201
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Li P, Shi R, Zhang QC. icSHAPE-pipe: A comprehensive toolkit for icSHAPE data analysis and evaluation. Methods 2019; 178:96-103. [PMID: 31606387 DOI: 10.1016/j.ymeth.2019.09.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 09/04/2019] [Accepted: 09/30/2019] [Indexed: 01/25/2023] Open
Abstract
RNA molecules have the intrinsic ability to fold into complex structures that are important in regulating many biological processes, including transcription, translation, processing and degradation. However, our knowledge for RNA structures remains very limited. Previously, we developed icSHAPE, a high-throughput method to probe single-stranded RNA nucleotide in cells. To recover the structural profile of an RNA or a transcript by icSHAPE, it is essential to accurately calculate an icSHAPE reactivity as the RNA structure score for each base. Here, we present icSHAPE-pipe, a comprehensive toolkit for the analysis of RNA structure sequencing data obtained from icSHAPE experiments. Compared to the original icSHAPE data processing protocol, icSHAPE-pipe calculates RNA structural information with higher accuracy and achieves higher coverage of the transcriptome. In addition, icSHAPE-pipe can perform quality control, and generate reports on sequencing data and the statistics of results. In sum, icSHAPE-pipe provides a convenient workflow for researchers to analyze RNA structural data from icSHAPE sequencing experiments.
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Affiliation(s)
- Pan Li
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Ruoyao Shi
- BioKnow Health Informatics Lab, College of Life Science, Jilin University, Changchun 130012, China.
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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202
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Owens MC, Clark SC, Yankey A, Somarowthu S. Identifying Structural Domains and Conserved Regions in the Long Non-Coding RNA lncTCF7. Int J Mol Sci 2019; 20:ijms20194770. [PMID: 31561429 PMCID: PMC6801803 DOI: 10.3390/ijms20194770] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNA (lncRNA) biology is a rapidly growing area of study. Thousands of lncRNAs are implicated as key players in cellular pathways and cancer biology. However, the structure–function relationships of these novel biomolecules are not well understood. Recent structural studies suggest that lncRNAs contain modular structural domains, which play a crucial role in their function. Here, we hypothesized that such structural domains exist in lncTCF7, a conserved lncRNA implicated in the development and progression of several cancers. To understand the structure–function relationship of lncTCF7, we characterized its secondary structure using chemical probing methods. Our model revealed structural domains and conserved regions in lncTCF7. One of the modular domains identified here coincides with a known protein-interacting domain. The model reported herein is, to our knowledge, the first structural model of lncTCF7 and thus will serve to direct future studies that will provide fundamental insights into the function of this lncRNA.
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Affiliation(s)
- Michael C Owens
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19101, USA.
| | - Sean C Clark
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19101, USA.
| | - Allison Yankey
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19101, USA.
| | - Srinivas Somarowthu
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19101, USA.
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203
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Zhou H, Rauch S, Dai Q, Cui X, Zhang Z, Nachtergaele S, Sepich C, He C, Dickinson BC. Evolution of a reverse transcriptase to map N 1-methyladenosine in human messenger RNA. Nat Methods 2019; 16:1281-1288. [PMID: 31548705 PMCID: PMC6884687 DOI: 10.1038/s41592-019-0550-4] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 08/05/2019] [Indexed: 11/09/2022]
Abstract
Chemical modifications to messenger RNA are increasingly recognized as a critical regulatory layer in the flow of genetic information, but quantitative tools to monitor RNA modifications in a whole-transcriptome and site-specific manner are lacking. Here we describe a versatile platform for directed evolution that rapidly selects for reverse transcriptases that install mutations at sites of a given type of RNA modification during reverse transcription, allowing for site-specific identification of the modification. To develop and validate the platform, we evolved the HIV-1 reverse transcriptase against N1-methyladenosine (m1A). Iterative rounds of selection yielded reverse transcriptases with both robust read-through and high mutation rates at m1A sites. The optimal evolved reverse transcriptase enabled detection of well-characterized m1A sites and revealed hundreds of m1A sites in human mRNA. This work develops and validates the reverse transcriptase evolution platform, and provides new tools, analysis methods and datasets to study m1A biology.
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Affiliation(s)
- Huiqing Zhou
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Simone Rauch
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Qing Dai
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | - Xiaolong Cui
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Zijie Zhang
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | - Sigrid Nachtergaele
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | - Caraline Sepich
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.,University of Chicago Medical Scientist Training Program, Chicago, USA
| | - Chuan He
- Department of Chemistry, University of Chicago, Chicago, IL, USA. .,Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA. .,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA. .,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA.
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204
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Mitchell D, Assmann SM, Bevilacqua PC. Probing RNA structure in vivo. Curr Opin Struct Biol 2019; 59:151-158. [PMID: 31521910 DOI: 10.1016/j.sbi.2019.07.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/26/2019] [Accepted: 07/30/2019] [Indexed: 01/30/2023]
Abstract
RNA structure underpins many essential functions in biology. New chemical reagents and techniques for probing RNA structure in living cells have emerged in recent years. High-throughput, genome-wide techniques such as Structure-seq2 and DMS-MaPseq exploit nucleobase modification by dimethylsulfate (DMS) to obtain complete structuromes, and are applicable to multiple domains of life and conditions. New reagents such as 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC), glyoxal, and nicotinoyl azide (NAz) greatly expand the capabilities of nucleobase probing in cells. Additionally, ribose-targeting reagents in selective 2'-hydroxyl acylation and primer extension (SHAPE) detect RNA flexibility in vivo. These techniques, coupled with crosslinking nucleobases in psoralen analysis of RNA interactions and structures (PARIS), provide new and diverse ways to elucidate RNA secondary and tertiary structure in vivo and genome-wide.
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Affiliation(s)
- David Mitchell
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA; Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Sarah M Assmann
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Philip C Bevilacqua
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA; Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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205
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Martin S, Blankenship C, Rausch JW, Sztuba-Solinska J. Using SHAPE-MaP to probe small molecule-RNA interactions. Methods 2019; 167:105-116. [DOI: 10.1016/j.ymeth.2019.04.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/20/2019] [Accepted: 04/16/2019] [Indexed: 01/14/2023] Open
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206
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Moqtaderi Z, Geisberg JV. Probing In Vivo Structure of Individual mRNA 3' Isoforms Using Dimethyl Sulfate. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2019; 128:e99. [PMID: 31503415 PMCID: PMC6777956 DOI: 10.1002/cpmb.99] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The DMS region extraction and deep sequencing (DREADS) procedure was designed to probe RNA structure in vivo and to link this structural information to specific 3' isoforms. Growing cells are treated with the alkylating agent dimethyl sulfate (DMS), which enters easily into cells and modifies RNA molecules at solvent-exposed A and C residues. RNA is isolated, and sequencing libraries are constructed in a manner that preserves the identities of individual mRNA isoforms arising from alternative cleavage/polyadenylation sites. During the cDNA synthesis step of library construction, the progress of reverse transcriptase (RT) is blocked when it encounters a DMS modification on the RNA, leading to disproportionate cDNA termination adjacent to DMS-modified positions. After paired-end deep sequencing, the downstream end of each sequenced fragment is mapped to a specific cleavage/poly(A) site representing an individual mRNA 3' isoform. The upstream mapped end of the sequenced fragment defines where the RT reaction stopped. Over the population of all sequenced fragments derived from a particular isoform, A and C positions that are overrepresented next to the upstream endpoints in the DMS sample (relative to a parallel untreated control) are inferred to have been DMS modified, and hence solvent exposed. This method thus allows in vivo structural information obtained using DMS to be linked to individual mRNA 3' isoforms. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Zarmik Moqtaderi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Joseph V Geisberg
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
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207
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Zinshteyn B, Chan D, England W, Feng C, Green R, Spitale RC. Assaying RNA structure with LASER-Seq. Nucleic Acids Res 2019; 47:43-55. [PMID: 30476193 PMCID: PMC6326810 DOI: 10.1093/nar/gky1172] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 11/17/2018] [Indexed: 01/06/2023] Open
Abstract
Chemical probing methods are crucial to our understanding of the structure and function of RNA molecules. The majority of chemical methods used to probe RNA structure report on Watson–Crick pairing, but tertiary structure parameters such as solvent accessibility can provide an additional layer of structural information, particularly in RNA-protein complexes. Herein we report the development of Light Activated Structural Examination of RNA by high-throughput sequencing, or LASER-Seq, for measuring RNA structure in cells with deep sequencing. LASER relies on a light-generated nicotinoyl nitrenium ion to form covalent adducts with the C8 position of adenosine and guanosine. Reactivity is governed by the accessibility of C8 to the light-generated probe. We compare structure probing by RT-stop and mutational profiling (MaP), demonstrating that LASER can be integrated with both platforms for RNA structure analyses. We find that LASER reactivity correlates with solvent accessibility across the entire ribosome, and that LASER can be used to rapidly survey for ligand binding sites in an unbiased fashion. LASER has a particular advantage in this last application, as it readily modifies paired nucleotides, enabling the identification of binding sites and conformational changes in highly structured RNA.
