1
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Huang E, Frydman C, Xiao X. Navigating the landscape of epitranscriptomics and host immunity. Genome Res 2024; 34:515-529. [PMID: 38702197 PMCID: PMC11146601 DOI: 10.1101/gr.278412.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2024]
Abstract
RNA modifications, also termed epitranscriptomic marks, encompass chemical alterations to individual nucleotides, including processes such as methylation and editing. These marks contribute to a wide range of biological processes, many of which are related to host immune system defense. The functions of immune-related RNA modifications can be categorized into three main groups: regulation of immunogenic RNAs, control of genes involved in innate immune response, and facilitation of adaptive immunity. Here, we provide an overview of recent research findings that elucidate the contributions of RNA modifications to each of these processes. We also discuss relevant methods for genome-wide identification of RNA modifications and their immunogenic substrates. Finally, we highlight recent advances in cancer immunotherapies that aim to reduce cancer cell viability by targeting the enzymes responsible for RNA modifications. Our presentation of these dynamic research avenues sets the stage for future investigations in this field.
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Affiliation(s)
- Elaine Huang
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California 90095, USA
| | - Clara Frydman
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California 90095, USA
| | - Xinshu Xiao
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California 90095, USA;
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California 90095, USA
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, California 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
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2
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Spitale RC, Incarnato D. Probing the dynamic RNA structurome and its functions. Nat Rev Genet 2023; 24:178-196. [PMID: 36348050 PMCID: PMC9644009 DOI: 10.1038/s41576-022-00546-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2022] [Indexed: 11/09/2022]
Abstract
RNA is a key regulator of almost every cellular process, and the structures adopted by RNA molecules are thought to be central to their functions. The recent fast-paced evolution of high-throughput sequencing-based RNA structure mapping methods has enabled the rapid in vivo structural interrogation of entire cellular transcriptomes. Collectively, these studies are shedding new light on the long underestimated complexity of the structural organization of the transcriptome - the RNA structurome. Moreover, recent analyses are challenging the view that the RNA structurome is a static entity by revealing how RNA molecules establish intricate networks of alternative intramolecular and intermolecular interactions and that these ensembles of RNA structures are dynamically regulated to finely tune RNA functions in living cells. This new understanding of how RNA can shape cell phenotypes has important implications for the development of RNA-targeted therapeutic strategies.
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Affiliation(s)
- Robert C. Spitale
- grid.266093.80000 0001 0668 7243Department of Pharmaceutical Sciences, University of California, Irvine, CA USA
| | - Danny Incarnato
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands.
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3
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Huang Y, Luo J, Jing R, Li M. Multi-model predictive analysis of RNA solvent accessibility based on modified residual attention mechanism. Brief Bioinform 2022; 23:6775603. [PMID: 36305428 DOI: 10.1093/bib/bbac470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/09/2022] [Accepted: 09/30/2022] [Indexed: 12/14/2022] Open
Abstract
Predicting RNA solvent accessibility using only primary sequence data can be regarded as sequence-based prediction work. Currently, the established studies for sequence-based RNA solvent accessibility prediction are limited due to the available number of datasets and black box prediction. To improve these issues, we first expanded the available RNA structures and then developed a sequence-based model using modified attention layers with different receptive fields to conform to the stem-loop structure of RNA chains. We measured the improvement with an extended dataset and further explored the model's interpretability by analysing the model structures, attention values and hyperparameters. Finally, we found that the developed model regarded the pieces of a sequence as templates during the training process. This work will be helpful for researchers who would like to build RNA attribute prediction models using deep learning in the future.
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Affiliation(s)
- Yuyao Huang
- College of Chemistry, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Jiesi Luo
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Runyu Jing
- School of Cyber Science and Engineering, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, Sichuan, 610065, China
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4
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Predicting RNA solvent accessibility from multi-scale context feature via multi-shot neural network. Anal Biochem 2022; 654:114802. [PMID: 35809650 DOI: 10.1016/j.ab.2022.114802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/11/2022] [Accepted: 06/28/2022] [Indexed: 11/24/2022]
Abstract
Knowledge of RNA solvent accessibility has recently become attractive due to the increasing awareness of its importance for key biological process. Accurately predicting the solvent accessibility of RNA is crucial for understanding its 3D structure and biological function. In this study, we develop a novel computational method, termed M2pred, for accurately predicting the solvent accessibility of RNA from sequence-based multi-scale context feature. In M2pred, three single-view features, i.e., base-pairing probabilities, position-specific frequency matrix, and a binary one-hot encoding, are first generated as three feature sources, and immediately concatenated to engender a super feature. Secondly, for the super feature, the matrix-format features of each nucleotide are extracted using an initialized sliding window technique, and regularly stacked into a cube-format feature. Then, using multi-scale context feature extraction strategy, a pyramid feature constructed of contextual feature of four scales related to target nucleotides is extracted from the cube-format feature. Finally, a customized multi-shot neural network framework, which is equipped with four different scales of receptive fields mainly integrating several residual attention blocks, is designed to dig discrimination information from the contextual pyramid feature. Experimental results demonstrate that the proposed M2pred achieve a high prediction performance and outperforms existing state-of-the-art prediction methods of RNA solvent accessibility.
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5
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Solayman M, Litfin T, Singh J, Paliwal K, Zhou Y, Zhan J. Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives. Brief Bioinform 2022; 23:6554125. [PMID: 35348613 PMCID: PMC9116373 DOI: 10.1093/bib/bbac112] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/30/2022] Open
Abstract
Characterizing RNA structures and functions have mostly been focused on 2D, secondary and 3D, tertiary structures. Recent advances in experimental and computational techniques for probing or predicting RNA solvent accessibility make this 1D representation of tertiary structures an increasingly attractive feature to explore. Here, we provide a survey of these recent developments, which indicate the emergence of solvent accessibility as a simple 1D property, adding to secondary and tertiary structures for investigating complex structure–function relations of RNAs.
