introduce Shapify, a novel algorithm that given an RNA sequence incorporates structural reactivity (SHAPE) data and partial structure information to output an RNA secondary structure prediction within a biologically sound hierarchical folding approach. Shapify enhances our understanding of SARS-CoV-2 -1 PRF pseudoknot conformations by providing energetically favourable predictions that are relevant to structure-function and may correlate with -1 PRF efficiency. Applied to the SARS-CoV-2 -1 PRF pseudoknot, Shapify unveils previously unknown paths from initial stems to pseudoknotted structures. By contextualizing our work with available experimental data, our structure predictions motivate future RNA structure-function research and can aid 3-D modeling of pseudoknots.
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Affiliation(s)
- Luke Trinity
- Department of Computer Science, University of Victoria, Victoria, British Columbia, Canada
| | - Ian Wark
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
| | - Lance Lansing
- Department of Computer Science, University of Victoria, Victoria, British Columbia, Canada
| | - Hosna Jabbari
- Department of Computer Science, University of Victoria, Victoria, British Columbia, Canada
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
- Institute on Aging and Lifelong Health, Victoria, British Columbia, Canada
| | - Ulrike Stege
- Department of Computer Science, University of Victoria, Victoria, British Columbia, Canada
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17
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Ma H, Pham P, Luo B, Rangan R, Kappel K, Su Z, Das R. Auto-DRRAFTER: Automated RNA Modeling Based on Cryo-EM Density. Methods Mol Biol 2023; 2568:193-211. [PMID: 36227570 DOI: 10.1007/978-1-0716-2687-0_13] [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] [Indexed: 05/14/2023]
Abstract
RNA three-dimensional structures provide rich and vital information for understanding their functions. Recent advances in cryogenic electron microscopy (cryo-EM) allow structure determination of RNAs and ribonucleoprotein (RNP) complexes. However, limited global and local resolutions of RNA cryo-EM maps pose great challenges in tracing RNA coordinates. The Rosetta-based "auto-DRRAFTER" method builds RNA models into moderate-resolution RNA cryo-EM density as part of the Ribosolve pipeline. Here, we describe a step-by-step protocol for auto-DRRAFTER using a glycine riboswitch from Fusobacterium nucleatum as an example. Successful implementation of this protocol allows automated RNA modeling into RNA cryo-EM density, accelerating our understanding of RNA structure-function relationships. Input and output files are being made available at https://github.com/auto-DRRAFTER/springer-chapter .
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Affiliation(s)
- Haiyun Ma
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Phillip Pham
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Bingnan Luo
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ramya Rangan
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Kalli Kappel
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Zhaoming Su
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Rhiju Das
- Biophysics Program, Stanford University, Stanford, CA, USA.
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18
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Abstract
The landscape paradigm is revisited in the light of evolution in simple systems. A brief overview of different classes of fitness landscapes is followed by a more detailed discussion of the RNA model, which is currently the only evolutionary model that allows for a comprehensive molecular analysis of a fitness landscape. Neutral networks of genotypes are indispensable for the success of evolution. Important insights into the evolutionary mechanism are gained by considering the topology of sequence and shape spaces. The dynamic concept of molecular quasispecies is viewed in the light of the landscape paradigm. The distribution of fitness values in state space is mirrored by the population structures of mutant distributions. Two classes of thresholds for replication error or mutations are important: (i) the-conventional-genotypic error threshold, which separates ordered replication from random drift on neutral networks, and (ii) a phenotypic error threshold above which the molecular phenotype is lost. Empirical landscapes are reviewed and finally, the implications of the landscape concept for virus evolution are discussed.
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Affiliation(s)
- Peter Schuster
- Institut für Theoretische Chemie der Universität Wien, Währingerstraße 17, 1090, Wien, Austria.
| | - Peter F Stadler
- Institut für Informatik der Universität Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany.,The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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19
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Myatt DP, Wharram L, Graham C, Liddell J, Branton H, Pizzey C, Cowieson N, Rambo R, Shattock RJ. Biophysical characterization of the structure of a SARS-CoV-2 self-amplifying RNA (saRNA) vaccine. Biol Methods Protoc 2023; 8:bpad001. [PMID: 36915370 PMCID: PMC10008065 DOI: 10.1093/biomethods/bpad001] [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: 10/07/2022] [Revised: 01/13/2023] [Accepted: 02/13/2023] [Indexed: 02/16/2023] Open
Abstract
The current SARS-Covid-2 (SARS-CoV-2) pandemic has led to an acceleration of messenger ribonucleic acid (mRNA) vaccine technology. The development of production processes for these large mRNA molecules, especially self-amplifying mRNA (saRNA), has required concomitant development of analytical characterization techniques. Characterizing the purity, shape and structure of these biomolecules is key to their successful performance as drug products. This article describes the biophysical characterization of the Imperial College London Self-amplifying viral RNA vaccine (IMP-1) developed for SARS-CoV-2. A variety of analytical techniques have been used to characterize the IMP-1 RNA molecule. In this article, we use ultraviolet spectroscopy, dynamic light scattering, size-exclusion chromatography small-angle X-ray scattering and circular dichroism to determine key biophysical attributes of IMP-1. Each technique provides important information about the concentration, size, shape, structure and purity of the molecule.