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Affiliation(s)
- Boris Zinshteyn
- Department of Molecular Biology and Genetics, Johns Hopkins University. Baltimore, MD 21205, USA
| | - Dalen Chan
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Whitney England
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Chao Feng
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University. Baltimore, MD 21205, USA.,Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA.,Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
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208
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Incarnato D, Morandi E, Simon LM, Oliviero S. RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications. Nucleic Acids Res 2019; 46:e97. [PMID: 29893890 PMCID: PMC6144828 DOI: 10.1093/nar/gky486] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 05/23/2018] [Indexed: 12/24/2022] Open
Abstract
RNA is emerging as a key regulator of a plethora of biological processes. While its study has remained elusive for decades, the recent advent of high-throughput sequencing technologies provided the unique opportunity to develop novel techniques for the study of RNA structure and post-transcriptional modifications. Nonetheless, most of the required downstream bioinformatics analyses steps are not easily reproducible, thus making the application of these techniques a prerogative of few laboratories. Here we introduce RNA Framework, an all-in-one toolkit for the analysis of most NGS-based RNA structure probing and post-transcriptional modification mapping experiments. To prove the extreme versatility of RNA Framework, we applied it to both an in-house generated DMS-MaPseq dataset, and to a series of literature available experiments. Notably, when starting from publicly available datasets, our software easily allows replicating authors' findings. Collectively, RNA Framework provides the most complete and versatile toolkit to date for a rapid and streamlined analysis of the RNA epistructurome. RNA Framework is available for download at: http://www.rnaframework.com.
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Affiliation(s)
- Danny Incarnato
- Italian Institute for Genomic Medicine (IIGM), Via Nizza 52, 10126 Torino, Italy.,Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, Torino, Italy
| | - Edoardo Morandi
- Italian Institute for Genomic Medicine (IIGM), Via Nizza 52, 10126 Torino, Italy.,Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, Torino, Italy
| | - Lisa Marie Simon
- Italian Institute for Genomic Medicine (IIGM), Via Nizza 52, 10126 Torino, Italy.,Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, Torino, Italy
| | - Salvatore Oliviero
- Italian Institute for Genomic Medicine (IIGM), Via Nizza 52, 10126 Torino, Italy.,Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, Torino, Italy
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209
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Simon LM, Morandi E, Luganini A, Gribaudo G, Martinez-Sobrido L, Turner DH, Oliviero S, Incarnato D. In vivo analysis of influenza A mRNA secondary structures identifies critical regulatory motifs. Nucleic Acids Res 2019; 47:7003-7017. [PMID: 31053845 PMCID: PMC6648356 DOI: 10.1093/nar/gkz318] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/15/2019] [Accepted: 04/23/2019] [Indexed: 02/05/2023] Open
Abstract
The influenza A virus (IAV) is a continuous health threat to humans as well as animals due to its recurring epidemics and pandemics. The IAV genome is segmented and the eight negative-sense viral RNAs (vRNAs) are transcribed into positive sense complementary RNAs (cRNAs) and viral messenger RNAs (mRNAs) inside infected host cells. A role for the secondary structure of IAV mRNAs has been hypothesized and debated for many years, but knowledge on the structure mRNAs adopt in vivo is currently missing. Here we solve, for the first time, the in vivo secondary structure of IAV mRNAs in living infected cells. We demonstrate that, compared to the in vitro refolded structure, in vivo IAV mRNAs are less structured but exhibit specific locally stable elements. Moreover, we show that the targeted disruption of these high-confidence structured domains results in an extraordinary attenuation of IAV replicative capacity. Collectively, our data provide the first comprehensive map of the in vivo structural landscape of IAV mRNAs, hence providing the means for the development of new RNA-targeted antivirals.
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Affiliation(s)
- Lisa Marie Simon
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123 Torino, Italy
| | - Edoardo Morandi
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123 Torino, Italy
| | - Anna Luganini
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123 Torino, Italy
| | - Giorgio Gribaudo
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123 Torino, Italy
| | - Luis Martinez-Sobrido
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Douglas H Turner
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, NY 14627, USA
| | - Salvatore Oliviero
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123 Torino, Italy
| | - Danny Incarnato
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123 Torino, Italy
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
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210
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Stark R, Grzelak M, Hadfield J. RNA sequencing: the teenage years. Nat Rev Genet 2019; 20:631-656. [DOI: 10.1038/s41576-019-0150-2] [Citation(s) in RCA: 679] [Impact Index Per Article: 135.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2019] [Indexed: 12/12/2022]
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211
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Abstract
RNA performs and regulates a diverse range of cellular processes, with new functional roles being uncovered at a rapid pace. Interest is growing in how these functions are linked to RNA structures that form in the complex cellular environment. A growing suite of technologies that use advances in RNA structural probes, high-throughput sequencing and new computational approaches to interrogate RNA structure at unprecedented throughput are beginning to provide insights into RNA structures at new spatial, temporal and cellular scales.
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Affiliation(s)
- Eric J Strobel
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Angela M Yu
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Julius B Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
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212
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Shenasa H, Hertel KJ. Combinatorial regulation of alternative splicing. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194392. [PMID: 31276857 DOI: 10.1016/j.bbagrm.2019.06.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 12/23/2022]
Abstract
The generation of protein coding mRNAs from pre-mRNA is a fundamental biological process that is required for gene expression. Alternative pre-mRNA splicing is responsible for much of the transcriptomic and proteomic diversity observed in higher order eukaryotes. Aberrations that disrupt regular alternative splicing patterns are known to cause human diseases, including various cancers. Alternative splicing is a combinatorial process, meaning many factors affect which two splice sites are ligated together. The features that dictate exon inclusion are comprised of splice site strength, intron-exon architecture, RNA secondary structure, splicing regulatory elements, promoter use and transcription speed by RNA polymerase and the presence of post-transcriptional nucleotide modifications. A comprehensive view of all of the factors that influence alternative splicing decisions is necessary to predict splicing outcomes and to understand the molecular basis of disease. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Affiliation(s)
- Hossein Shenasa
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA 92697, United States of America
| | - Klemens J Hertel
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA 92697, United States of America.
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213
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Lin C, Miles WO. Beyond CLIP: advances and opportunities to measure RBP-RNA and RNA-RNA interactions. Nucleic Acids Res 2019; 47:5490-5501. [PMID: 31076772 PMCID: PMC6582316 DOI: 10.1093/nar/gkz295] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 04/08/2019] [Accepted: 04/11/2019] [Indexed: 12/14/2022] Open
Abstract
RNA is an essential player in almost all biological processes, and has an ever-growing number of roles in regulating cellular growth and organization. RNA functions extend far beyond just coding for proteins and RNA has been shown to function in signaling events, chromatin organization and transcriptional regulation. Dissecting how the complex network of RNA-binding proteins (RBPs) and regulatory RNAs interact with their substrates within the cell is a real, but exciting, challenge for the RNA community. Investigating these biological questions has fueled the development of new quantitative technologies to measure how RNA and RBPs interact both locally and on a global scale. In this review, we provide an assessment of available approaches to enable researchers to select the protocol most applicable for their experimental question.
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Affiliation(s)
- Chenyu Lin
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Wayne O Miles
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
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214
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Busan S, Weidmann CA, Sengupta A, Weeks KM. Guidelines for SHAPE Reagent Choice and Detection Strategy for RNA Structure Probing Studies. Biochemistry 2019; 58:2655-2664. [PMID: 31117385 DOI: 10.1021/acs.biochem.8b01218] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chemical probing is an important tool for characterizing the complex folded structures of RNA molecules, many of which play key cellular roles. Electrophilic SHAPE reagents create adducts at the 2'-hydroxyl position on the RNA backbone of flexible ribonucleotides with relatively little dependence on nucleotide identity. Strategies for adduct detection such as mutational profiling (MaP) allow accurate, automated calculation of relative adduct frequencies for each nucleotide in a given RNA or group of RNAs. A number of alternative reagents and adduct detection strategies have been proposed, especially for use in living cells. Here we evaluate five SHAPE reagents: three previously well-validated reagents 1M7 (1-methyl-7-nitroisatoic anhydride), 1M6 (1-methyl-6-nitroisatoic anhydride), and NMIA ( N-methylisatoic anhydride), one more recently proposed NAI (2-methylnicotinic acid imidazolide), and one novel reagent 5NIA (5-nitroisatoic anhydride). We clarify the importance of carefully designed software in reading out SHAPE experiments using massively parallel sequencing approaches. We examine SHAPE modification in living cells in diverse cell lines, compare MaP and reverse transcription-truncation as SHAPE adduct detection strategies, make recommendations for SHAPE reagent choice, and outline areas for future development.