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Affiliation(s)
- Md Solayman
- Institute for Glycomics, Griffith University, Parklands Dr. Southport, QLD 4222, Australia
| | - Thomas Litfin
- Institute for Glycomics, Griffith University, Parklands Dr. Southport, QLD 4222, Australia
| | - Jaswinder Singh
- Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University, Brisbane, QLD 4111, Australia
| | - Kuldip Paliwal
- Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University, Brisbane, QLD 4111, Australia
| | - Yaoqi Zhou
- Institute for Glycomics, Griffith University, Parklands Dr. Southport, QLD 4222, Australia.,Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.,Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Jian Zhan
- Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
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6
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Solayman M, Litfin T, Zhou Y, Zhan J. High-throughput mapping of RNA solvent accessibility at the single-nucleotide resolution by RtcB ligation between a fixed 5'-OH-end linker and unique 3'-P-end fragments from hydroxyl radical cleavage. RNA Biol 2022; 19:1179-1189. [PMID: 36369947 PMCID: PMC9662193 DOI: 10.1080/15476286.2022.2145098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Given the challenges for the experimental determination of RNA tertiary structures, probing solvent accessibility has become increasingly important to gain functional insights. Among various chemical probes developed, backbone-cleaving hydroxyl radical is the only one that can provide unbiased detection of all accessible nucleotides. However, the readouts have been based on reverse transcription (RT) stop at the cleaving sites, which are prone to false positives due to PCR amplification bias, early drop-off of reverse transcriptase, and the use of random primers in RT reaction. Here, we introduced a fixed-primer method called RL-Seq by performing RtcB Ligation (RL) between a fixed 5'-OH-end linker and unique 3'-P-end fragments from hydroxyl radical cleavage prior to high-throughput sequencing. The application of this method to E. coli ribosomes confirmed its ability to accurately probe solvent accessibility with high sensitivity (low required sequencing depth) and accuracy (strong correlation to structure-derived values) at the single-nucleotide resolution. Moreover, a near-perfect correlation was found between the experiments with and without using unique molecular identifiers, indicating negligible PCR biases in RL-Seq. Further improvement of RL-Seq and its potential transcriptome-wide applications are discussed.
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Affiliation(s)
- Md Solayman
- Institute for Glycomics, Griffith University, Parklands Dr, Southport, QLD, Australia
| | - Thomas Litfin
- Institute for Glycomics, Griffith University, Parklands Dr, Southport, QLD, Australia
| | - Yaoqi Zhou
- Institute for Glycomics, Griffith University, Parklands Dr, Southport, QLD, Australia,Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China,CONTACT Yaoqi Zhou Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Jian Zhan
- Institute for Glycomics, Griffith University, Parklands Dr, Southport, QLD, Australia,Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China,Jian Zhan Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen518055, China
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7
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Amirloo B, Staroseletz Y, Yousaf S, Clarke DJ, Brown T, Aojula H, Zenkova MA, Bichenkova EV. "Bind, cleave and leave": multiple turnover catalysis of RNA cleavage by bulge-loop inducing supramolecular conjugates. Nucleic Acids Res 2021; 50:651-673. [PMID: 34967410 PMCID: PMC8789077 DOI: 10.1093/nar/gkab1273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 12/23/2022] Open
Abstract
Antisense sequence-specific knockdown of pathogenic RNA offers opportunities to find new solutions for therapeutic treatments. However, to gain a desired therapeutic effect, the multiple turnover catalysis is critical to inactivate many copies of emerging RNA sequences, which is difficult to achieve without sacrificing the sequence-specificity of cleavage. Here, engineering two or three catalytic peptides into the bulge-loop inducing molecular framework of antisense oligonucleotides achieved catalytic turnover of targeted RNA. Different supramolecular configurations revealed that cleavage of the RNA backbone upon sequence-specific hybridization with the catalyst accelerated with increase in the number of catalytic guanidinium groups, with almost complete demolition of target RNA in 24 h. Multiple sequence-specific cuts at different locations within and around the bulge-loop facilitated release of the catalyst for subsequent attacks of at least 10 further RNA substrate copies, such that delivery of only a few catalytic molecules could be sufficient to maintain knockdown of typical RNA copy numbers. We have developed fluorescent assay and kinetic simulation tools to characterise how the limited availability of different targets and catalysts had restrained catalytic reaction progress considerably, and to inform how to accelerate the catalytic destruction of shorter linear and larger RNAs even further.
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Affiliation(s)
- Bahareh Amirloo
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Yaroslav Staroseletz
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090 Novosibirsk, Russian Federation
| | - Sameen Yousaf
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - David J Clarke
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Harmesh Aojula
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090 Novosibirsk, Russian Federation
| | - Elena V Bichenkova
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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8
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Gilmer O, Quignon E, Jousset AC, Paillart JC, Marquet R, Vivet-Boudou V. Chemical and Enzymatic Probing of Viral RNAs: From Infancy to Maturity and Beyond. Viruses 2021; 13:1894. [PMID: 34696322 PMCID: PMC8537439 DOI: 10.3390/v13101894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022] Open
Abstract
RNA molecules are key players in a variety of biological events, and this is particularly true for viral RNAs. To better understand the replication of those pathogens and try to block them, special attention has been paid to the structure of their RNAs. Methods to probe RNA structures have been developed since the 1960s; even if they have evolved over the years, they are still in use today and provide useful information on the folding of RNA molecules, including viral RNAs. The aim of this review is to offer a historical perspective on the structural probing methods used to decipher RNA structures before the development of the selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) methodology and to show how they have influenced the current probing techniques. Actually, these technological breakthroughs, which involved advanced detection methods, were made possible thanks to the development of next-generation sequencing (NGS) but also to the previous works accumulated in the field of structural RNA biology. Finally, we will also discuss how high-throughput SHAPE (hSHAPE) paved the way for the development of sophisticated RNA structural techniques.
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Affiliation(s)
| | | | | | | | - Roland Marquet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR9002, F-67000 Strasbourg, France; (O.G.); (E.Q.); (A.-C.J.); (J.-C.P.)
| | - Valérie Vivet-Boudou
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR9002, F-67000 Strasbourg, France; (O.G.); (E.Q.); (A.-C.J.); (J.-C.P.)