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Affiliation(s)
- Daniel P Myatt
- The National Biologics Manufacturing Centre (NBMC), The Centre for Process Innovation, Darlington DL1 1GL, UK
| | - Lewis Wharram
- The National Biologics Manufacturing Centre (NBMC), The Centre for Process Innovation, Darlington DL1 1GL, UK
| | - Charlotte Graham
- The National Biologics Manufacturing Centre (NBMC), The Centre for Process Innovation, Darlington DL1 1GL, UK
| | - John Liddell
- The National Biologics Manufacturing Centre (NBMC), The Centre for Process Innovation, Darlington DL1 1GL, UK
| | - Harvey Branton
- The National Biologics Manufacturing Centre (NBMC), The Centre for Process Innovation, Darlington DL1 1GL, UK
| | - Claire Pizzey
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, UK
| | - Nathan Cowieson
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, UK
| | - Robert Rambo
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, UK
| | - Robin J Shattock
- Department of Infectious Disease, Imperial College London, London W21PG, UK
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20
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Catacalos C, Krohannon A, Somalraju S, Meyer KD, Janga SC, Chakrabarti K. Epitranscriptomics in parasitic protists: Role of RNA chemical modifications in posttranscriptional gene regulation. PLoS Pathog 2022; 18:e1010972. [PMID: 36548245 PMCID: PMC9778586 DOI: 10.1371/journal.ppat.1010972] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
"Epitranscriptomics" is the new RNA code that represents an ensemble of posttranscriptional RNA chemical modifications, which can precisely coordinate gene expression and biological processes. There are several RNA base modifications, such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), and pseudouridine (Ψ), etc. that play pivotal roles in fine-tuning gene expression in almost all eukaryotes and emerging evidences suggest that parasitic protists are no exception. In this review, we primarily focus on m6A, which is the most abundant epitranscriptomic mark and regulates numerous cellular processes, ranging from nuclear export, mRNA splicing, polyadenylation, stability, and translation. We highlight the universal features of spatiotemporal m6A RNA modifications in eukaryotic phylogeny, their homologs, and unique processes in 3 unicellular parasites-Plasmodium sp., Toxoplasma sp., and Trypanosoma sp. and some technological advances in this rapidly developing research area that can significantly improve our understandings of gene expression regulation in parasites.
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Affiliation(s)
- Cassandra Catacalos
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Alexander Krohannon
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, Indiana, United States of America
| | - Sahiti Somalraju
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, Indiana, United States of America
| | - Kate D. Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Sarath Chandra Janga
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, Indiana, United States of America
| | - Kausik Chakrabarti
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
- * E-mail:
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21
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Liang W, Wang S, Wang H, Li X, Meng Q, Zhao Y, Zheng C. When 3D genome technology meets viral infection, including SARS-CoV-2. J Med Virol 2022; 94:5627-5639. [PMID: 35916043 PMCID: PMC9538846 DOI: 10.1002/jmv.28040] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/09/2022] [Accepted: 07/30/2022] [Indexed: 01/06/2023]
Abstract
Mammalian chromosomes undergo varying degrees of compression to form three-dimensional genome structures. These three-dimensional structures undergo dynamic and precise chromatin interactions to achieve precise spatial and temporal regulation of gene expression. Most eukaryotic DNA viruses can invade their genomes into the nucleus. However, it is still poorly understood how the viral genome is precisely positioned after entering the host cell nucleus to find the most suitable location and whether it can specifically interact with the host genome to hijack the host transcriptional factories or even integrate into the host genome to complete its transcription and replication rapidly. Chromosome conformation capture technology can reveal long-range chromatin interactions between different chromosomal sites in the nucleus, potentially providing a reference for viral DNA-host chromatin interactions. This review summarized the research progress on the three-dimensional interaction between virus and host genome and the impact of virus integration into the host genome on gene transcription regulation, aiming to provide new insights into chromatin interaction and viral gene transcription regulation, laying the foundation for the treatment of infectious diseases.
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Affiliation(s)
- Weizheng Liang
- Central LaboratoryThe First Affiliated Hospital of Hebei North UniversityZhangjiakouChina
- Department of Immunology, School of Basic Medical SciencesFujian Medical UniversityFuzhouChina
| | - Shuangqing Wang
- Department of NeurologyShenzhen University General Hospital, Shenzhen UniversityShenzhen, Guangdong ProvinceChina
| | - Hao Wang
- Department of Obstetrics and GynecologyShenzhen University General HospitalShenzhen, GuangdongChina
| | - Xiushen Li
- Department of Obstetrics and GynecologyShenzhen University General HospitalShenzhen, GuangdongChina
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical EngineeringShenzhen University Health Science CenterShenzhen, GuangdongChina
- Shenzhen Key LaboratoryShenzhen University General HospitalShenzhen, GuangdongChina
| | - Qingxue Meng
- Central LaboratoryThe First Affiliated Hospital of Hebei North UniversityZhangjiakouChina
| | - Yan Zhao
- Department of Mathematics and Computer ScienceFree University BerlinBerlinGermany
| | - Chunfu Zheng
- Department of Immunology, School of Basic Medical SciencesFujian Medical UniversityFuzhouChina
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryAlbertaCanada
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
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22
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Huang Y, Luo J, Jing R, Li M. Multi-model predictive analysis of RNA solvent accessibility based on modified residual attention mechanism. Brief Bioinform 2022; 23:6775603. [PMID: 36305428 DOI: 10.1093/bib/bbac470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/09/2022] [Accepted: 09/30/2022] [Indexed: 12/14/2022] Open
Abstract
Predicting RNA solvent accessibility using only primary sequence data can be regarded as sequence-based prediction work. Currently, the established studies for sequence-based RNA solvent accessibility prediction are limited due to the available number of datasets and black box prediction. To improve these issues, we first expanded the available RNA structures and then developed a sequence-based model using modified attention layers with different receptive fields to conform to the stem-loop structure of RNA chains. We measured the improvement with an extended dataset and further explored the model's interpretability by analysing the model structures, attention values and hyperparameters. Finally, we found that the developed model regarded the pieces of a sequence as templates during the training process. This work will be helpful for researchers who would like to build RNA attribute prediction models using deep learning in the future.