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Affiliation(s)
- Steven Busan
- Department of Chemistry , University of North Carolina , Chapel Hill , North Carolina 27599-3290 , United States
| | - Chase A Weidmann
- Department of Chemistry , University of North Carolina , Chapel Hill , North Carolina 27599-3290 , United States
| | - Arnab Sengupta
- Department of Chemistry , University of North Carolina , Chapel Hill , North Carolina 27599-3290 , United States
| | - Kevin M Weeks
- Department of Chemistry , University of North Carolina , Chapel Hill , North Carolina 27599-3290 , United States
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215
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Yeung PY, Zhao J, Chow EYC, Mou X, Hong H, Chen L, Chan TF, Kwok CK. Systematic evaluation and optimization of the experimental steps in RNA G-quadruplex structure sequencing. Sci Rep 2019; 9:8091. [PMID: 31147619 PMCID: PMC6542847 DOI: 10.1038/s41598-019-44541-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 05/20/2019] [Indexed: 11/24/2022] Open
Abstract
cDNA library preparation is important for many high-throughput sequencing applications, such as RNA G-quadruplex structure sequencing (rG4-seq). A systematic evaluation of the procedures of the experimental pipeline, however, is lacking. Herein, we perform a comprehensive assessment of the 5 key experimental steps involved in the cDNA library preparation of rG4-seq, and identify better reaction conditions and/or enzymes to carry out each of these key steps. Notably, we apply the improved methods to fragmented cellular RNA, and show reduced RNA input requirement, lower transcript abundance variations between biological replicates, as well as lower transcript coverage bias when compared to prior arts. In addition, the time to perform these steps is substantially reduced to hours. Our method and results can be directly applied in protocols that require cDNA library preparation, and provide insights to the further development of simple and efficient cDNA library preparation for different biological applications.
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Affiliation(s)
- Pui Yan Yeung
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Jieyu Zhao
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Eugene Yui-Ching Chow
- School of Life Sciences, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Xi Mou
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - HuiQi Hong
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117549, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.,Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117594, Singapore
| | - Ting-Fung Chan
- School of Life Sciences, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
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216
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Improved TGIRT-seq methods for comprehensive transcriptome profiling with decreased adapter dimer formation and bias correction. Sci Rep 2019; 9:7953. [PMID: 31138886 PMCID: PMC6538698 DOI: 10.1038/s41598-019-44457-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 05/17/2019] [Indexed: 02/08/2023] Open
Abstract
Thermostable group II intron reverse transcriptases (TGIRTs) with high fidelity and processivity have been used for a variety of RNA sequencing (RNA-seq) applications, including comprehensive profiling of whole-cell, exosomal, and human plasma RNAs; quantitative tRNA-seq based on the ability of TGIRT enzymes to give full-length reads of tRNAs and other structured small ncRNAs; high-throughput mapping of post-transcriptional modifications; and RNA structure mapping. Here, we improved TGIRT-seq methods for comprehensive transcriptome profiling by rationally designing RNA-seq adapters that minimize adapter dimer formation. Additionally, we developed biochemical and computational methods for remediating 5′- and 3′-end biases, the latter based on a random forest regression model that provides insight into the contribution of different factors to these biases. These improvements, some of which may be applicable to other RNA-seq methods, increase the efficiency of TGIRT-seq library construction and improve coverage of very small RNAs, such as miRNAs. Our findings provide insight into the biochemical basis of 5′- and 3′-end biases in RNA-seq and suggest general approaches for remediating biases and decreasing adapter dimer formation.
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217
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Frezza E, Courban A, Allouche D, Sargueil B, Pasquali S. The interplay between molecular flexibility and RNA chemical probing reactivities analyzed at the nucleotide level via an extensive molecular dynamics study. Methods 2019; 162-163:108-127. [PMID: 31145972 DOI: 10.1016/j.ymeth.2019.05.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 05/22/2019] [Accepted: 05/22/2019] [Indexed: 12/20/2022] Open
Abstract
Determination of the tridimensional structure of ribonucleic acid molecules is fundamental for understanding their function in the cell. A common method to investigate RNA structures of large molecules is the use of chemical probes such as SHAPE (2'-hydroxyl acylation analyzed by primer extension) reagents, DMS (dimethyl sulfate) and CMCT (1-cyclohexyl-3-(2-morpholinoethyl) carbodiimide metho-p-toluene sulfate), the reaction of which is dependent on the local structural properties of each nucleotide. In order to understand the interplay between local flexibility, sugar pucker, canonical pairing and chemical reactivity of the probes, we performed all-atom molecular dynamics simulations on a set of RNA molecules for which both tridimensional structure and chemical probing data are available and we analyzed the correlations between geometrical parameters and the chemical reactivity. Our study confirms that SHAPE reactivity is guided by the local flexibility of the different chemical moieties but suggests that a combination of multiple parameters is needed to better understand the implications of the reactivity at the molecular level. This is also the case for DMS and CMCT for which the reactivity appears to be more complex than commonly accepted.
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Affiliation(s)
- Elisa Frezza
- Faculté de Pharmacie de Paris, Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 - CNRS, Université Paris Descartes, 4 Avenue de l'Observatoire 75270 PARIS CEDEX 06, France.
| | - Antoine Courban
- Faculté de Pharmacie de Paris, Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 - CNRS, Université Paris Descartes, 4 Avenue de l'Observatoire 75270 PARIS CEDEX 06, France
| | - Delphine Allouche
- Faculté de Pharmacie de Paris, Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 - CNRS, Université Paris Descartes, 4 Avenue de l'Observatoire 75270 PARIS CEDEX 06, France
| | - Bruno Sargueil
- Faculté de Pharmacie de Paris, Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 - CNRS, Université Paris Descartes, 4 Avenue de l'Observatoire 75270 PARIS CEDEX 06, France.
| | - Samuela Pasquali
- Faculté de Pharmacie de Paris, Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 - CNRS, Université Paris Descartes, 4 Avenue de l'Observatoire 75270 PARIS CEDEX 06, France.
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218
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Yu H, Meng W, Mao Y, Zhang Y, Sun Q, Tao S. Deciphering the rules of mRNA structure differentiation in Saccharomyces cerevisiae in vivo and in vitro with deep neural networks. RNA Biol 2019; 16:1044-1054. [PMID: 31119975 PMCID: PMC6602416 DOI: 10.1080/15476286.2019.1612692] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The structure of mRNA in vivo is unwound to some extent in response to multiple factors involved in the translation process, resulting in significant differences from the structure of the same mRNA in vitro. In this study, we have proposed a novel application of deep neural networks, named DeepDRU, to predict the degree of mRNA structure unwinding in vivo by fitting five quantifiable features that may affect mRNA folding: ribosome density (RD), minimum folding free energy (MFE), GC content, translation initiation ribosome density (INI) and mRNA structure position (POS). mRNA structures with adjustment of the simulated structural features were designed and then fed into the trained DeepDRU model. We found unique effect regions of these five features on mRNA structure in vivo. Strikingly, INI is the most critical factor affecting the structure of mRNA in vivo, and structural sequence features, including MFE and GC content, have relatively smaller effects. DeepDRU provides a new paradigm for predicting the unwinding capability of mRNA structure in vivo. This improved knowledge about the mechanisms of factors influencing the structural capability of mRNA to unwind will facilitate the design and functional analysis of mRNA structure in vivo.
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Affiliation(s)
- Haopeng Yu
- a College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas , Northwest A&F University , Yangling , Shaanxi , China.,b Bioinformatics Center , Northwest A&F University , Yangling , Shaanxi , China
| | - Wenjing Meng
- a College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas , Northwest A&F University , Yangling , Shaanxi , China.,b Bioinformatics Center , Northwest A&F University , Yangling , Shaanxi , China
| | - Yuanhui Mao
- a College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas , Northwest A&F University , Yangling , Shaanxi , China.,b Bioinformatics Center , Northwest A&F University , Yangling , Shaanxi , China
| | - Yi Zhang
- a College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas , Northwest A&F University , Yangling , Shaanxi , China.,b Bioinformatics Center , Northwest A&F University , Yangling , Shaanxi , China
| | - Qing Sun
- a College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas , Northwest A&F University , Yangling , Shaanxi , China.,b Bioinformatics Center , Northwest A&F University , Yangling , Shaanxi , China
| | - Shiheng Tao
- a College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas , Northwest A&F University , Yangling , Shaanxi , China.,b Bioinformatics Center , Northwest A&F University , Yangling , Shaanxi , China
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219
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Unveiling the druggable RNA targets and small molecule therapeutics. Bioorg Med Chem 2019; 27:2149-2165. [PMID: 30981606 PMCID: PMC7126819 DOI: 10.1016/j.bmc.2019.03.057] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/25/2019] [Accepted: 03/29/2019] [Indexed: 12/15/2022]
Abstract
The increasing appreciation for the crucial roles of RNAs in infectious and non-infectious human diseases makes them attractive therapeutic targets. Coding and non-coding RNAs frequently fold into complex conformations which, if effectively targeted, offer opportunities to therapeutically modulate numerous cellular processes, including those linked to undruggable protein targets. Despite the considerable skepticism as to whether RNAs can be targeted with small molecule therapeutics, overwhelming evidence suggests the challenges we are currently facing are not outside the realm of possibility. In this review, we highlight the most recent advances in molecular techniques that have sparked a revolution in understanding the RNA structure-to-function relationship. We bring attention to the application of these modern techniques to identify druggable RNA targets and to assess small molecule binding specificity. Finally, we discuss novel screening methodologies that support RNA drug discovery and present examples of therapeutically valuable RNA targets.