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9
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Hanumanthappa AK, Singh J, Paliwal K, Singh J, Zhou Y. Single-sequence and profile-based prediction of RNA solvent accessibility using dilated convolutional neural network. Bioinformatics 2021; 36:5169-5176. [PMID: 33106872 DOI: 10.1093/bioinformatics/btaa652] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 06/30/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022] Open
Abstract
MOTIVATION RNA solvent accessibility, similar to protein solvent accessibility, reflects the structural regions that are accessible to solvents or other functional biomolecules, and plays an important role for structural and functional characterization. Unlike protein solvent accessibility, only a few tools are available for predicting RNA solvent accessibility despite the fact that millions of RNA transcripts have unknown structures and functions. Also, these tools have limited accuracy. Here, we have developed RNAsnap2 that uses a dilated convolutional neural network with a new feature, based on predicted base-pairing probabilities from LinearPartition. RESULTS Using the same training set from the recent predictor RNAsol, RNAsnap2 provides an 11% improvement in median Pearson Correlation Coefficient (PCC) and 9% improvement in mean absolute errors for the same test set of 45 RNA chains. A larger improvement (22% in median PCC) is observed for 31 newly deposited RNA chains that are non-redundant and independent from the training and the test sets. A single-sequence version of RNAsnap2 (i.e. without using sequence profiles generated from homology search by Infernal) has achieved comparable performance to the profile-based RNAsol. In addition, RNAsnap2 has achieved comparable performance for protein-bound and protein-free RNAs. Both RNAsnap2 and RNAsnap2 (SingleSeq) are expected to be useful for searching structural signatures and locating functional regions of non-coding RNAs. AVAILABILITY AND IMPLEMENTATION Standalone-versions of RNAsnap2 and RNAsnap2 (SingleSeq) are available at https://github.com/jaswindersingh2/RNAsnap2. Direct prediction can also be made at https://sparks-lab.org/server/rnasnap2. The datasets used in this research can also be downloaded from the GITHUB and the webserver mentioned above. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Anil Kumar Hanumanthappa
- Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University, Brisbane, QLD 4111, Australia
| | - Jaswinder Singh
- Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University, Brisbane, QLD 4111, Australia
| | - Kuldip Paliwal
- Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University, Brisbane, QLD 4111, Australia
| | - Jaspreet Singh
- Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University, Brisbane, QLD 4111, Australia
| | - Yaoqi Zhou
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Southport, QLD 4222, Australia
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10
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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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11
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Excess primer degradation by Exo I improves the preparation of 3' cDNA ligation-based sequencing libraries. Biotechniques 2019; 67:110-116. [PMID: 31208218 DOI: 10.2144/btn-2018-0178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
RNA sequencing library construction using single-stranded ligation of a DNA adapter to 3' ends of cDNAs often produces primer-adapter byproducts, which compete with cDNA-adapter ligation products during library amplification and, therefore, reduces the number of informative sequencing reads. We find that Escherichia coli Exo I digestion efficiently and selectively removes surplus reverse transcription primer and thereby reduces the primer-adapter product contamination in 3' cDNA ligation-based sequencing libraries, including small RNA libraries, which are typically similar in size to the primer-adapter products. We further demonstrate that Exo I treatment does not lead to trimming of the cDNA 3' end when duplexed with the RNA template. Exo I digestion is easy to perform and implement in other protocols and could facilitate a more widespread use of 3' cDNA ligation for sequencing-based applications.
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12
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Ponce-Salvatierra A, Astha, Merdas K, Nithin C, Ghosh P, Mukherjee S, Bujnicki JM. Computational modeling of RNA 3D structure based on experimental data. Biosci Rep 2019; 39:BSR20180430. [PMID: 30670629 PMCID: PMC6367127 DOI: 10.1042/bsr20180430] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 01/02/2023] Open
Abstract
RNA molecules are master regulators of cells. They are involved in a variety of molecular processes: they transmit genetic information, sense cellular signals and communicate responses, and even catalyze chemical reactions. As in the case of proteins, RNA function is dictated by its structure and by its ability to adopt different conformations, which in turn is encoded in the sequence. Experimental determination of high-resolution RNA structures is both laborious and difficult, and therefore the majority of known RNAs remain structurally uncharacterized. To address this problem, predictive computational methods were developed based on the accumulated knowledge of RNA structures determined so far, the physical basis of the RNA folding, and taking into account evolutionary considerations, such as conservation of functionally important motifs. However, all theoretical methods suffer from various limitations, and they are generally unable to accurately predict structures for RNA sequences longer than 100-nt residues unless aided by additional experimental data. In this article, we review experimental methods that can generate data usable by computational methods, as well as computational approaches for RNA structure prediction that can utilize data from experimental analyses. We outline methods and data types that can be potentially useful for RNA 3D structure modeling but are not commonly used by the existing software, suggesting directions for future development.
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Affiliation(s)
- Almudena Ponce-Salvatierra
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, Warsaw PL-02-109, Poland
| | - Astha
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, Warsaw PL-02-109, Poland
| | - Katarzyna Merdas
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, Warsaw PL-02-109, Poland
| | - Chandran Nithin
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, Warsaw PL-02-109, Poland
| | - Pritha Ghosh
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, Warsaw PL-02-109, Poland
| | - Sunandan Mukherjee
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, Warsaw PL-02-109, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, Warsaw PL-02-109, Poland
- Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, Poznan PL-61-614, Poland
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13
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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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14
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Sauter B, Gillingham D. Profiling the Nucleobase and Structure Selectivity of Anticancer Drugs and other DNA Alkylating Agents by RNA Sequencing. Chembiochem 2018; 19:1638-1642. [PMID: 29732707 DOI: 10.1002/cbic.201800235] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Indexed: 01/10/2023]
Abstract
Drugs that covalently modify DNA are components of most chemotherapy regimens, often serving as first-line treatments. Classically, the reactivity and selectivity of DNA alkylating agents has been determined in vitro with short oligonucleotides. A statistically sound analysis of sequence preferences of alkylating agents is untenable with serial analysis methods because of the combinatorial explosion of sequence possibilities. Next-generation sequencing (NGS) is ideally suited for the broad characterization of sequence or structure selectivities because it analyzes many sequences at once. Herein, NGS is used to report on the chemoselectivity of alkylating agents on RNA and this technology is applied to the previously uncharacterized alkylating agent trimethylsilyl diazomethane.
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Affiliation(s)
- Basilius Sauter
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland
| | - Dennis Gillingham
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland
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15
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Hao Y, Bohon J, Hulscher R, Rappé MC, Gupta S, Adilakshmi T, Woodson SA. Time-Resolved Hydroxyl Radical Footprinting of RNA with X-Rays. ACTA ACUST UNITED AC 2018; 73:e52. [PMID: 29927103 DOI: 10.1002/cpnc.52] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
RNA footprinting by hydroxyl radical cleavage provides 'snapshots' of RNA tertiary structure or protein interactions that bury the RNA backbone. Generation of hydroxyl radicals with a high-flux synchrotron X-ray beam provides analysis on a short timescale (5-100 msec), which enables the structures of folding intermediates or other transient conformational states to be determined in biochemical solutions or cells. This article provides protocols for using synchrotron beamlines for hydroxyl radical footprinting. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Yumeng Hao
- Johns Hopkins University, Baltimore, Maryland
| | - Jen Bohon
- Center for Synchrotron Biosciences, Case Western Reserve University, Cleveland, Ohio
| | | | | | - Sayan Gupta
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California
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16
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Schuller AP, Zinshteyn B, Enam SU, Green R. Directed hydroxyl radical probing reveals Upf1 binding to the 80S ribosomal E site rRNA at the L1 stalk. Nucleic Acids Res 2018; 46:2060-2073. [PMID: 29253221 PMCID: PMC5829565 DOI: 10.1093/nar/gkx1263] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/04/2017] [Accepted: 12/06/2017] [Indexed: 01/02/2023] Open
Abstract
Upf1 is an SF1-family RNA helicase that is essential for the nonsense-mediated decay (NMD) process in eukaryotes. While Upf1 has been shown to interact with 80S ribosomes, the molecular details of this interaction were unknown. Using purified recombinant proteins and high-throughput sequencing combined with Fe-BABE directed hydroxyl radical probing (HTS-BABE) we have characterized the interaction between Upf1 and the yeast 80S ribosome. We identify the 1C domain of Upf1, an alpha-helical insertion in the RecA helicase core, to be essential for ribosome binding, and determine that the L1 stalk of 25S rRNA is the binding site for Upf1 on the ribosome. Using the cleavage sites identified by hydroxyl radical probing and high-resolution structures of both yeast Upf1 and the human 80S ribosome, we provide a model of a Upf1:80S structure. Our model requires that the L1 stalk adopt an open configuration as adopted by an un-rotated, or classical-state, ribosome. Our results shed light on the interaction between Upf1 and the ribosome, and suggest that Upf1 may specifically engage a classical-state ribosome during translation.