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Affiliation(s)
- Yuyao Huang
- College of Chemistry, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Jiesi Luo
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Runyu Jing
- School of Cyber Science and Engineering, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, Sichuan, 610065, China
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23
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Sharma P, Mondal K, Kumar S, Tamang S, Najar IN, Das S, Thakur N. RNA thermometers in bacteria: Role in thermoregulation. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - GENE REGULATORY MECHANISMS 2022; 1865:194871. [DOI: 10.1016/j.bbagrm.2022.194871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/09/2022] [Accepted: 08/21/2022] [Indexed: 04/09/2023]
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24
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Matarrese MAG, Loppini A, Nicoletti M, Filippi S, Chiodo L. Assessment of tools for RNA secondary structure prediction and extraction: a final-user perspective. J Biomol Struct Dyn 2022:1-20. [DOI: 10.1080/07391102.2022.2116110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Margherita A. G. Matarrese
- Engineering Department, Campus Bio-Medico University of Rome, Rome, Italy
- Jane and John Justin Neurosciences Center, Cook Children’s Health Care System, TX, USA
- Department of Bioengineering, The University of Texas at Arlington, Arlington, TX, USA
| | - Alessandro Loppini
- Engineering Department, Campus Bio-Medico University of Rome, Rome, Italy
- Center for Life Nano & Neuroscience, Italian Institute of Technology, Rome, Italy
| | - Martina Nicoletti
- Engineering Department, Campus Bio-Medico University of Rome, Rome, Italy
- Center for Life Nano & Neuroscience, Italian Institute of Technology, Rome, Italy
| | - Simonetta Filippi
- Engineering Department, Campus Bio-Medico University of Rome, Rome, Italy
| | - Letizia Chiodo
- Engineering Department, Campus Bio-Medico University of Rome, Rome, Italy
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25
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Mukherjee D, Maiti S, Gouda PK, Sharma R, Roy P, Bhattacharyya D. RNABPDB: Molecular Modeling of RNA Structure-From Base Pair Analysis in Crystals to Structure Prediction. Interdiscip Sci 2022; 14:759-774. [PMID: 35705797 DOI: 10.1007/s12539-022-00528-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/05/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
The stable three-dimensional structure of RNA is known to play several important biochemical roles, from post-transcriptional gene regulation to enzymatic action. These structures contain double-helical regions, which often have different types of non-canonical base pairs in addition to Watson-Crick base pairs. Hence, it is important to study their structures from experimentally obtained or even predicted ones, to understand their role, or to develop a drug against the potential targets. Molecular Modeling of RNA double helices containing non-canonical base pairs is a difficult process, particularly due to the unavailability of structural features of non-Watson-Crick base pairs. Here we show a composite web-server with an associated database that allows one to generate the structure of RNA double helix containing non-canonical base pairs using consensus parameters obtained from the database. The database classification is followed by an evaluation of the central tendency of the structural parameters as well as a quantitative estimation of interaction strengths. These parameters are used to construct three-dimensional structures of double helices composed of Watson-Crick and/or non-canonical base pairs. Our benchmark study to regenerate double-helical fragments of many experimentally derived RNA structures indicate very high accuracy. This composite server is expected to be highly useful in understanding functions of various pre-miRNA by modeling structures of the molecules and estimating binding efficiency. The database can be accessed from http://hdrnas.saha.ac.in/rnabpdb .
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Affiliation(s)
- Debasish Mukherjee
- Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India.
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Satyabrata Maiti
- Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
- Homi Bhaba National Institute, Anushaktinagar, Mumbai, 400094, India
| | - Prasanta Kumar Gouda
- Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
| | - Richa Sharma
- Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
| | - Parthajit Roy
- Department of Computer Science, The University of Burdwan, Golapbag, Burdwan, 713104, India
| | - Dhananjay Bhattacharyya
- Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
- Homi Bhaba National Institute, Anushaktinagar, Mumbai, 400094, India
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26
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Gumna J, Antczak M, Adamiak RW, Bujnicki JM, Chen SJ, Ding F, Ghosh P, Li J, Mukherjee S, Nithin C, Pachulska-Wieczorek K, Ponce-Salvatierra A, Popenda M, Sarzynska J, Wirecki T, Zhang D, Zhang S, Zok T, Westhof E, Miao Z, Szachniuk M, Rybarczyk A. Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models. Int J Mol Sci 2022; 23:ijms23179630. [PMID: 36077037 PMCID: PMC9455975 DOI: 10.3390/ijms23179630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 01/19/2023] Open
Abstract
RNA is a unique biomolecule that is involved in a variety of fundamental biological functions, all of which depend solely on its structure and dynamics. Since the experimental determination of crystal RNA structures is laborious, computational 3D structure prediction methods are experiencing an ongoing and thriving development. Such methods can lead to many models; thus, it is necessary to build comparisons and extract common structural motifs for further medical or biological studies. Here, we introduce a computational pipeline dedicated to reference-free high-throughput comparative analysis of 3D RNA structures. We show its application in the RNA-Puzzles challenge, in which five participating groups attempted to predict the three-dimensional structures of 5'- and 3'-untranslated regions (UTRs) of the SARS-CoV-2 genome. We report the results of this puzzle and discuss the structural motifs obtained from the analysis. All simulated models and tools incorporated into the pipeline are open to scientific and academic use.
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Affiliation(s)
- Julita Gumna
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Maciej Antczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Ryszard W. Adamiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Janusz M. Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Pritha Ghosh
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Jun Li
- Department of Physics, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Sunandan Mukherjee
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Chandran Nithin
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
- Laboratory of Computational Biology, Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02-089 Warsaw, Poland
| | | | - Almudena Ponce-Salvatierra
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Mariusz Popenda
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Tomasz Wirecki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Dong Zhang
- Department of Physics, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Sicheng Zhang
- Department of Physics, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Tomasz Zok
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Eric Westhof
- Architecture et Réactivité de l’ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg, France
| | - Zhichao Miao
- Translational Research Institute of Brain and Brain-Like Intelligence, Department of Anesthesiology, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Shanghai 200081, China
- Correspondence: (Z.M.); (A.R.)
| | - Marta Szachniuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Agnieszka Rybarczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
- Correspondence: (Z.M.); (A.R.)