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220
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Zhang H, Keane SC. Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1541. [PMID: 31025514 PMCID: PMC7169810 DOI: 10.1002/wrna.1541] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/18/2019] [Accepted: 04/02/2019] [Indexed: 12/22/2022]
Abstract
The characterization of functional yet nonprotein coding (nc) RNAs has expanded the role of RNA in the cell from a passive player in the central dogma of molecular biology to an active regulator of gene expression. The misregulation of ncRNA function has been linked with a variety of diseases and disorders ranging from cancers to neurodegeneration. However, a detailed molecular understanding of how ncRNAs function has been limited; due, in part, to the difficulties associated with obtaining high-resolution structures of large RNAs. Tertiary structure determination of RNA as a whole is hampered by various technical challenges, all of which are exacerbated as the size of the RNA increases. Namely, RNAs tend to be highly flexible and dynamic molecules, which are difficult to crystallize. Biomolecular nuclear magnetic resonance (NMR) spectroscopy offers a viable alternative to determining the structure of large RNA molecules that do not readily crystallize, but is itself hindered by some technical limitations. Recently, a series of advancements have allowed the biomolecular NMR field to overcome, at least in part, some of these limitations. These advances include improvements in sample preparation strategies as well as methodological improvements. Together, these innovations pave the way for the study of ever larger RNA molecules that have important biological function. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Huaqun Zhang
- Biophysics Program, University of Michigan, Ann Arbor, Michigan
| | - Sarah C Keane
- Biophysics Program, University of Michigan, Ann Arbor, Michigan.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan
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221
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Adams RL, Huston NC, Tavares RCA, Pyle AM. Sensitive detection of structural features and rearrangements in long, structured RNA molecules. Methods Enzymol 2019; 623:249-289. [PMID: 31239050 DOI: 10.1016/bs.mie.2019.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Technical innovations in structural probing have drastically advanced the field of RNA structure analysis. These advances have led to parallel approaches developed in separate labs for analyzing RNA structure and dynamics. With the wealth of methodologies available, it can be difficult to determine which is best suited for a given application. Here, using a long, highly structured viral RNA as an example (the positive strand genome of Hepatitis C Virus), we present a semi-comprehensive analysis and describe the major approaches for analyzing the architecture of RNA that is modified with structure-sensitive probes. Additionally, we present an updated method for generating in vitro transcribed and folded RNA that maintains native secondary structures in long RNA molecules. We anticipate that the methods described here will streamline the use of current approaches and help investigators who are unfamiliar with structure probing, obviating the need for time-consuming and expensive optimization.
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Affiliation(s)
- Rebecca L Adams
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, United States
| | - Nicholas C Huston
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, United States
| | - Rafael C A Tavares
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, United States; Department of Chemistry, Yale University, New Haven, CT, United States
| | - Anna M Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, United States; Department of Chemistry, Yale University, New Haven, CT, United States; Howard Hughes Medical Institute, Chevy Chase, MD, United States.
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222
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Belfort M, Lambowitz AM. Group II Intron RNPs and Reverse Transcriptases: From Retroelements to Research Tools. Cold Spring Harb Perspect Biol 2019; 11:11/4/a032375. [PMID: 30936187 DOI: 10.1101/cshperspect.a032375] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Group II introns, self-splicing retrotransposons, serve as both targets of investigation into their structure, splicing, and retromobility and a source of tools for genome editing and RNA analysis. Here, we describe the first cryo-electron microscopy (cryo-EM) structure determination, at 3.8-4.5 Å, of a group II intron ribozyme complexed with its encoded protein, containing a reverse transcriptase (RT), required for RNA splicing and retromobility. We also describe a method called RIG-seq using a retrotransposon indicator gene for high-throughput integration profiling of group II introns and other retrotransposons. Targetrons, RNA-guided gene targeting agents widely used for bacterial genome engineering, are described next. Finally, we detail thermostable group II intron RTs, which synthesize cDNAs with high accuracy and processivity, for use in various RNA-seq applications and relate their properties to a 3.0-Å crystal structure of the protein poised for reverse transcription. Biological insights from these group II intron revelations are discussed.
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Affiliation(s)
- Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, State University of New York, Albany, New York 12222
| | - Alan M Lambowitz
- Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712
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223
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RNA structure maps across mammalian cellular compartments. Nat Struct Mol Biol 2019; 26:322-330. [PMID: 30886404 PMCID: PMC6640855 DOI: 10.1038/s41594-019-0200-7] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/07/2019] [Indexed: 11/15/2022]
Abstract
RNA structure is intimately connected to each step of gene expression. Recent advances have enabled transcriptome-wide maps of RNA secondary structure, termed RNA structuromes. However, previous whole-cell analyses lacked the resolution to unravel the landscape and also the regulatory mechanisms of RNA structural changes across subcellular compartments. Here we reveal the RNA structuromes in three compartments — chromatin, nucleoplasm and cytoplasm in human and mouse cells. The cytotopic structuromes substantially expand RNA structural information, and enable detailed investigation of the central role of RNA structure in linking transcription, translation, and RNA decay. We develop a resource to visualize the interplay of RNA-protein interactions, RNA modifications, and RNA structure, and predict both direct and indirect reader proteins of RNA modifications. We also validate a novel role of the RNA binding protein LIN28A as an N6-methyladenosine modification “anti-reader”. Our results highlight the dynamic nature of RNA structures and its functional significance in gene regulation.
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224
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Choudhary K, Lai YH, Tran EJ, Aviran S. dStruct: identifying differentially reactive regions from RNA structurome profiling data. Genome Biol 2019; 20:40. [PMID: 30791935 PMCID: PMC6385470 DOI: 10.1186/s13059-019-1641-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/24/2019] [Indexed: 12/16/2022] Open
Abstract
RNA biology is revolutionized by recent developments of diverse high-throughput technologies for transcriptome-wide profiling of molecular RNA structures. RNA structurome profiling data can be used to identify differentially structured regions between groups of samples. Existing methods are limited in scope to specific technologies and/or do not account for biological variation. Here, we present dStruct which is the first broadly applicable method for differential analysis accounting for biological variation in structurome profiling data. dStruct is compatible with diverse profiling technologies, is validated with experimental data and simulations, and outperforms existing methods.
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Affiliation(s)
- Krishna Choudhary
- Department of Biomedical Engineering and Genome Center, University of California, Davis, One Shields Avenue, Davis, 95616 CA USA
| | - Yu-Hsuan Lai
- Department of Biochemistry, Purdue University, BCHM 305, 175 S. University Street, West Lafayette, 47907-2063 IN USA
| | - Elizabeth J. Tran
- Department of Biochemistry, Purdue University, BCHM 305, 175 S. University Street, West Lafayette, 47907-2063 IN USA
- Purdue University Center for Cancer Research, Purdue University, Hansen Life Sciences Research Building, Room 141, 201 S. University Street, West Lafayette, 47907-2064 IN USA
| | - Sharon Aviran
- Department of Biomedical Engineering and Genome Center, University of California, Davis, One Shields Avenue, Davis, 95616 CA USA
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225
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High-Resolution Ribosome Profiling Defines Discrete Ribosome Elongation States and Translational Regulation during Cellular Stress. Mol Cell 2019; 73:959-970.e5. [PMID: 30686592 DOI: 10.1016/j.molcel.2018.12.009] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/25/2018] [Accepted: 12/12/2018] [Indexed: 12/19/2022]
Abstract
Ribosomes undergo substantial conformational changes during translation elongation to accommodate incoming aminoacyl-tRNAs and translocate along the mRNA template. We used multiple elongation inhibitors and chemical probing to define ribosome conformational states corresponding to differently sized ribosome-protected mRNA fragments (RPFs) generated by ribosome profiling. We show, using various genetic and environmental perturbations, that short 20-22 or classical 27-29 nucleotide RPFs correspond to ribosomes with open or occupied ribosomal A sites, respectively. These distinct states of translation elongation are readily discerned by ribosome profiling in all eukaryotes we tested, including fungi, worms, and mammals. This high-resolution ribosome profiling approach reveals mechanisms of translation-elongation arrest during distinct stress conditions. Hyperosmotic stress inhibits translocation through Rck2-dependent eEF2 phosphorylation, whereas oxidative stress traps ribosomes in a pre-translocation state, independent of Rck2-driven eEF2 phosphorylation. These results provide insights and approaches for defining the molecular events that impact translation elongation throughout biology.
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226
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Wang PY, Sexton AN, Culligan WJ, Simon MD. Carbodiimide reagents for the chemical probing of RNA structure in cells. RNA (NEW YORK, N.Y.) 2019; 25:135-146. [PMID: 30389828 PMCID: PMC6298570 DOI: 10.1261/rna.067561.118] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/18/2018] [Indexed: 05/09/2023]
Abstract
Deciphering the conformations of RNAs in their cellular environment allows identification of RNA elements with potentially functional roles within biological contexts. Insight into the conformation of RNA in cells has been achieved using chemical probes that were developed to react specifically with flexible RNA nucleotides, or the Watson-Crick face of single-stranded nucleotides. The most widely used probes are either selective SHAPE (2'-hydroxyl acylation and primer extension) reagents that probe nucleotide flexibility, or dimethyl sulfate (DMS), which probes the base-pairing at adenine and cytosine but is unable to interrogate guanine or uracil. The constitutively charged carbodiimide N-cyclohexyl-N'-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMC) is widely used for probing G and U nucleotides, but has not been established for probing RNA in cells. Here, we report the use of a smaller and conditionally charged reagent, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC), as a chemical probe of RNA conformation, and the first reagent validated for structure probing of unpaired G and U nucleotides in intact cells. We showed that EDC demonstrates similar reactivity to CMC when probing transcripts in vitro. We found that EDC specifically reacted with accessible nucleotides in the 7SK noncoding RNA in intact cells. We probed structured regions within the Xist lncRNA with EDC and integrated these data with DMS probing data. Together, EDC and DMS allowed us to refine predicted structure models for the 3' extension of repeat C within Xist. These results highlight how complementing DMS probing experiments with EDC allows the analysis of Watson-Crick base-pairing at all four nucleotides of RNAs in their cellular context.