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Affiliation(s)
- Anthony P Schuller
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Boris Zinshteyn
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Syed Usman Enam
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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17
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Ritchey LE, Su Z, Tang Y, Tack DC, Assmann SM, Bevilacqua PC. Structure-seq2: sensitive and accurate genome-wide profiling of RNA structure in vivo. Nucleic Acids Res 2017. [PMID: 28637286 PMCID: PMC5737731 DOI: 10.1093/nar/gkx533] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
RNA serves many functions in biology such as splicing, temperature sensing, and innate immunity. These functions are often determined by the structure of RNA. There is thus a pressing need to understand RNA structure and how it changes during diverse biological processes both in vivo and genome-wide. Here, we present Structure-seq2, which provides nucleotide-resolution RNA structural information in vivo and genome-wide. This optimized version of our original Structure-seq method increases sensitivity by at least 4-fold and improves data quality by minimizing formation of a deleterious by-product, reducing ligation bias, and improving read coverage. We also present a variation of Structure-seq2 in which a biotinylated nucleotide is incorporated during reverse transcription, which greatly facilitates the protocol by eliminating two PAGE purification steps. We benchmark Structure-seq2 on both mRNA and rRNA structure in rice (Oryza sativa). We demonstrate that Structure-seq2 can lead to new biological insights. Our Structure-seq2 datasets uncover hidden breaks in chloroplast rRNA and identify a previously unreported N1-methyladenosine (m1A) in a nuclear-encoded Oryza sativa rRNA. Overall, Structure-seq2 is a rapid, sensitive, and unbiased method to probe RNA in vivo and genome-wide that facilitates new insights into RNA biology.
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Affiliation(s)
- Laura E Ritchey
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.,Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Zhao Su
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Yin Tang
- Bioinformatics and Genomics Graduate Program, Pennsylvania State University, University Park, PA 16802, USA
| | - David C Tack
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Philip C Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.,Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.,Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
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18
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Piao M, Sun L, Zhang QC. RNA Regulations and Functions Decoded by Transcriptome-wide RNA Structure Probing. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:267-278. [PMID: 29031843 PMCID: PMC5673676 DOI: 10.1016/j.gpb.2017.05.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 05/09/2017] [Accepted: 05/27/2017] [Indexed: 01/07/2023]
Abstract
RNA folds into intricate structures that are crucial for its functions and regulations. To date, a multitude of approaches for probing structures of the whole transcriptome, i.e., RNA structuromes, have been developed. Applications of these approaches to different cell lines and tissues have generated a rich resource for the study of RNA structure–function relationships at a systems biology level. In this review, we first introduce the designs of these methods and their applications to study different RNA structuromes. We emphasize their technological differences especially their unique advantages and caveats. We then summarize the structural insights in RNA functions and regulations obtained from the studies of RNA structuromes. And finally, we propose potential directions for future improvements and studies.
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Affiliation(s)
- Meiling Piao
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lei Sun
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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19
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Hagedorn PH, Hansen BR, Koch T, Lindow M. Managing the sequence-specificity of antisense oligonucleotides in drug discovery. Nucleic Acids Res 2017; 45:2262-2282. [PMID: 28426096 PMCID: PMC5389529 DOI: 10.1093/nar/gkx056] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 01/21/2017] [Indexed: 01/06/2023] Open
Abstract
All drugs perturb the expression of many genes in the cells that are exposed to them. These gene expression changes can be divided into effects resulting from engaging the intended target and effects resulting from engaging unintended targets. For antisense oligonucleotides, developments in bioinformatics algorithms, and the quality of sequence databases, allow oligonucleotide sequences to be analyzed computationally, in terms of the predictability of their interactions with intended and unintended RNA targets. Applying these tools enables selection of sequence-specific oligonucleotides where no- or only few unintended RNA targets are expected. To evaluate oligonucleotide sequence-specificity experimentally, we recommend a transcriptomics protocol where two or more oligonucleotides targeting the same RNA molecule, but with entirely different sequences, are evaluated together. This helps to clarify which changes in cellular RNA levels result from downstream processes of engaging the intended target, and which are likely to be related to engaging unintended targets. As required for all classes of drugs, the toxic potential of oligonucleotides must be evaluated in cell- and animal models before clinical testing. Since potential adverse effects related to unintended targeting are sequence-dependent and therefore species-specific, in vitro toxicology assays in human cells are especially relevant in oligonucleotide drug discovery.
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Affiliation(s)
- Peter H Hagedorn
- Roche Pharmaceutical Discovery and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, Hørsholm 2970, Denmark.,Center for Computational and Applied Transcriptomics, Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Bo R Hansen
- Roche Pharmaceutical Discovery and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, Hørsholm 2970, Denmark
| | - Troels Koch
- Roche Pharmaceutical Discovery and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, Hørsholm 2970, Denmark
| | - Morten Lindow
- Roche Pharmaceutical Discovery and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, Hørsholm 2970, Denmark.,Center for Computational and Applied Transcriptomics, Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark.,The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
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20
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Dawn of the in vivo RNA structurome and interactome. Biochem Soc Trans 2017; 44:1395-1410. [PMID: 27911722 DOI: 10.1042/bst20160075] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 06/19/2016] [Accepted: 07/04/2016] [Indexed: 12/11/2022]
Abstract
RNA is one of the most fascinating biomolecules in living systems given its structural versatility to fold into elaborate architectures for important biological functions such as gene regulation, catalysis, and information storage. Knowledge of RNA structures and interactions can provide deep insights into their functional roles in vivo For decades, RNA structural studies have been conducted on a transcript-by-transcript basis. The advent of next-generation sequencing (NGS) has enabled the development of transcriptome-wide structural probing methods to profile the global landscape of RNA structures and interactions, also known as the RNA structurome and interactome, which transformed our understanding of the RNA structure-function relationship on a transcriptomic scale. In this review, molecular tools and NGS methods used for RNA structure probing are presented, novel insights uncovered by RNA structurome and interactome studies are highlighted, and perspectives on current challenges and potential future directions are discussed. A more complete understanding of the RNA structures and interactions in vivo will help illuminate the novel roles of RNA in gene regulation, development, and diseases.