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27
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Ma H, Wen H, Xue Z, Li G, Zhang Z. RNANetMotif: Identifying sequence-structure RNA network motifs in RNA-protein binding sites. PLoS Comput Biol 2022; 18:e1010293. [PMID: 35819951 PMCID: PMC9275694 DOI: 10.1371/journal.pcbi.1010293] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 06/09/2022] [Indexed: 11/19/2022] Open
Abstract
RNA molecules can adopt stable secondary and tertiary structures, which are essential in mediating physical interactions with other partners such as RNA binding proteins (RBPs) and in carrying out their cellular functions. In vivo and in vitro experiments such as RNAcompete and eCLIP have revealed in vitro binding preferences of RBPs to RNA oligomers and in vivo binding sites in cells. Analysis of these binding data showed that the structure properties of the RNAs in these binding sites are important determinants of the binding events; however, it has been a challenge to incorporate the structure information into an interpretable model. Here we describe a new approach, RNANetMotif, which takes predicted secondary structure of thousands of RNA sequences bound by an RBP as input and uses a graph theory approach to recognize enriched subgraphs. These enriched subgraphs are in essence shared sequence-structure elements that are important in RBP-RNA binding. To validate our approach, we performed RNA structure modeling via coarse-grained molecular dynamics folding simulations for selected 4 RBPs, and RNA-protein docking for LIN28B. The simulation results, e.g., solvent accessibility and energetics, further support the biological relevance of the discovered network subgraphs. RNA binding proteins (RBPs) regulate every aspect of RNA biology, including splicing, translation, transportation, and degradation. High-throughput technologies such as eCLIP have identified thousands of binding sites for a given RBP throughout the genome. It has been shown by earlier studies that, in addition to nucleotide sequences, the structure and conformation of RNAs also play important role in RBP-RNA interactions. Analogous to protein-protein interactions or protein-DNA interactions, it is likely that there exist intrinsic sequence-structure motifs common to these RNAs that underlie their binding specificity to specific RBPs. It is known that RNAs form energetically favorable secondary structures, which can be represented as graphs, with nucleotides being nodes and backbone covalent bonds and base-pairing hydrogen bonds representing edges. We hypothesize that these graphs can be mined by graph theory approaches to identify sequence-structure motifs as enriched sub-graphs. In this article, we described the details of this approach, termed RNANetMotif and associated new concepts, namely EKS (Extended K-mer Subgraph) and GraphK graph algorithm. To test the utility of our approach, we conducted 3D structure modeling of selected RNA sequences through molecular dynamics (MD) folding simulation and evaluated the significance of the discovered RNA motifs by comparing their spatial exposure with other regions on the RNA. We believe that this approach has the novelty of treating the RNA sequence as a graph and RBP binding sites as enriched subgraph, which has broader applications beyond RBP-RNA interactions.
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Affiliation(s)
- Hongli Ma
- Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, China
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- School of Mathematics, Shandong University, Jinan, China
| | - Han Wen
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Zhiyuan Xue
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China
| | - Guojun Li
- Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, China
- School of Mathematics, Shandong University, Jinan, China
- School of Mathematical Science, Liaocheng University, Liaocheng, China
| | - Zhaolei Zhang
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
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Wiedemann J, Kaczor J, Milostan M, Zok T, Blazewicz J, Szachniuk M, Antczak M. RNAloops: a database of RNA multiloops. Bioinformatics 2022; 38:4200-4205. [PMID: 35809063 PMCID: PMC9438955 DOI: 10.1093/bioinformatics/btac484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/26/2022] [Accepted: 07/06/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Knowledge of the 3D structure of RNA supports discovering its functions and is crucial for designing drugs and modern therapeutic solutions. Thus, much attention is devoted to experimental determination and computational prediction targeting the global fold of RNA and its local substructures. The latter include multi-branched loops-functionally significant elements that highly affect the spatial shape of the entire molecule. Unfortunately, their computational modeling constitutes a weak point of structural bioinformatics. A remedy for this is in collecting these motifs and analyzing their features. RESULTS RNAloops is a self-updating database that stores multi-branched loops identified in the PDB-deposited RNA structures. A description of each loop includes angular data-planar and Euler angles computed between pairs of adjacent helices to allow studying their mutual arrangement in space. The system enables search and analysis of multiloops, presents their structure details numerically and visually, and computes data statistics. AVAILABILITY AND IMPLEMENTATION RNAloops is freely accessible at https://rnaloops.cs.put.poznan.pl. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jakub Wiedemann
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Jacek Kaczor
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Maciej Milostan
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland,Poznan Supercomputing and Networking Center, 61-131 Poznan, Poland
| | - Tomasz Zok
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland,Poznan Supercomputing and Networking Center, 61-131 Poznan, Poland
| | - Jacek Blazewicz
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland,Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
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Li X, Bhullar AS, Binzel DW, Guo P. The dynamic, motile and deformative properties of RNA nanoparticles facilitate the third milestone of drug development. Adv Drug Deliv Rev 2022; 186:114316. [PMID: 35526663 DOI: 10.1016/j.addr.2022.114316] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/25/2022] [Accepted: 04/29/2022] [Indexed: 12/13/2022]
Abstract
Besides mRNA, rRNA, and tRNA, cells contain many other noncoding RNA that display critical roles in the regulation of cellular functions. Human genome sequencing revealed that the majority of non-protein-coding DNA actually codes for non-coding RNAs. The dynamic nature of RNA results in its motile and deformative behavior. These conformational transitions such as the change of base-pairing, breathing within complemented strands, and pseudoknot formation at the 2D level as well as the induced-fit and conformational capture at the 3D level are important for their biological functions including regulation, translation, and catalysis. The dynamic, motile and catalytic activity has led to a belief that RNA is the origin of life. We have recently reported that the deformative property of RNA nanoparticles enhances their penetration through the leaky blood vessel of cancers which leads to highly efficient tumor accumulation. This special deformative property also enables RNA nanoparticles to pass the glomerulus, overcoming the filtration size limit, resulting in fast renal excretion and rapid body clearance, thus low or no toxicity. The biodistribution of RNA nanoparticles can be further improved by the incorporation of ligands for cancer targeting. In addition to the favorable biodistribution profiles, RNA nanoparticles possess other properties including self-assembly, negative charge, programmability, and multivalency; making it a great material for pharmaceutical applications. The intrinsic negative charge of RNA nanoparticles decreases the toxicity of drugs by preventing nonspecific binding to the negative charged cell membrane and enhancing the solubility of hydrophobic drugs. The polyvalent property of RNA nanoparticles allows the multi-functionalization which can apply to overcome drug resistance. This review focuses on the summary of these unique properties of RNA nanoparticles, which describes the mechanism of RNA dynamic, motile and deformative properties, and elucidates and prepares to welcome the RNA therapeutics as the third milestone in pharmaceutical drug development.