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Affiliation(s)
- Peter Y Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
- Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Alec N Sexton
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
- Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - William J Culligan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
- Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA
- Department of Cell Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
- Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA
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227
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Katz N, Cohen R, Solomon O, Kaufmann B, Atar O, Yakhini Z, Goldberg S, Amit R. An in Vivo Binding Assay for RNA-Binding Proteins Based on Repression of a Reporter Gene. ACS Synth Biol 2018; 7:2765-2774. [PMID: 30408420 DOI: 10.1021/acssynbio.8b00378] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We study translation repression in bacteria by engineering a regulatory circuit that functions as a binding assay for RNA binding proteins (RBP) in vivo. We do so by inducing expression of a fluorescent protein-RBP chimera, together with encoding its binding site at various positions within the ribosomal initiation region (+11-13 nt from the AUG) of a reporter module. We show that when bound by their cognate RBPs, the phage coat proteins for PP7 (PCP) and Qβ (QCP), strong repression is observed for all hairpin positions within the initiation region. Yet, a sharp transition to no-effect is observed when positioned in the elongation region, at a single-nucleotide resolution. Employing in vivo Selective 2'-hydroxyl acylation analyzed by primer extension followed by sequencing (SHAPE-seq) for a representative construct, established that in the translationally active state the mRNA molecule is nonstructured, while in the repressed state a structured signature was detected. We then utilize this regulatory phenomena to quantify the binding affinity of the coat proteins of phages MS2, PP7, GA, and Qβ to 14 cognate and noncognate binding sites in vivo. Using our circuit, we demonstrate qualitative differences between in vitro to in vivo binding characteristics for various variants when comparing to past studies. Furthermore, by introducing a simple mutation to the loop region for the Qβ-wt site, MCP binding is abolished, creating the first high-affinity QCP site that is completely orthogonal to MCP. Consequently, we demonstrate that our hybrid transcriptional-post-transcriptional circuit can be utilized as a binding assay to quantify RNA-RBP interactions in vivo.
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Affiliation(s)
- Noa Katz
- Department of Biotechnology and Food Engineering, Technion − Israel Institute of Technology, Haifa 32000, Israel
| | - Roni Cohen
- Department of Biotechnology and Food Engineering, Technion − Israel Institute of Technology, Haifa 32000, Israel
| | - Oz Solomon
- Department of Biotechnology and Food Engineering, Technion − Israel Institute of Technology, Haifa 32000, Israel
- School of Computer Science, Interdisciplinary Center, Herzeliya 46150, Israel
| | - Beate Kaufmann
- Department of Biotechnology and Food Engineering, Technion − Israel Institute of Technology, Haifa 32000, Israel
| | - Orna Atar
- Department of Biotechnology and Food Engineering, Technion − Israel Institute of Technology, Haifa 32000, Israel
| | - Zohar Yakhini
- Department of Computer Science, Technion − Israel Institute of Technology, Haifa 32000, Israel
- School of Computer Science, Interdisciplinary Center, Herzeliya 46150, Israel
| | - Sarah Goldberg
- Department of Biotechnology and Food Engineering, Technion − Israel Institute of Technology, Haifa 32000, Israel
| | - Roee Amit
- Department of Biotechnology and Food Engineering, Technion − Israel Institute of Technology, Haifa 32000, Israel
- Russell Berrie Nanotechnology Institute, Technion − Israel Institute of Technology, Haifa 32000, Israel
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228
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Moqtaderi Z, Geisberg JV, Struhl K. Extensive Structural Differences of Closely Related 3' mRNA Isoforms: Links to Pab1 Binding and mRNA Stability. Mol Cell 2018; 72:849-861.e6. [PMID: 30318446 PMCID: PMC6289678 DOI: 10.1016/j.molcel.2018.08.044] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 07/05/2018] [Accepted: 08/29/2018] [Indexed: 12/24/2022]
Abstract
Alternative polyadenylation generates numerous 3' mRNA isoforms that can vary in biological properties, such as stability and localization. We developed methods to obtain transcriptome-scale structural information and protein binding on individual 3' mRNA isoforms in vivo. Strikingly, near-identical mRNA isoforms can possess dramatically different structures throughout the 3' UTR. Analyses of identical mRNAs in different species or refolded in vitro indicate that structural differences in vivo are often due to trans-acting factors. The level of Pab1 binding to poly(A)-containing isoforms is surprisingly variable, and differences in Pab1 binding correlate with the extent of structural variation for closely spaced isoforms. A pattern encompassing single-strandedness near the 3' terminus, double-strandedness of the poly(A) tail, and low Pab1 binding is associated with mRNA stability. Thus, individual 3' mRNA isoforms can be remarkably different physical entities in vivo. Sequences responsible for isoform-specific structures, differential Pab1 binding, and mRNA stability are evolutionarily conserved, indicating biological function.
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Affiliation(s)
- Zarmik Moqtaderi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph V Geisberg
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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229
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Genome-wide probing RNA structure with the modified DMS-MaPseq in Arabidopsis. Methods 2018; 155:30-40. [PMID: 30503825 DOI: 10.1016/j.ymeth.2018.11.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 11/20/2018] [Accepted: 11/27/2018] [Indexed: 11/20/2022] Open
Abstract
Transcripts have intrinsic propensity to form stable secondary structure that is fundamental to regulate RNA transcription, splicing, translation, RNA localization and turnover. Numerous methods that integrate chemical reactions with next-generation sequencing (NGS) have been applied to study in vivo RNA structure, providing new insights into RNA biology. Dimethyl sulfate (DMS) probing coupled with mutational profiling through NGS (DMS-MaPseq) is a newly developed method for revealing genome-wide or target-specific RNA structure. Herein, we present our experimental protocol of a modified DMS-MaPseq method for plant materials. The DMS treatment condition was optimized, and library preparation procedures were simplified. We also provided custom scripts for bioinformatic analysis of genome-wide DMS-MaPseq data. Bioinformatic results showed that our method could generate high-quality and reproducible data. Further, we assessed sequencing depth and coverage for genome-wide RNA structure profiling in Arabidopsis, and provided two examples of in vivo structure of mobile RNAs. We hope that our modified DMS-MaPseq method will serve as a powerful tool for analyzing in vivo RNA structurome in plants.
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230
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Mailler E, Paillart JC, Marquet R, Smyth RP, Vivet-Boudou V. The evolution of RNA structural probing methods: From gels to next-generation sequencing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1518. [PMID: 30485688 DOI: 10.1002/wrna.1518] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/13/2018] [Accepted: 10/17/2018] [Indexed: 01/09/2023]
Abstract
RNA molecules are important players in all domains of life and the study of the relationship between their multiple flexible states and the associated biological roles has increased in recent years. For several decades, chemical and enzymatic structural probing experiments have been used to determine RNA structure. During this time, there has been a steady improvement in probing reagents and experimental methods, and today the structural biologist community has a large range of tools at its disposal to probe the secondary structure of RNAs in vitro and in cells. Early experiments used radioactive labeling and polyacrylamide gel electrophoresis as read-out methods. This was superseded by capillary electrophoresis, and more recently by next-generation sequencing. Today, powerful structural probing methods can characterize RNA structure on a genome-wide scale. In this review, we will provide an overview of RNA structural probing methodologies from a historical and technical perspective. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Methods > RNA Analyses in vitro and In Silico RNA Methods > RNA Analyses in Cells.
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Affiliation(s)
- Elodie Mailler
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Strasbourg, France
| | | | - Roland Marquet
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Strasbourg, France
| | - Redmond P Smyth
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Strasbourg, France
| | - Valerie Vivet-Boudou
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Strasbourg, France
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231
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Qian X, Zhao J, Yeung PY, Zhang QC, Kwok CK. Revealing lncRNA Structures and Interactions by Sequencing-Based Approaches. Trends Biochem Sci 2018; 44:33-52. [PMID: 30459069 DOI: 10.1016/j.tibs.2018.09.012] [Citation(s) in RCA: 290] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 09/11/2018] [Accepted: 09/19/2018] [Indexed: 11/28/2022]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as significant players in almost every level of gene function and regulation. Thus, characterizing the structures and interactions of lncRNAs is essential for understanding their mechanistic roles in cells. Through a combination of (bio)chemical approaches and automated capillary and high-throughput sequencing (HTS), the complexity and diversity of RNA structures and interactions has been revealed in the transcriptomes of multiple species. These methods have uncovered important biological insights into the mechanistic and functional roles of lncRNA in gene expression and RNA metabolism, as well as in development and disease. In this review, we summarize the latest sequencing strategies to reveal RNA structure, RNA-RNA, RNA-DNA, and RNA-protein interactions, and highlight the recent applications of these approaches to map functional lncRNAs. We discuss the advantages and limitations of these strategies, and provide recommendations to further advance methodologies capable of mapping RNA structure and interactions in order to discover new biology of lncRNAs and decipher their molecular mechanisms and implication in diseases.