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21
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Structural transitions during large ribosomal subunit maturation analyzed by tethered nuclease structure probing in S. cerevisiae. PLoS One 2017; 12:e0179405. [PMID: 28686620 PMCID: PMC5501410 DOI: 10.1371/journal.pone.0179405] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 05/30/2017] [Indexed: 11/19/2022] Open
Abstract
Yeast large ribosomal subunit (LSU) precursors are subject to substantial changes in protein composition during their maturation due to coordinated transient interactions with a large number of ribosome biogenesis factors and due to the assembly of ribosomal proteins. These compositional changes go along with stepwise processing of LSU rRNA precursors and with specific rRNA folding events, as revealed by recent cryo-electron microscopy analyses of late nuclear and cytoplasmic LSU precursors. Here we aimed to analyze changes in the spatial rRNA surrounding of selected ribosomal proteins during yeast LSU maturation. For this we combined a recently developed tethered tertiary structure probing approach with both targeted and high throughput readout strategies. Several structural features of late LSU precursors were faithfully detected by this procedure. In addition, the obtained data let us suggest that early rRNA precursor processing events are accompanied by a global transition from a flexible to a spatially restricted rRNA conformation. For intermediate LSU precursors a number of structural hallmarks could be addressed which include the fold of the internal transcribed spacer between 5.8S rRNA and 25S rRNA, the orientation of the central protuberance and the spatial organization of the interface between LSU rRNA domains I and III.
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22
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Abstract
The discoveries of myriad non-coding RNA molecules, each transiting through multiple flexible states in cells or virions, present major challenges for structure determination. Advances in high-throughput chemical mapping give new routes for characterizing entire transcriptomes in vivo, but the resulting one-dimensional data generally remain too information-poor to allow accurate de novo structure determination. Multidimensional chemical mapping (MCM) methods seek to address this challenge. Mutate-and-map (M2), RNA interaction groups by mutational profiling (RING-MaP and MaP-2D analysis) and multiplexed •OH cleavage analysis (MOHCA) measure how the chemical reactivities of every nucleotide in an RNA molecule change in response to modifications at every other nucleotide. A growing body of in vitro blind tests and compensatory mutation/rescue experiments indicate that MCM methods give consistently accurate secondary structures and global tertiary structures for ribozymes, ribosomal domains and ligand-bound riboswitch aptamers up to 200 nucleotides in length. Importantly, MCM analyses provide detailed information on structurally heterogeneous RNA states, such as ligand-free riboswitches that are functionally important but difficult to resolve with other approaches. The sequencing requirements of currently available MCM protocols scale at least quadratically with RNA length, precluding general application to transcriptomes or viral genomes at present. We propose a modify-cross-link-map (MXM) expansion to overcome this and other current limitations to resolving the in vivo 'RNA structurome'.
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23
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Choudhary K, Deng F, Aviran S. Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions. QUANTITATIVE BIOLOGY 2017; 5:3-24. [PMID: 28717530 PMCID: PMC5510538 DOI: 10.1007/s40484-017-0093-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 12/08/2016] [Accepted: 12/15/2016] [Indexed: 12/30/2022]
Abstract
BACKGROUND Structure profiling experiments provide single-nucleotide information on RNA structure. Recent advances in chemistry combined with application of high-throughput sequencing have enabled structure profiling at transcriptome scale and in living cells, creating unprecedented opportunities for RNA biology. Propelled by these experimental advances, massive data with ever-increasing diversity and complexity have been generated, which give rise to new challenges in interpreting and analyzing these data. RESULTS We review current practices in analysis of structure profiling data with emphasis on comparative and integrative analysis as well as highlight emerging questions. Comparative analysis has revealed structural patterns across transcriptomes and has become an integral component of recent profiling studies. Additionally, profiling data can be integrated into traditional structure prediction algorithms to improve prediction accuracy. CONCLUSIONS To keep pace with experimental developments, methods to facilitate, enhance and refine such analyses are needed. Parallel advances in analysis methodology will complement profiling technologies and help them reach their full potential.
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Affiliation(s)
| | | | - Sharon Aviran
- Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA 95616, USA
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24
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Incarnato D, Oliviero S. The RNA Epistructurome: Uncovering RNA Function by Studying Structure and Post-Transcriptional Modifications. Trends Biotechnol 2016; 35:318-333. [PMID: 27988057 DOI: 10.1016/j.tibtech.2016.11.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/11/2016] [Accepted: 11/21/2016] [Indexed: 01/15/2023]
Abstract
A large fraction of higher metazoan genomes transcribe RNA molecules whose functions extend far beyond carrying instructions for protein synthesis. Although RNA is apparently a simple molecule, the ways in which it performs many of its functions have remained highly elusive for decades. As learned from studying ribosomal and transfer RNAs, two of the key features influencing the function of RNA are its structure and post-transcriptional modifications. A deep understanding of RNA function therefore requires rapid and straightforward approaches to study the complex and intricate landscape of RNA structures and modifications. In this review we summarize and discuss the most recent methods and findings in the field of RNA biology, with an eye toward new frontiers and open questions.