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Affiliation(s)
- Xin Li
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Abhjeet S Bhullar
- Interdisciplinary Biophysics Graduate Program, College of Art and Science, The Ohio State University, Columbus, OH 43210, United States
| | - Daniel W Binzel
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States.
| | - Peixuan Guo
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, United States; James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, United States; College of Medicine, The Ohio State University, Columbus, OH 43210, United States.
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30
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Giarimoglou N, Kouvela A, Patsi I, Zhang J, Stamatopoulou V, Stathopoulos C. Lineage-specific insertions in T-box riboswitches modulate antibiotic binding and action. Nucleic Acids Res 2022; 50:5834-5849. [PMID: 35580054 PMCID: PMC9177973 DOI: 10.1093/nar/gkac359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/21/2022] [Accepted: 05/11/2022] [Indexed: 01/27/2023] Open
Abstract
T-box riboswitches (T-boxes) are essential RNA regulatory elements with a remarkable structural diversity, especially among bacterial pathogens. In staphylococci, all glyS T-boxes synchronize glycine supply during synthesis of nascent polypeptides and cell wall formation and are characterized by a conserved and unique insertion in their antiterminator/terminator domain, termed stem Sa. Interestingly, in Staphylococcus aureus the stem Sa can accommodate binding of specific antibiotics, which in turn induce robust and diverse effects on T-box-mediated transcription. In the present study, domain swap mutagenesis and probing analysis were performed to decipher the role of stem Sa. Deletion of stem Sa significantly reduces both the S. aureus glyS T-box-mediated transcription readthrough levels and the ability to discriminate among tRNAGly isoacceptors, both in vitro and in vivo. Moreover, the deletion inverted the previously reported stimulatory effects of specific antibiotics. Interestingly, stem Sa insertion in the terminator/antiterminator domain of Geobacillus kaustophilus glyS T-box, which lacks this domain, resulted in elevated transcription in the presence of tigecycline and facilitated discrimination among proteinogenic and nonproteinogenic tRNAGly isoacceptors. Overall, stem Sa represents a lineage-specific structural feature required for efficient staphylococcal glyS T-box-mediated transcription and it could serve as a species-selective druggable target through its ability to modulate antibiotic binding.
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Affiliation(s)
- Nikoleta Giarimoglou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Adamantia Kouvela
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Ioanna Patsi
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
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From single-omics to interactomics: How can ligand-induced perturbations modulate single-cell phenotypes? ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 131:45-83. [PMID: 35871896 DOI: 10.1016/bs.apcsb.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Cells suffer from perturbations by different stimuli, which, consequently, rise to individual alterations in their profile and function that may end up affecting the tissue as a whole. This is no different if we consider the effect of a therapeutic agent on a biological system. As cells are exposed to external ligands their profile can change at different single-omics levels. Detecting how these changes take place through different sequencing technologies is key to a better understanding of the effects of therapeutic agents. Single-cell RNA-sequencing stands out as one of the most common approaches for cell profiling and perturbation analysis. As a result, single-cell transcriptomics data can be integrated with other omics data sources, such as proteomics and epigenomics data, to clarify the perturbation effects and mechanism at the cell level. Appropriate computational tools are key to process and integrate the available information. This chapter focuses on the recent advances on ligand-induced perturbation and single-cell omics computational tools and algorithms, their current limitations, and how the deluge of data can be used to improve the current process of drug research and development.
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32
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Solayman M, Litfin T, Singh J, Paliwal K, Zhou Y, Zhan J. Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives. Brief Bioinform 2022; 23:6554125. [PMID: 35348613 PMCID: PMC9116373 DOI: 10.1093/bib/bbac112] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/30/2022] Open
Abstract
Characterizing RNA structures and functions have mostly been focused on 2D, secondary and 3D, tertiary structures. Recent advances in experimental and computational techniques for probing or predicting RNA solvent accessibility make this 1D representation of tertiary structures an increasingly attractive feature to explore. Here, we provide a survey of these recent developments, which indicate the emergence of solvent accessibility as a simple 1D property, adding to secondary and tertiary structures for investigating complex structure–function relations of RNAs.
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Affiliation(s)
- Md Solayman
- Institute for Glycomics, Griffith University, Parklands Dr. Southport, QLD 4222, Australia
| | - Thomas Litfin
- Institute for Glycomics, Griffith University, Parklands Dr. Southport, QLD 4222, Australia
| | - Jaswinder Singh
- Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University, Brisbane, QLD 4111, Australia
| | - Kuldip Paliwal
- Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University, Brisbane, QLD 4111, Australia
| | - Yaoqi Zhou
- Institute for Glycomics, Griffith University, Parklands Dr. Southport, QLD 4222, Australia.,Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.,Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Jian Zhan
- Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
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Olson SW, Turner AMW, Arney JW, Saleem I, Weidmann CA, Margolis DM, Weeks KM, Mustoe AM. Discovery of a large-scale, cell-state-responsive allosteric switch in the 7SK RNA using DANCE-MaP. Mol Cell 2022; 82:1708-1723.e10. [PMID: 35320755 PMCID: PMC9081252 DOI: 10.1016/j.molcel.2022.02.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/29/2021] [Accepted: 02/02/2022] [Indexed: 12/17/2022]
Abstract
7SK is a conserved noncoding RNA that regulates transcription by sequestering the transcription factor P-TEFb. 7SK function entails complex changes in RNA structure, but characterizing RNA dynamics in cells remains an unsolved challenge. We developed a single-molecule chemical probing strategy, DANCE-MaP (deconvolution and annotation of ribonucleic conformational ensembles), that defines per-nucleotide reactivity, direct base pairing interactions, tertiary interactions, and thermodynamic populations for each state in RNA structural ensembles from a single experiment. DANCE-MaP reveals that 7SK RNA encodes a large-scale structural switch that couples dissolution of the P-TEFb binding site to structural remodeling at distal release factor binding sites. The 7SK structural equilibrium shifts in response to cell growth and stress and can be targeted to modulate expression of P-TEFbresponsive genes. Our study reveals that RNA structural dynamics underlie 7SK function as an integrator of diverse cellular signals to control transcription and establishes the power of DANCE-MaP to define RNA dynamics in cells.