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Affiliation(s)
- Xingyang Qian
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; These authors contributed equally to this work
| | - Jieyu Zhao
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China; These authors contributed equally to this work
| | - Pui Yan Yeung
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China; These authors contributed equally to this work
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
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232
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Kiefer L, Schofield JA, Simon MD. Expanding the Nucleoside Recoding Toolkit: Revealing RNA Population Dynamics with 6-Thioguanosine. J Am Chem Soc 2018; 140:14567-14570. [PMID: 30353734 PMCID: PMC6779120 DOI: 10.1021/jacs.8b08554] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
RNA-sequencing (RNA-seq) measures RNA abundance in a biological sample but does not provide temporal information about the sequenced RNAs. Metabolic labeling can be used to distinguish newly made RNAs from pre-existing RNAs. Mutations induced from chemical recoding of the hydrogen bonding pattern of the metabolic label can reveal which RNAs are new in the context of a sequencing experiment. These nucleotide recoding strategies have been developed for a single uridine analogue, 4-thiouridine (s4U), limiting the scope of these experiments. Here we report the first use of nucleoside recoding with a guanosine analogue, 6-thioguanosine (s6G). Using TimeLapse sequencing (TimeLapse-seq), s6G can be recoded under RNA-friendly oxidative nucleophilic-aromatic substitution conditions to produce adenine analogues (substituted 2-aminoadenosines). We demonstrate the first use of s6G recoding experiments to reveal transcriptome-wide RNA population dynamics.
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Affiliation(s)
- Lea Kiefer
- Department of Molecular Biophysics & Biochemistry, Yale University,
New Haven, CT 06511, USA
- Chemical Biology Institute, Yale University, West Haven, CT 06516,
USA
| | - Jeremy A. Schofield
- Department of Molecular Biophysics & Biochemistry, Yale University,
New Haven, CT 06511, USA
- Chemical Biology Institute, Yale University, West Haven, CT 06516,
USA
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233
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Sas-Chen A, Schwartz S. Misincorporation signatures for detecting modifications in mRNA: Not as simple as it sounds. Methods 2018; 156:53-59. [PMID: 30359724 DOI: 10.1016/j.ymeth.2018.10.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/04/2018] [Accepted: 10/21/2018] [Indexed: 12/11/2022] Open
Abstract
Post-transcriptional modification on mRNA has become a field of intense interest in recent years, and next-generation sequencing based technologies are constantly emerging to detect an increasing number of modifications at a transcriptome-wide level. Some of these approaches are based on identification of misincorporation events induced by reverse transcriptase at modified sites. Although conceptually trivial, sensitive and specific identification of such events is a challenge prone to a surprising number of artifacts, which can lead to substantially inflated estimates of the abundance of diverse modifications. Here we discuss the sources of some of these artifacts and delineate approaches to overcome them.
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Affiliation(s)
- Aldema Sas-Chen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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234
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Mizrahi O, Nachshon A, Shitrit A, Gelbart IA, Dobesova M, Brenner S, Kahana C, Stern-Ginossar N. Virus-Induced Changes in mRNA Secondary Structure Uncover cis-Regulatory Elements that Directly Control Gene Expression. Mol Cell 2018; 72:862-874.e5. [PMID: 30318442 DOI: 10.1016/j.molcel.2018.09.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/16/2018] [Accepted: 08/31/2018] [Indexed: 11/25/2022]
Abstract
mRNAs carry two layers of information, the genetic code and the information that dictates their post-transcriptional fate. The latter function relies on a complex interplay between cis-elements and trans-regulators, and unbiased identification of these elements is still challenging. To identify cis-elements that control gene expression, we use dimethyl sulfate (DMS) mutational profiling with sequencing and map changes in mRNA secondary structure following viral infection. Our dynamic structural data reveal a major role for ribosomes in unwinding secondary structures, which is further supported by the relationship we uncover between structure and translation efficiency. Moreover, our analysis revealed dozens of regions in viral and cellular mRNAs that exhibit changes in secondary structure. In-depth analysis of these regions reveals cis-elements in 3' UTRs that regulate mRNA stability and elements within coding sequences that control translation. Overall, our study demonstrates how mapping dynamic changes in mRNA structure allows unbiased identification of functional regulatory elements.
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Affiliation(s)
- Orel Mizrahi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Aharon Nachshon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Alina Shitrit
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Idit A Gelbart
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Martina Dobesova
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shirly Brenner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Chaim Kahana
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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235
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Bevilacqua PC, Assmann SM. Technique Development for Probing RNA Structure In Vivo and Genome-Wide. Cold Spring Harb Perspect Biol 2018; 10:a032250. [PMID: 30275275 PMCID: PMC6169808 DOI: 10.1101/cshperspect.a032250] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
How organisms perceive and respond to their surroundings is one of the great questions in biology. It is clear that RNA plays key roles in sensing. Cellular and environmental cues that RNA responds to include temperature, ions, metabolites, and biopolymers. Recent advances in next-generation sequencing and in vivo chemical probing have provided unprecedented insights into RNA folding in vivo and genome-wide. Patterns of chemical reactivity have implicated control of gene expression by RNA and aided prediction of RNA structure. Central to these advances has been development of molecular biological and chemical techniques. Key advances are improvements in the quality, cost, and throughput of library preparation; availability of a wider array of chemicals for probing RNA structure in vivo; and robustness and user friendliness of data analysis. Insights from probing transcriptomes and future directions are provided.
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Affiliation(s)
- Philip C Bevilacqua
- Departments of Chemistry and Biochemistry & Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802
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236
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Kwok CK, Marsico G, Balasubramanian S. Detecting RNA G-Quadruplexes (rG4s) in the Transcriptome. Cold Spring Harb Perspect Biol 2018; 10:10/7/a032284. [PMID: 29967010 DOI: 10.1101/cshperspect.a032284] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RNA G-quadruplex (rG4) secondary structures are proposed to play key roles in fundamental biological processes that include the modulation of transcriptional, co-transcriptional, and posttranscriptional events. Recent methodological developments that include predictive algorithms and structure-based sequencing have enabled the detection and mapping of rG4 structures on a transcriptome-wide scale at high sensitivity and resolution. The data generated by these studies provide valuable insights into the potentially diverse roles of rG4s in biology and open up a number of mechanistic hypotheses. Herein we highlight these methodologies and discuss the associated findings in relation to rG4-related biological mechanisms.
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Affiliation(s)
- Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - Giovanni Marsico
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom.,Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom.,Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
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237
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The helicase Ded1p controls use of near-cognate translation initiation codons in 5' UTRs. Nature 2018; 559:130-134. [PMID: 29950728 PMCID: PMC6226265 DOI: 10.1038/s41586-018-0258-0] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/08/2018] [Indexed: 12/21/2022]
Abstract
The conserved and essential DEAD-box RNA helicase Ded1p from yeast and its mammalian orthologue DDX3 are critical for the initiation of translation1. Mutations in DDX3 are linked to tumorigenesis2-4 and intellectual disability5, and the enzyme is targeted by a range of viruses6. How Ded1p and its orthologues engage RNAs during the initiation of translation is unknown. Here we show, by integrating transcriptome-wide analyses of translation, RNA structure and Ded1p-RNA binding, that the effects of Ded1p on the initiation of translation are connected to near-cognate initiation codons in 5' untranslated regions. Ded1p associates with the translation pre-initiation complex at the mRNA entry channel and repressing the activity of Ded1p leads to the accumulation of RNA structure in 5' untranslated regions, the initiation of translation from near-cognate start codons immediately upstream of these structures and decreased protein synthesis from the corresponding main open reading frames. The data reveal a program for the regulation of translation that links Ded1p, the activation of near-cognate start codons and mRNA structure. This program has a role in meiosis, in which a marked decrease in the levels of Ded1p is accompanied by the activation of the alternative translation initiation sites that are seen when the activity of Ded1p is repressed. Our observations indicate that Ded1p affects translation initiation by controlling the use of near-cognate initiation codons that are proximal to mRNA structure in 5' untranslated regions.