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Affiliation(s)
- Danny Incarnato
- Human Genetics Foundation (HuGeF), 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
- Human Genetics Foundation (HuGeF), 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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25
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Robust statistical modeling improves sensitivity of high-throughput RNA structure probing experiments. Nat Methods 2016; 14:83-89. [DOI: 10.1038/nmeth.4068] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 10/03/2016] [Indexed: 12/20/2022]
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26
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Choudhary K, Shih NP, Deng F, Ledda M, Li B, Aviran S. Metrics for rapid quality control in RNA structure probing experiments. Bioinformatics 2016; 32:3575-3583. [PMID: 27497441 DOI: 10.1093/bioinformatics/btw501] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 07/02/2016] [Accepted: 07/26/2016] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The diverse functionalities of RNA can be attributed to its capacity to form complex and varied structures. The recent proliferation of new structure probing techniques coupled with high-throughput sequencing has helped RNA studies expand in both scope and depth. Despite differences in techniques, most experiments face similar challenges in reproducibility due to the stochastic nature of chemical probing and sequencing. As these protocols expand to transcriptome-wide studies, quality control becomes a more daunting task. General and efficient methodologies are needed to quantify variability and quality in the wide range of current and emerging structure probing experiments. RESULTS We develop metrics to rapidly and quantitatively evaluate data quality from structure probing experiments, demonstrating their efficacy on both small synthetic libraries and transcriptome-wide datasets. We use a signal-to-noise ratio concept to evaluate replicate agreement, which has the capacity to identify high-quality data. We also consider and compare two methods to assess variability inherent in probing experiments, which we then utilize to evaluate the coverage adjustments needed to meet desired quality. The developed metrics and tools will be useful in summarizing large-scale datasets and will help standardize quality control in the field. AVAILABILITY AND IMPLEMENTATION The data and methods used in this article are freely available at: http://bme.ucdavis.edu/aviranlab/SPEQC_software CONTACT: saviran@ucdavis.eduSupplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Krishna Choudhary
- Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA
| | - Nathan P Shih
- Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA
| | - Fei Deng
- Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA
| | - Mirko Ledda
- Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA
| | - Bo Li
- Center for RNA Systems Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Sharon Aviran
- Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA
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27
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Deng F, Ledda M, Vaziri S, Aviran S. Data-directed RNA secondary structure prediction using probabilistic modeling. RNA (NEW YORK, N.Y.) 2016; 22:1109-1119. [PMID: 27251549 PMCID: PMC4931104 DOI: 10.1261/rna.055756.115] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/26/2016] [Indexed: 06/05/2023]
Abstract
Structure dictates the function of many RNAs, but secondary RNA structure analysis is either labor intensive and costly or relies on computational predictions that are often inaccurate. These limitations are alleviated by integration of structure probing data into prediction algorithms. However, existing algorithms are optimized for a specific type of probing data. Recently, new chemistries combined with advances in sequencing have facilitated structure probing at unprecedented scale and sensitivity. These novel technologies and anticipated wealth of data highlight a need for algorithms that readily accommodate more complex and diverse input sources. We implemented and investigated a recently outlined probabilistic framework for RNA secondary structure prediction and extended it to accommodate further refinement of structural information. This framework utilizes direct likelihood-based calculations of pseudo-energy terms per considered structural context and can readily accommodate diverse data types and complex data dependencies. We use real data in conjunction with simulations to evaluate performances of several implementations and to show that proper integration of structural contexts can lead to improvements. Our tests also reveal discrepancies between real data and simulations, which we show can be alleviated by refined modeling. We then propose statistical preprocessing approaches to standardize data interpretation and integration into such a generic framework. We further systematically quantify the information content of data subsets, demonstrating that high reactivities are major drivers of SHAPE-directed predictions and that better understanding of less informative reactivities is key to further improvements. Finally, we provide evidence for the adaptive capability of our framework using mock probe simulations.
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Affiliation(s)
- Fei Deng
- Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, California 95616, USA
| | - Mirko Ledda
- Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, California 95616, USA
| | - Sana Vaziri
- Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, California 95616, USA
| | - Sharon Aviran
- Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, California 95616, USA
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28
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Hulscher RM, Bohon J, Rappé MC, Gupta S, D'Mello R, Sullivan M, Ralston CY, Chance MR, Woodson SA. Probing the structure of ribosome assembly intermediates in vivo using DMS and hydroxyl radical footprinting. Methods 2016; 103:49-56. [PMID: 27016143 PMCID: PMC4921310 DOI: 10.1016/j.ymeth.2016.03.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/09/2016] [Accepted: 03/21/2016] [Indexed: 01/01/2023] Open
Abstract
The assembly of the Escherichia coli ribosome has been widely studied and characterized in vitro. Despite this, ribosome biogenesis in living cells is only partly understood because assembly is coupled with transcription, modification and processing of the pre-ribosomal RNA. We present a method for footprinting and isolating pre-rRNA as it is synthesized in E. coli cells. Pre-rRNA synthesis is synchronized by starvation, followed by nutrient upshift. RNA synthesized during outgrowth is metabolically labeled to facilitate isolation of recent transcripts. Combining this technique with two in vivo RNA probing methods, hydroxyl radical and DMS footprinting, allows the structure of nascent RNA to be probed over time. Together, these can be used to determine changes in the structures of ribosome assembly intermediates as they fold in vivo.
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Affiliation(s)
- Ryan M Hulscher
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Jen Bohon
- Center for Proteomics and Bioinformatics and Center for Synchrotron Biosciences, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106, USA
| | - Mollie C Rappé
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Sayan Gupta
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Rhijuta D'Mello
- Center for Proteomics and Bioinformatics and Center for Synchrotron Biosciences, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106, USA
| | - Michael Sullivan
- Center for Proteomics and Bioinformatics and Center for Synchrotron Biosciences, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106, USA
| | - Corie Y Ralston
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mark R Chance
- Center for Proteomics and Bioinformatics and Center for Synchrotron Biosciences, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106, USA
| | - Sarah A Woodson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA.
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29
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Lorenz R, Wolfinger MT, Tanzer A, Hofacker IL. Predicting RNA secondary structures from sequence and probing data. Methods 2016; 103:86-98. [PMID: 27064083 DOI: 10.1016/j.ymeth.2016.04.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 03/29/2016] [Accepted: 04/04/2016] [Indexed: 01/08/2023] Open
Abstract
RNA secondary structures have proven essential for understanding the regulatory functions performed by RNA such as microRNAs, bacterial small RNAs, or riboswitches. This success is in part due to the availability of efficient computational methods for predicting RNA secondary structures. Recent advances focus on dealing with the inherent uncertainty of prediction by considering the ensemble of possible structures rather than the single most stable one. Moreover, the advent of high-throughput structural probing has spurred the development of computational methods that incorporate such experimental data as auxiliary information.
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Affiliation(s)
- Ronny Lorenz
- University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstrasse 17, 1090 Vienna, Austria.
| | - Michael T Wolfinger
- University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstrasse 17, 1090 Vienna, Austria; Medical University of Vienna, Center for Anatomy and Cell Biology, Währingerstraße 13, 1090 Vienna, Austria.
| | - Andrea Tanzer
- University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstrasse 17, 1090 Vienna, Austria.
| | - Ivo L Hofacker
- University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstrasse 17, 1090 Vienna, Austria; University of Vienna, Faculty of Computer Science, Research Group Bioinformatics and Computational Biology, Währingerstr. 29, 1090 Vienna, Austria.
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30
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Uzilov AV, Underwood JG. High-Throughput Nuclease Probing of RNA Structures Using FragSeq. Methods Mol Biol 2016; 1490:105-34. [PMID: 27665596 DOI: 10.1007/978-1-4939-6433-8_8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
High-throughput sequencing of cDNA (RNA-Seq) can be used to generate nuclease accessibility data for many distinct transcripts in the same mixture simultaneously. Such assays accelerate RNA structure analysis and provide researchers with new technologies to tackle biological questions on a transcriptome-wide scale. FragSeq is an experimental assay for transcriptome-wide RNA structure probing using RNA-Seq, coupled with data analysis tools that allow quantitative determination of nuclease accessibility at single-base resolution. We provide a practical guide to designing and carrying out FragSeq experiments and data analysis.