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Affiliation(s)
- Samuel W Olson
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Anne-Marie W Turner
- Department of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; UNC HIV Cure Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - J Winston Arney
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Irfana Saleem
- Verna and Marrs McClean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, TX 77030, USA
| | - Chase A Weidmann
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - David M Margolis
- Department of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; UNC HIV Cure Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA.
| | - Anthony M Mustoe
- Verna and Marrs McClean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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34
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He W, Henning-Knechtel A, Kirmizialtin S. Visualizing RNA Structures by SAXS-Driven MD Simulations. FRONTIERS IN BIOINFORMATICS 2022; 2:781949. [PMID: 36304317 PMCID: PMC9580860 DOI: 10.3389/fbinf.2022.781949] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/04/2022] [Indexed: 12/26/2022] Open
Abstract
The biological role of biomolecules is intimately linked to their structural dynamics. Experimental or computational techniques alone are often insufficient to determine accurate structural ensembles in atomic detail. We use all-atom molecular dynamics (MD) simulations and couple it to small-angle X-ray scattering (SAXS) experiments to resolve the structural dynamics of RNA molecules. To accomplish this task, we utilize a set of re-weighting and biasing techniques tailored for RNA molecules. To showcase our approach, we study two RNA molecules: a riboswitch that shows structural variations upon ligand binding, and a two-way junction RNA that displays structural heterogeneity and sensitivity to salt conditions. Integration of MD simulations and experiments allows the accurate construction of conformational ensembles of RNA molecules. We observe a dynamic change of the SAM-I riboswitch conformations depending on its binding partners. The binding of SAM and Mg2+ cations stabilizes the compact state. The absence of Mg2+ or SAM leads to the loss of tertiary contacts, resulting in a dramatic expansion of the riboswitch conformations. The sensitivity of RNA structures to the ionic strength demonstrates itself in the helix junction helix (HJH). The HJH shows non-monotonic compaction as the ionic strength increases. The physics-based picture derived from the experimentally guided MD simulations allows biophysical characterization of RNA molecules. All in all, SAXS-guided MD simulations offer great prospects for studying RNA structural dynamics.
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Affiliation(s)
- Weiwei He
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department of Chemistry, New York University, New York, NY, United States
| | - Anja Henning-Knechtel
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Serdal Kirmizialtin
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- *Correspondence: Serdal Kirmizialtin,
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35
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Przanowska RK, Weidmann CA, Saha S, Cichewicz MA, Jensen KN, Przanowski P, Irving PS, Janes KA, Guertin MJ, Weeks KM, Dutta A. Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors. Cell Rep 2022; 38:110361. [PMID: 35172143 PMCID: PMC8937029 DOI: 10.1016/j.celrep.2022.110361] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/03/2021] [Accepted: 01/19/2022] [Indexed: 12/27/2022] Open
Abstract
Many lncRNAs have been discovered using transcriptomic data; however, it is unclear what fraction of lncRNAs is functional and what structural properties affect their phenotype. MUNC lncRNA (also known as DRReRNA) acts as an enhancer RNA for the Myod1 gene in cis and stimulates the expression of other promyogenic genes in trans by recruiting the cohesin complex. Here, experimental probing of the RNA structure revealed that MUNC contains multiple structural domains not detected by prediction algorithms in the absence of experimental information. We show that these specific and structurally distinct domains are required for induction of promyogenic genes, for binding genomic sites and gene expression regulation, and for binding the cohesin complex. Myod1 induction and cohesin interaction comprise only a subset of MUNC phenotype. Our study reveals unexpectedly complex, structure-driven functions for the MUNC lncRNA and emphasizes the importance of experimentally determined structures for understanding structure-function relationships in lncRNAs.
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Affiliation(s)
- Roza K Przanowska
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Biomedical Engineering, University of Virginia School of Engineering, Charlottesville, VA 22908, USA
| | - Chase A Weidmann
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biological Chemistry and Center for RNA Biomedicine, University of Michigan Medical School, Ann Arbor, MI 48103, USA
| | - Shekhar Saha
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Magdalena A Cichewicz
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Kate N Jensen
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Piotr Przanowski
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Biomedical Engineering, University of Virginia School of Engineering, Charlottesville, VA 22908, USA
| | - Patrick S Irving
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kevin A Janes
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Biomedical Engineering, University of Virginia School of Engineering, Charlottesville, VA 22908, USA
| | - Michael J Guertin
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut, Farmington, CT 06030, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Genetics, University of Alabama, Birmingham, AL 35233, USA.
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Carrascoza F, Antczak M, Miao Z, Westhof E, Szachniuk M. Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions. RNA (NEW YORK, N.Y.) 2022; 28:250-262. [PMID: 34819324 PMCID: PMC8906551 DOI: 10.1261/rna.078685.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
In silico prediction is a well-established approach to derive a general shape of an RNA molecule based on its sequence or secondary structure. This paper reports an analysis of the stereochemical quality of the RNA three-dimensional models predicted using dedicated computer programs. The stereochemistry of 1052 RNA 3D structures, including 1030 models predicted by fully automated and human-guided approaches within 22 RNA-Puzzles challenges and reference structures, is analyzed. The evaluation is based on standards of RNA stereochemistry that the Protein Data Bank requires from deposited experimental structures. Deviations from standard bond lengths and angles, planarity, or chirality are quantified. A reduction in the number of such deviations should help in the improvement of RNA 3D structure modeling approaches.