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238
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Automated Recognition of RNA Structure Motifs by Their SHAPE Data Signatures. Genes (Basel) 2018; 9:genes9060300. [PMID: 29904019 PMCID: PMC6027059 DOI: 10.3390/genes9060300] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/04/2018] [Accepted: 06/13/2018] [Indexed: 02/03/2023] Open
Abstract
High-throughput structure profiling (SP) experiments that provide information at nucleotide resolution are revolutionizing our ability to study RNA structures. Of particular interest are RNA elements whose underlying structures are necessary for their biological functions. We previously introduced patteRNA, an algorithm for rapidly mining SP data for patterns characteristic of such motifs. This work provided a proof-of-concept for the detection of motifs and the capability of distinguishing structures displaying pronounced conformational changes. Here, we describe several improvements and automation routines to patteRNA. We then consider more elaborate biological situations starting with the comparison or integration of results from searches for distinct motifs and across datasets. To facilitate such analyses, we characterize patteRNA’s outputs and describe a normalization framework that regularizes results. We then demonstrate that our algorithm successfully discerns between highly similar structural variants of the human immunodeficiency virus type 1 (HIV-1) Rev response element (RRE) and readily identifies its exact location in whole-genome structure profiles of HIV-1. This work highlights the breadth of information that can be gleaned from SP data and broadens the utility of data-driven methods as tools for the detection of novel RNA elements.
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239
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Stojković V, Chu T, Therizols G, Weinberg DE, Fujimori DG. miCLIP-MaPseq, a Substrate Identification Approach for Radical SAM RNA Methylating Enzymes. J Am Chem Soc 2018; 140:7135-7143. [PMID: 29782154 DOI: 10.1021/jacs.8b02618] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Although present across bacteria, the large family of radical SAM RNA methylating enzymes is largely uncharacterized. Escherichia coli RlmN, the founding member of the family, methylates an adenosine in 23S rRNA and several tRNAs to yield 2-methyladenosine (m2A). However, varied RNA substrate specificity among RlmN enzymes, combined with the ability of certain family members to generate 8-methyladenosine (m8A), makes functional predictions across this family challenging. Here, we present a method for unbiased substrate identification that exploits highly efficient, mechanism-based cross-linking between the enzyme and its RNA substrates. Additionally, by determining that the thermostable group II intron reverse transcriptase introduces mismatches at the site of the cross-link, we have identified the precise positions of RNA modification using mismatch profiling. These results illustrate the capability of our method to define enzyme-substrate pairs and determine modification sites of the largely uncharacterized radical SAM RNA methylating enzyme family.
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Affiliation(s)
- Vanja Stojković
- Department of Cellular and Molecular Pharmacology , University of California , San Francisco , California 94158 , United States
| | - Tongyue Chu
- Department of Cellular and Molecular Pharmacology , University of California , San Francisco , California 94158 , United States
| | - Gabriel Therizols
- Department of Cellular and Molecular Pharmacology , University of California , San Francisco , California 94158 , United States
| | - David E Weinberg
- Department of Cellular and Molecular Pharmacology , University of California , San Francisco , California 94158 , United States
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology , University of California , San Francisco , California 94158 , United States.,Department of Pharmaceutical Chemistry , University of California , 600 16th Street, MC2280 San Francisco , California 94158 , United States
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240
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Yang X, Yang M, Deng H, Ding Y. New Era of Studying RNA Secondary Structure and Its Influence on Gene Regulation in Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:671. [PMID: 29872445 PMCID: PMC5972288 DOI: 10.3389/fpls.2018.00671] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/02/2018] [Indexed: 05/29/2023]
Abstract
The dynamic structure of RNA plays a central role in post-transcriptional regulation of gene expression such as RNA maturation, degradation, and translation. With the rise of next-generation sequencing, the study of RNA structure has been transformed from in vitro low-throughput RNA structure probing methods to in vivo high-throughput RNA structure profiling. The development of these methods enables incremental studies on the function of RNA structure to be performed, revealing new insights of novel regulatory mechanisms of RNA structure in plants. Genome-wide scale RNA structure profiling allows us to investigate general RNA structural features over 10s of 1000s of mRNAs and to compare RNA structuromes between plant species. Here, we provide a comprehensive and up-to-date overview of: (i) RNA structure probing methods; (ii) the biological functions of RNA structure; (iii) genome-wide RNA structural features corresponding to their regulatory mechanisms; and (iv) RNA structurome evolution in plants.
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Affiliation(s)
- Xiaofei Yang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Minglei Yang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Hongjing Deng
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
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241
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SWI2/SNF2 ATPase CHR2 remodels pri-miRNAs via Serrate to impede miRNA production. Nature 2018; 557:516-521. [DOI: 10.1038/s41586-018-0135-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 03/09/2018] [Indexed: 12/22/2022]
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242
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Hurst T, Xu X, Zhao P, Chen SJ. Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis. J Phys Chem B 2018; 122:4771-4783. [PMID: 29659274 DOI: 10.1021/acs.jpcb.8b00575] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) method probes RNA local structural and dynamic information at single nucleotide resolution. To gain quantitative insights into the relationship between nucleotide flexibility, RNA 3D structure, and SHAPE reactivity, we develop a 3D Structure-SHAPE Relationship model (3DSSR) to rebuild SHAPE profiles from 3D structures. The model starts from RNA structures and combines nucleotide interaction strength and conformational propensity, ligand (SHAPE reagent) accessibility, and base-pairing pattern through a composite function to quantify the correlation between SHAPE reactivity and nucleotide conformational stability. The 3DSSR model shows the relationship between SHAPE reactivity and RNA structure and energetics. Comparisons between the 3DSSR-predicted SHAPE profile and the experimental SHAPE data show correlation, suggesting that the extracted analytical function may have captured the key factors that determine the SHAPE reactivity profile. Furthermore, the theory offers an effective method to sieve RNA 3D models and exclude models that are incompatible with experimental SHAPE data.
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Affiliation(s)
- Travis Hurst
- Department of Physics, Department of Biochemistry , and University of Missouri Informatics Institute , University of Missouri , Columbia , Missouri 65211 , United States
| | - Xiaojun Xu
- Department of Physics, Department of Biochemistry , and University of Missouri Informatics Institute , University of Missouri , Columbia , Missouri 65211 , United States
| | - Peinan Zhao
- Department of Physics, Department of Biochemistry , and University of Missouri Informatics Institute , University of Missouri , Columbia , Missouri 65211 , United States
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry , and University of Missouri Informatics Institute , University of Missouri , Columbia , Missouri 65211 , United States
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243
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Plakos K, DeRose VJ. Mapping platinum adducts on yeast ribosomal RNA using high-throughput sequencing. Chem Commun (Camb) 2018; 53:12746-12749. [PMID: 29099140 DOI: 10.1039/c7cc06708a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Methods to map small-molecule binding sites on cellular RNAs are important for understanding interactions with both endogenous and exogenous compounds. Pt(ii) reagents are well-known DNA and RNA crosslinking agents, but sequence-specific and genome-wide identification of Pt targets following in-cell treatment is challenging. Here we describe application of high-throughput 'Pt-Seq' to identify Pt-rRNA adducts following treatment of S. cerevisiae with cisplatin.
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Affiliation(s)
- Kory Plakos
- Department of Chemistry and Biochemistry and Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
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244
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Zhang Y, Burkhardt DH, Rouskin S, Li GW, Weissman JS, Gross CA. A Stress Response that Monitors and Regulates mRNA Structure Is Central to Cold Shock Adaptation. Mol Cell 2018; 70:274-286.e7. [PMID: 29628307 DOI: 10.1016/j.molcel.2018.02.035] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 01/19/2018] [Accepted: 02/27/2018] [Indexed: 11/16/2022]
Abstract
Temperature influences the structural and functional properties of cellular components, necessitating stress responses to restore homeostasis following temperature shift. Whereas the circuitry controlling the heat shock response is well understood, that controlling the E. coli cold shock adaptation program is not. We found that during the growth arrest phase (acclimation) that follows shift to low temperature, protein synthesis increases, and open reading frame (ORF)-wide mRNA secondary structure decreases. To identify the regulatory system controlling this process, we screened for players required for increased translation. We identified a two-member mRNA surveillance system that enables recovery of translation during acclimation: RNase R assures appropriate mRNA degradation and the Csps dynamically adjust mRNA secondary structure to globally modulate protein expression level. An autoregulatory switch in which Csps tune their own expression to cellular demand enables dynamic control of global translation. The universality of Csps in bacteria suggests broad utilization of this control mechanism.
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Affiliation(s)
- Yan Zhang
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David H Burkhardt
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Graduate Group in Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute of Quantitative Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Silvi Rouskin
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute of Quantitative Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Gene-Wei Li
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute of Quantitative Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute of Quantitative Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Carol A Gross
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute of Quantitative Biology, University of California, San Francisco, San Francisco, CA 94158, USA.