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Affiliation(s)
- Andrew V Uzilov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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31
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Fang R, Moss WN, Rutenberg-Schoenberg M, Simon MD. Probing Xist RNA Structure in Cells Using Targeted Structure-Seq. PLoS Genet 2015; 11:e1005668. [PMID: 26646615 PMCID: PMC4672913 DOI: 10.1371/journal.pgen.1005668] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 10/24/2015] [Indexed: 11/19/2022] Open
Abstract
The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5’-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function. To do their jobs, many RNAs need to fold into structures (through base-paring). We were interested in the conformation of a specific mammalian RNA, Xist, when it is inside a cell. Xist is a very large non-coding RNA (lncRNA), that is >17,000 nt long. Xist is particularly important because it is one of the first lncRNAs to be discovered, and turns genes off across an entire chromosome. To figure out how Xist RNA is folded in mouse cells, we developed a new approach, Targeted Structure-Seq, to examine the conformation of large RNAs like Xist. Using computer modeling, we identified parts of Xist that are base paired into RNA duplexes. We also determined which parts of the Xist RNA are likely to be structured. This work provides a new tool for studying the secondary structure of any large RNA, and helps us understand what the important pieces of Xist look like while Xist does its work in the cell.
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Affiliation(s)
- Rui Fang
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Chemical Biology Institute, Yale University, West Haven, Connecticut, United States of America
| | - Walter N. Moss
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Michael Rutenberg-Schoenberg
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Chemical Biology Institute, Yale University, West Haven, Connecticut, United States of America
| | - Matthew D. Simon
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Chemical Biology Institute, Yale University, West Haven, Connecticut, United States of America
- * E-mail:
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Dumont E, Monari A. Understanding DNA under oxidative stress and sensitization: the role of molecular modeling. Front Chem 2015; 3:43. [PMID: 26236706 PMCID: PMC4500984 DOI: 10.3389/fchem.2015.00043] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/29/2015] [Indexed: 12/12/2022] Open
Abstract
DNA is constantly exposed to damaging threats coming from oxidative stress, i.e., from the presence of free radicals and reactive oxygen species. Sensitization from exogenous and endogenous compounds that strongly enhance the frequency of light-induced lesions also plays an important role. The experimental determination of DNA lesions, though a difficult subject, is somehow well established and allows to elucidate even extremely rare DNA lesions. In parallel, molecular modeling has become fundamental to clearly understand the fine mechanisms related to DNA defects induction. Indeed, it offers an unprecedented possibility to get access to an atomistic or even electronic resolution. Ab initio molecular dynamics may also describe the time-evolution of the molecular system and its reactivity. Yet the modeling of DNA (photo-)reactions does necessitate elaborate multi-scale methodologies to tackle a damage induction reactivity that takes place in a complex environment. The double-stranded DNA environment is first characterized by a very high flexibility, but also a strongly inhomogeneous electrostatic embedding. Additionally, one aims at capturing more subtle effects, such as the sequence selectivity which is of critical important for DNA damage. The structure and dynamics of the DNA/sensitizers complexes, as well as the photo-induced electron- and energy-transfer phenomena taking place upon sensitization, should be carefully modeled. Finally the factors inducing different repair ratios for different lesions should also be rationalized. In this review we will critically analyze the different computational strategies used to model DNA lesions. A clear picture of the complex interplay between reactivity and structural factors will be sketched. The use of proper multi-scale modeling leads to the in-depth comprehension of DNA lesions mechanisms and also to the rational design of new chemo-therapeutic agents.
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Affiliation(s)
- Elise Dumont
- Laboratoire de Chimie, UMR 5182 Centre National de la Recherche Scientifique, École Normale Supérieure de Lyon Lyon, France
| | - Antonio Monari
- Université de Lorraine - Nancy, Theory-Modeling-Simulation, Structure et Réactivité des Systèmes Moléculaires Complexes (SRSMC) Vandoeuvre-les-Nancy, France ; Centre National de la Recherche Scientifique, Theory-Modeling-Simulation, Structure et Réactivité des Systèmes Moléculaires Complexes (SRSMC) Vandoeuvre-les-Nancy, France
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Solem AC, Halvorsen M, Ramos SBV, Laederach A. The potential of the riboSNitch in personalized medicine. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:517-32. [PMID: 26115028 PMCID: PMC4543445 DOI: 10.1002/wrna.1291] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 03/25/2015] [Accepted: 05/13/2015] [Indexed: 01/28/2023]
Abstract
RNA conformation plays a significant role in stability, ligand binding, transcription, and translation. Single nucleotide variants (SNVs) have the potential to disrupt specific structural elements because RNA folds in a sequence-specific manner. A riboSNitch is an element of RNA structure with a specific function that is disrupted by an SNV or a single nucleotide polymorphism (SNP; or polymorphism; SNVs occur with low frequency in the population, <1%). The riboSNitch is analogous to a riboswitch, where binding of a small molecule rather than mutation alters the structure of the RNA to control gene regulation. RiboSNitches are particularly relevant to interpreting the results of genome-wide association studies (GWAS). Often GWAS identify SNPs associated with a phenotype mapping to noncoding regions of the genome. Because a majority of the human genome is transcribed, significant subsets of GWAS SNPs are putative riboSNitches. The extent to which the transcriptome is tolerant of SNP-induced structure change is still poorly understood. Recent advances in ultra high-throughput structure probing begin to reveal the structural complexities of mutation-induced structure change. This review summarizes our current understanding of SNV and SNP-induced structure change in the human transcriptome and discusses the importance of riboSNitch discovery in interpreting GWAS results and massive sequencing projects.
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Affiliation(s)
- Amanda C Solem
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Matthew Halvorsen
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Silvia B V Ramos
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Bioinformatics and Computational Biology Program, University of North Carolina, Chapel Hill, NC, USA
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Abstract
The range of roles played by structured RNAs in biological systems is vast. At the same time as we are learning more about the importance of RNA structure, recent advances in reagents, methods and technology mean that RNA secondary structural probing has become faster and more accurate. As a result, the capabilities of laboratories that already perform this type of structural analysis have increased greatly, and it has also become more widely accessible. The present review summarizes established and recently developed techniques. The information we can derive from secondary structural analysis is assessed, together with the areas in which we are likely to see exciting developments in the near future.