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Affiliation(s)
- Francisco Carrascoza
- Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, 60-965 Poznan, Poland
| | - Maciej Antczak
- Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, 60-965 Poznan, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Zhichao Miao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
- Translational Research Institute of Brain and Brain-Like Intelligence, Department of Anesthesiology, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai 200081, China
| | - Eric Westhof
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire CNRS, Architecture et Réactivité de l'ARN, 67084 Strasbourg, France
| | - Marta Szachniuk
- Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, 60-965 Poznan, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
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Zeke A, Schád É, Horváth T, Abukhairan R, Szabó B, Tantos A. Deep structural insights into RNA-binding disordered protein regions. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1714. [PMID: 35098694 PMCID: PMC9539567 DOI: 10.1002/wrna.1714] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/22/2021] [Accepted: 01/07/2022] [Indexed: 12/11/2022]
Abstract
Recent efforts to identify RNA binding proteins in various organisms and cellular contexts have yielded a large collection of proteins that are capable of RNA binding in the absence of conventional RNA recognition domains. Many of the recently identified RNA interaction motifs fall into intrinsically disordered protein regions (IDRs). While the recognition mode and specificity of globular RNA binding elements have been thoroughly investigated and described, much less is known about the way IDRs can recognize their RNA partners. Our aim was to summarize the current state of structural knowledge on the RNA binding modes of disordered protein regions and to propose a classification system based on their sequential and structural properties. Through a detailed structural analysis of the complexes that contain disordered protein regions binding to RNA, we found two major binding modes that represent different recognition strategies and, most likely, functions. We compared these examples with DNA binding disordered proteins and found key differences stemming from the nucleic acids as well as similar binding strategies, implying a broader substrate acceptance by these proteins. Due to the very limited number of known structures, we integrated molecular dynamics simulations in our study, whose results support the proposed structural preferences of specific RNA‐binding IDRs. To broaden the scope of our review, we included a brief analysis of RNA‐binding small molecules and compared their structural characteristics and RNA recognition strategies to the RNA‐binding IDRs. This article is categorized under:RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Interactions with Proteins and Other Molecules > Protein–RNA Recognition RNA Interactions with Proteins and Other Molecules > Small Molecule–RNA Interactions
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Affiliation(s)
- András Zeke
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Éva Schád
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Tamás Horváth
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Rawan Abukhairan
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Beáta Szabó
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
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Poblete S, Božič A, Kanduč M, Podgornik R, Guzman HV. RNA Secondary Structures Regulate Adsorption of Fragments onto Flat Substrates. ACS OMEGA 2021; 6:32823-32831. [PMID: 34901632 PMCID: PMC8655909 DOI: 10.1021/acsomega.1c04774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/04/2021] [Indexed: 06/14/2023]
Abstract
RNA is a functionally rich molecule with multilevel, hierarchical structures whose role in the adsorption to molecular substrates is only beginning to be elucidated. Here, we introduce a multiscale simulation approach that combines a tractable coarse-grained RNA structural model with an interaction potential of a structureless flat adsorbing substrate. Within this approach, we study the specific role of stem-hairpin and multibranch RNA secondary structure motifs on its adsorption phenomenology. Our findings identify a dual regime of adsorption for short RNA fragments with and without the secondary structure and underline the adsorption efficiency in both cases as a function of the surface interaction strength. The observed behavior results from an interplay between the number of contacts formed at the surface and the conformational entropy of the RNA molecule. The adsorption phenomenology of RNA seems to persist also for much longer RNAs as qualitatively observed by comparing the trends of our simulations with a theoretical approach based on an ideal semiflexible polymer chain.
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Affiliation(s)
- Simón Poblete
- Instituto
de Ciencias Físicas y Matemáticas, Universidad Austral de Chile, Valdivia 5091000, Chile
- Computational
Biology Lab, Fundación Ciencia &
Vida, Santiago 7780272, Chile
| | - Anže Božič
- Department
of Theoretical Physics, Jožef Stefan
Institute, SI-1000 Ljubljana, Slovenia
| | - Matej Kanduč
- Department
of Theoretical Physics, Jožef Stefan
Institute, SI-1000 Ljubljana, Slovenia
| | - Rudolf Podgornik
- School
of Physical Sciences and Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute
of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Wenzhou
Institute of the University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- Department
of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Horacio V. Guzman
- Department
of Theoretical Physics, Jožef Stefan
Institute, SI-1000 Ljubljana, Slovenia
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Poblete S, Guzman HV. Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models. Viruses 2021; 13:1555. [PMID: 34452420 PMCID: PMC8402887 DOI: 10.3390/v13081555] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
Three-dimensional RNA domain reconstruction is important for the assembly, disassembly and delivery functionalities of a packed proteinaceus capsid. However, to date, the self-association of RNA molecules is still an open problem. Recent chemical probing reports provide, with high reliability, the secondary structure of diverse RNA ensembles, such as those of viral genomes. Here, we present a method for reconstructing the complete 3D structure of RNA genomes, which combines a coarse-grained model with a subdomain composition scheme to obtain the entire genome inside proteinaceus capsids based on secondary structures from experimental techniques. Despite the amount of sampling involved in the folded and also unfolded RNA molecules, advanced microscope techniques can provide points of anchoring, which enhance our model to include interactions between capsid pentamers and RNA subdomains. To test our method, we tackle the satellite tobacco mosaic virus (STMV) genome, which has been widely studied by both experimental and computational communities. We provide not only a methodology to structurally analyze the tertiary conformations of the RNA genome inside capsids, but a flexible platform that allows the easy implementation of features/descriptors coming from both theoretical and experimental approaches.
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Affiliation(s)
- Simón Poblete
- Instituto de Ciencias Físicas y Matemáticas, Universidad Austral de Chile, Valdivia 5091000, Chile
- Chile and Computational Biology Lab, Fundación Ciencia & Vida, Santiago 7780272, Chile
| | - Horacio V. Guzman
- Department of Theoretical Physics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
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40
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Li J, Chen SJ. RNA 3D Structure Prediction Using Coarse-Grained Models. Front Mol Biosci 2021; 8:720937. [PMID: 34277713 PMCID: PMC8283274 DOI: 10.3389/fmolb.2021.720937] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 06/17/2021] [Indexed: 12/12/2022] Open
Abstract
The three-dimensional (3D) structures of Ribonucleic acid (RNA) molecules are essential to understanding their various and important biological functions. However, experimental determination of the atomic structures is laborious and technically difficult. The large gap between the number of sequences and the experimentally determined structures enables the thriving development of computational approaches to modeling RNAs. However, computational methods based on all-atom simulations are intractable for large RNA systems, which demand long time simulations. Facing such a challenge, many coarse-grained (CG) models have been developed. Here, we provide a review of CG models for modeling RNA 3D structures, compare the performance of the different models, and offer insights into potential future developments.