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245
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Lackey L, Coria A, Woods C, McArthur E, Laederach A. Allele-specific SHAPE-MaP assessment of the effects of somatic variation and protein binding on mRNA structure. RNA (NEW YORK, N.Y.) 2018; 24:513-528. [PMID: 29317542 PMCID: PMC5855952 DOI: 10.1261/rna.064469.117] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/04/2018] [Indexed: 05/22/2023]
Abstract
The impact of inherited and somatic mutations on messenger RNA (mRNA) structure remains poorly understood. Recent technological advances that leverage next-generation sequencing to obtain experimental structure data, such as SHAPE-MaP, can reveal structural effects of mutations, especially when these data are incorporated into structure modeling. Here, we analyze the ability of SHAPE-MaP to detect the relatively subtle structural changes caused by single-nucleotide mutations. We find that allele-specific sorting greatly improved our detection ability. Thus, we used SHAPE-MaP with a novel combination of clone-free robotic mutagenesis and allele-specific sorting to perform a rapid, comprehensive survey of noncoding somatic and inherited riboSNitches in two cancer-associated mRNAs, TPT1 and LCP1 Using rigorous thermodynamic modeling of the Boltzmann suboptimal ensemble, we identified a subset of mutations that change TPT1 and LCP1 RNA structure, with approximately 14% of all variants identified as riboSNitches. To confirm that these in vitro structures were biologically relevant, we tested how dependent TPT1 and LCP1 mRNA structures were on their environments. We performed SHAPE-MaP on TPT1 and LCP1 mRNAs in the presence or absence of cellular proteins and found that both mRNAs have similar overall folds in all conditions. RiboSNitches identified within these mRNAs in vitro likely exist under biological conditions. Overall, these data reveal a robust mRNA structural landscape where differences in environmental conditions and most sequence variants do not significantly alter RNA structural ensembles. Finally, predicting riboSNitches in mRNAs from sequence alone remains particularly challenging; these data will provide the community with benchmarks for further algorithmic development.
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Affiliation(s)
- Lela Lackey
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Aaztli Coria
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Chanin Woods
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Evonne McArthur
- School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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246
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Mustoe AM, Busan S, Rice GM, Hajdin CE, Peterson BK, Ruda VM, Kubica N, Nutiu R, Baryza JL, Weeks KM. Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing. Cell 2018; 173:181-195.e18. [PMID: 29551268 DOI: 10.1016/j.cell.2018.02.034] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/02/2018] [Accepted: 02/15/2018] [Indexed: 11/25/2022]
Abstract
mRNAs can fold into complex structures that regulate gene expression. Resolving such structures de novo has remained challenging and has limited our understanding of the prevalence and functions of mRNA structure. We use SHAPE-MaP experiments in living E. coli cells to derive quantitative, nucleotide-resolution structure models for 194 endogenous transcripts encompassing approximately 400 genes. Individual mRNAs have exceptionally diverse architectures, and most contain well-defined structures. Active translation destabilizes mRNA structure in cells. Nevertheless, mRNA structure remains similar between in-cell and cell-free environments, indicating broad potential for structure-mediated gene regulation. We find that the translation efficiency of endogenous genes is regulated by unfolding kinetics of structures overlapping the ribosome binding site. We discover conserved structured elements in 35% of UTRs, several of which we validate as novel protein binding motifs. RNA structure regulates every gene studied here in a meaningful way, implying that most functional structures remain to be discovered.
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Affiliation(s)
- Anthony M Mustoe
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA.
| | - Steven Busan
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Greggory M Rice
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA; Novartis Institutes for Biomedical Research, Inc., Cambridge, MA, USA
| | | | - Brant K Peterson
- Novartis Institutes for Biomedical Research, Inc., Cambridge, MA, USA
| | - Vera M Ruda
- Novartis Institutes for Biomedical Research, Inc., Cambridge, MA, USA
| | - Neil Kubica
- Novartis Institutes for Biomedical Research, Inc., Cambridge, MA, USA
| | - Razvan Nutiu
- Novartis Institutes for Biomedical Research, Inc., Cambridge, MA, USA
| | - Jeremy L Baryza
- Novartis Institutes for Biomedical Research, Inc., Cambridge, MA, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA.
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247
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Ledda M, Aviran S. PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures. Genome Biol 2018; 19:28. [PMID: 29495968 PMCID: PMC5833111 DOI: 10.1186/s13059-018-1399-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/30/2018] [Indexed: 02/08/2023] Open
Abstract
Establishing a link between RNA structure and function remains a great challenge in RNA biology. The emergence of high-throughput structure profiling experiments is revolutionizing our ability to decipher structure, yet principled approaches for extracting information on structural elements directly from these data sets are lacking. We present PATTERNA, an unsupervised pattern recognition algorithm that rapidly mines RNA structure motifs from profiling data. We demonstrate that PATTERNA detects motifs with an accuracy comparable to commonly used thermodynamic models and highlight its utility in automating data-directed structure modeling from large data sets. PATTERNA is versatile and compatible with diverse profiling techniques and experimental conditions.
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Affiliation(s)
- Mirko Ledda
- Department of Biomedical Engineering and Genome Center, UC Davis, 1 Shields Ave, Davis, 95616 USA
- Integrative Genetics and Genomics Graduate Group, UC Davis, 1 Shields Ave, Davis, 95616 USA
| | - Sharon Aviran
- Department of Biomedical Engineering and Genome Center, UC Davis, 1 Shields Ave, Davis, 95616 USA
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248
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Leppek K, Das R, Barna M. Functional 5' UTR mRNA structures in eukaryotic translation regulation and how to find them. Nat Rev Mol Cell Biol 2018; 19:158-174. [PMID: 29165424 PMCID: PMC5820134 DOI: 10.1038/nrm.2017.103] [Citation(s) in RCA: 482] [Impact Index Per Article: 80.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
RNA molecules can fold into intricate shapes that can provide an additional layer of control of gene expression beyond that of their sequence. In this Review, we discuss the current mechanistic understanding of structures in 5' untranslated regions (UTRs) of eukaryotic mRNAs and the emerging methodologies used to explore them. These structures may regulate cap-dependent translation initiation through helicase-mediated remodelling of RNA structures and higher-order RNA interactions, as well as cap-independent translation initiation through internal ribosome entry sites (IRESs), mRNA modifications and other specialized translation pathways. We discuss known 5' UTR RNA structures and how new structure probing technologies coupled with prospective validation, particularly compensatory mutagenesis, are likely to identify classes of structured RNA elements that shape post-transcriptional control of gene expression and the development of multicellular organisms.
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Affiliation(s)
- Kathrin Leppek
- Department of Developmental Biology, Stanford University, Stanford, California 94305, USA
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Rhiju Das
- Departments of Biochemistry and Physics, Stanford University, Stanford, California 94305, USA
| | - Maria Barna
- Department of Developmental Biology, Stanford University, Stanford, California 94305, USA
- Department of Genetics, Stanford University, Stanford, California 94305, USA
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249
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Moss WN. RNA2DMut: a web tool for the design and analysis of RNA structure mutations. RNA (NEW YORK, N.Y.) 2018; 24:273-286. [PMID: 29183923 PMCID: PMC5824348 DOI: 10.1261/rna.063933.117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/25/2017] [Indexed: 06/07/2023]
Abstract
With the widespread application of high-throughput sequencing, novel RNA sequences are being discovered at an astonishing rate. The analysis of function, however, lags behind. In both the cis- and trans-regulatory functions of RNA, secondary structure (2D base-pairing) plays essential regulatory roles. In order to test RNA function, it is essential to be able to design and analyze mutations that can affect structure. This was the motivation for the creation of the RNA2DMut web tool. With RNA2DMut, users can enter in RNA sequences to analyze, constrain mutations to specific residues, or limit changes to purines/pyrimidines. The sequence is analyzed at each base to determine the effect of every possible point mutation on 2D structure. The metrics used in RNA2DMut rely on the calculation of the Boltzmann structure ensemble and do not require a robust 2D model of RNA structure for designing mutations. This tool can facilitate a wide array of uses involving RNA: for example, in designing and evaluating mutants for biological assays, interrogating RNA-protein interactions, identifying key regions to alter in SELEX experiments, and improving RNA folding and crystallization properties for structural biology. Additional tools are available to help users introduce other mutations (e.g., indels and substitutions) and evaluate their effects on RNA structure. Example calculations are shown for five RNAs that require 2D structure for their function: the MALAT1 mascRNA, an influenza virus splicing regulatory motif, the EBER2 viral noncoding RNA, the Xist lncRNA repA region, and human Y RNA 5. RNA2DMut can be accessed at https://rna2dmut.bb.iastate.edu/.
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Affiliation(s)
- Walter N Moss
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
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250
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Statistical modeling of RNA structure profiling experiments enables parsimonious reconstruction of structure landscapes. Nat Commun 2018; 9:606. [PMID: 29426922 PMCID: PMC5807309 DOI: 10.1038/s41467-018-02923-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 01/09/2018] [Indexed: 11/23/2022] Open
Abstract
RNA plays key regulatory roles in diverse cellular processes, where its functionality often derives from folding into and converting between structures. Many RNAs further rely on co-existence of alternative structures, which govern their response to cellular signals. However, characterizing heterogeneous landscapes is difficult, both experimentally and computationally. Recently, structure profiling experiments have emerged as powerful and affordable structure characterization methods, which improve computational structure prediction. To date, efforts have centered on predicting one optimal structure, with much less progress made on multiple-structure prediction. Here, we report a probabilistic modeling approach that predicts a parsimonious set of co-existing structures and estimates their abundances from structure profiling data. We demonstrate robust landscape reconstruction and quantitative insights into structural dynamics by analyzing numerous data sets. This work establishes a framework for data-directed characterization of structure landscapes to aid experimentalists in performing structure-function studies. Different experimental and computational approaches can be used to study RNA structures. Here, the authors present a computational method for data-directed reconstruction of complex RNA structure landscapes, which predicts a parsimonious set of co-existing structures and estimates their abundances from structure profiling data.
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