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Affiliation(s)
| | - Shi-Jie Chen
- Departments of Physics and Biochemistry, and Institute of Data Science and Informatics, University of Missouri, Columbia, MO, United States
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Christy TW, Giannetti CA, Houlihan G, Smola MJ, Rice GM, Wang J, Dokholyan NV, Laederach A, Holliger P, Weeks KM. Direct Mapping of Higher-Order RNA Interactions by SHAPE-JuMP. Biochemistry 2021; 60:1971-1982. [PMID: 34121404 PMCID: PMC8256721 DOI: 10.1021/acs.biochem.1c00270] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Higher-order structure governs function for many RNAs. However, discerning this structure for large RNA molecules in solution is an unresolved challenge. Here, we present SHAPE-JuMP (selective 2'-hydroxyl acylation analyzed by primer extension and juxtaposed merged pairs) to interrogate through-space RNA tertiary interactions. A bifunctional small molecule is used to chemically link proximal nucleotides in an RNA structure. The RNA cross-link site is then encoded into complementary DNA (cDNA) in a single, direct step using an engineered reverse transcriptase that "jumps" across cross-linked nucleotides. The resulting cDNAs contain a deletion relative to the native RNA sequence, which can be detected by sequencing, that indicates the sites of cross-linked nucleotides. SHAPE-JuMP measures RNA tertiary structure proximity concisely across large RNA molecules at nanometer resolution. SHAPE-JuMP is especially effective at measuring interactions in multihelix junctions and loop-to-helix packing, enables modeling of the global fold for RNAs up to several hundred nucleotides in length, facilitates ranking of structural models by consistency with through-space restraints, and is poised to enable solution-phase structural interrogation and modeling of complex RNAs.
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Affiliation(s)
- Thomas W. Christy
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Catherine A. Giannetti
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - Gillian Houlihan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Matthew J. Smola
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - Greggory M. Rice
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - Jian Wang
- Departments of Pharmacology, and Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Nikolay V. Dokholyan
- Departments of Pharmacology, and Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, PA 17033, USA
- Departments of Chemistry, and Biomedical Engineering, Pennsylvania State University, University Park, PA 16802
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
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Abstract
RNA lies upstream of nearly all biology and functions as the central conduit of information exchange in all cells. RNA molecules encode information both in their primary sequences and in complex structures that form when an RNA folds back on itself. From the time of discovery of mRNA in the late 1950s until quite recently, we had only a rudimentary understanding of RNA structure across vast regions of most messenger and noncoding RNAs. This deficit is now rapidly being addressed, especially by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry, mutational profiling (MaP), and closely related platform technologies that, collectively, create chemical microscopes for RNA. These technologies make it possible to interrogate RNA structure, quantitatively, at nucleotide resolution, and at large scales, for entire mRNAs, noncoding RNAs, and viral RNA genomes. By applying comprehensive structure probing to diverse problems, we and others are showing that control of biological function mediated by RNA structure is ubiquitous across prokaryotic and eukaryotic organisms.Work over the past decade using SHAPE-based analyses has clarified key principles. First, the method of RNA structure probing matters. SHAPE-MaP, with its direct and one-step readout that probes nearly every nucleotide by reaction at the 2'-hydroxyl, gives a more detailed and accurate readout than alternatives. Second, comprehensive chemical probing is essential. Focusing on fragments of large RNAs or using meta-gene or statistical analyses to compensate for sparse data sets misses critical features and often yields structure models with poor predictive power. Finally, every RNA has its own internal structural personality. There are myriad ways in which RNA structure modulates sequence accessibility, protein binding, translation, splice-site choice, phase separation, and other fundamental biological processes. In essentially every instance where we have applied rigorous and quantitative SHAPE technologies to study RNA structure-function interrelationships, new insights regarding biological regulatory mechanisms have emerged. RNA elements with more complex higher-order structures appear more likely to contain high-information-content clefts and pockets that bind small molecules, broadly informing a vigorous field of RNA-targeted drug discovery.The broad implications of this collective work are twofold. First, it is long past time to abandon depiction of large RNAs as simple noodle-like or gently flowing molecules. Instead, we need to emphasize that nearly all RNAs are punctuated with distinctive internal structures, a subset of which modulate function in profound ways. Second, structure probing should be an integral component of any effort that seeks to understand the functional nexuses and biological roles of large RNAs.
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Affiliation(s)
- Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, United States
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An RNA-centric historical narrative around the Protein Data Bank. J Biol Chem 2021; 296:100555. [PMID: 33744291 PMCID: PMC8080527 DOI: 10.1016/j.jbc.2021.100555] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/17/2021] [Accepted: 03/16/2021] [Indexed: 01/06/2023] Open
Abstract
Some of the amazing contributions brought to the scientific community by the Protein Data Bank (PDB) are described. The focus is on nucleic acid structures with a bias toward RNA. The evolution and key roles in science of the PDB and other structural databases for nucleic acids illustrate how small initial ideas can become huge and indispensable resources with the unflinching willingness of scientists to cooperate globally. The progress in the understanding of the molecular interactions driving RNA architectures followed the rapid increase in RNA structures in the PDB. That increase was consecutive to improvements in chemical synthesis and purification of RNA molecules, as well as in biophysical methods for structure determination and computer technology. The RNA modeling efforts from the early beginnings are also described together with their links to the state of structural knowledge and technological development. Structures of RNA and of its assemblies are physical objects, which, together with genomic data, allow us to integrate present-day biological functions and the historical evolution in all living species on earth.
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