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Poulsen LD, Kielpinski LJ, Salama SR, Krogh A, Vinther J. SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data. RNA (NEW YORK, N.Y.) 2015; 21:1042-52. [PMID: 25805860 PMCID: PMC4408784 DOI: 10.1261/rna.047068.114] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 02/04/2015] [Indexed: 05/24/2023]
Abstract
Selective 2' Hydroxyl Acylation analyzed by Primer Extension (SHAPE) is an accurate method for probing of RNA secondary structure. In existing SHAPE methods, the SHAPE probing signal is normalized to a no-reagent control to correct for the background caused by premature termination of the reverse transcriptase. Here, we introduce a SHAPE Selection (SHAPES) reagent, N-propanone isatoic anhydride (NPIA), which retains the ability of SHAPE reagents to accurately probe RNA structure, but also allows covalent coupling between the SHAPES reagent and a biotin molecule. We demonstrate that SHAPES-based selection of cDNA-RNA hybrids on streptavidin beads effectively removes the large majority of background signal present in SHAPE probing data and that sequencing-based SHAPES data contain the same amount of RNA structure data as regular sequencing-based SHAPE data obtained through normalization to a no-reagent control. Moreover, the selection efficiently enriches for probed RNAs, suggesting that the SHAPES strategy will be useful for applications with high-background and low-probing signal such as in vivo RNA structure probing.
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Affiliation(s)
- Line Dahl Poulsen
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | | | - Sofie R Salama
- Center for Biomolecular Science and Engineering, and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Anders Krogh
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Jeppe Vinther
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
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The RNA structurome: transcriptome-wide structure probing with next-generation sequencing. Trends Biochem Sci 2015; 40:221-32. [DOI: 10.1016/j.tibs.2015.02.005] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 02/16/2015] [Accepted: 02/17/2015] [Indexed: 01/16/2023]
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Kielpinski LJ, Sidiropoulos N, Vinther J. Reproducible Analysis of Sequencing-Based RNA Structure Probing Data with User-Friendly Tools. Methods Enzymol 2015; 558:153-180. [PMID: 26068741 DOI: 10.1016/bs.mie.2015.01.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
RNA structure-probing data can improve the prediction of RNA secondary and tertiary structure and allow structural changes to be identified and investigated. In recent years, massive parallel sequencing has dramatically improved the throughput of RNA structure probing experiments, but at the same time also made analysis of the data challenging for scientists without formal training in computational biology. Here, we discuss different strategies for data analysis of massive parallel sequencing-based structure-probing data. To facilitate reproducible and standardized analysis of this type of data, we have made a collection of tools, which allow raw sequencing reads to be converted to normalized probing values using different published strategies. In addition, we also provide tools for visualization of the probing data in the UCSC Genome Browser and for converting RNA coordinates to genomic coordinates and vice versa. The collection is implemented as functions in the R statistical environment and as tools in the Galaxy platform, making them easily accessible for the scientific community. We demonstrate the usefulness of the collection by applying it to the analysis of sequencing-based hydroxyl radical probing data and comparing different normalization strategies.
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Affiliation(s)
- Lukasz Jan Kielpinski
- Section for RNA and Computational Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Nikolaos Sidiropoulos
- Section for RNA and Computational Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jeppe Vinther
- Section for RNA and Computational Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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Abstract
The diverse roles of RNAs depend on their ability to fold so as to form biologically functional structures. Thus, understanding the function of a given RNA molecule often requires experimental analysis of its secondary structure by in vitro RNA probing, which is more accurate than using prediction programs only. This chapter presents in vitro RNA probing protocols that we routinely use, from RNA transcript production and purification to RNA structure determination using enzymatic (RNases T1, T2, and V1) and chemical (DMS, CMCT, kethoxal, and Pb(2+)) probing performed on both unlabeled and end-labeled RNAs.
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Affiliation(s)
- Jean-Vincent Philippe
- CNRS UMR 7365 IMoPA, Université de Lorraine, Biopôle, 9 avenue de la Forêt de Haye, Vandoeuvre-lès-Nancy, 54506, France
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Aviran S, Pachter L. Rational experiment design for sequencing-based RNA structure mapping. RNA (NEW YORK, N.Y.) 2014; 20:1864-1877. [PMID: 25332375 PMCID: PMC4238353 DOI: 10.1261/rna.043844.113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Accepted: 09/07/2014] [Indexed: 05/30/2023]
Abstract
Structure mapping is a classic experimental approach for determining nucleic acid structure that has gained renewed interest in recent years following advances in chemistry, genomics, and informatics. The approach encompasses numerous techniques that use different means to introduce nucleotide-level modifications in a structure-dependent manner. Modifications are assayed via cDNA fragment analysis, using electrophoresis or next-generation sequencing (NGS). The recent advent of NGS has dramatically increased the throughput, multiplexing capacity, and scope of RNA structure mapping assays, thereby opening new possibilities for genome-scale, de novo, and in vivo studies. From an informatics standpoint, NGS is more informative than prior technologies by virtue of delivering direct molecular measurements in the form of digital sequence counts. Motivated by these new capabilities, we introduce a novel model-based in silico approach for quantitative design of large-scale multiplexed NGS structure mapping assays, which takes advantage of the direct and digital nature of NGS readouts. We use it to characterize the relationship between controllable experimental parameters and the precision of mapping measurements. Our results highlight the complexity of these dependencies and shed light on relevant tradeoffs and pitfalls, which can be difficult to discern by intuition alone. We demonstrate our approach by quantitatively assessing the robustness of SHAPE-Seq measurements, obtained by multiplexing SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) chemistry in conjunction with NGS. We then utilize it to elucidate design considerations in advanced genome-wide approaches for probing the transcriptome, which recently obtained in vivo information using dimethyl sulfate (DMS) chemistry.
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Affiliation(s)
- Sharon Aviran
- Biomedical Engineering Department and Genome Center, University of California at Davis, Davis, California 95616, USA
| | - Lior Pachter
- Center for Computational Biology and Departments of Molecular and Cell Biology and Mathematics, University of California at Berkeley, Berkeley, California 94720, USA
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40
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Ingle S, Azad RN, Jain SS, Tullius TD. Chemical probing of RNA with the hydroxyl radical at single-atom resolution. Nucleic Acids Res 2014; 42:12758-67. [PMID: 25313156 PMCID: PMC4227780 DOI: 10.1093/nar/gku934] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 09/17/2014] [Accepted: 09/24/2014] [Indexed: 12/02/2022] Open
Abstract
While hydroxyl radical cleavage is widely used to map RNA tertiary structure, lack of mechanistic understanding of strand break formation limits the degree of structural insight that can be obtained from this experiment. Here, we determine how individual ribose hydrogens of sarcin/ricin loop RNA participate in strand cleavage. We find that substituting deuterium for hydrogen at a ribose 5'-carbon produces a kinetic isotope effect on cleavage; the major cleavage product is an RNA strand terminated by a 5'-aldehyde. We conclude that hydroxyl radical abstracts a 5'-hydrogen atom, leading to RNA strand cleavage. We used this approach to obtain structural information for a GUA base triple, a common tertiary structural feature of RNA. Cleavage at U exhibits a large 5' deuterium kinetic isotope effect, a potential signature of a base triple. Others had noted a ribose-phosphate hydrogen bond involving the G 2'-OH and the U phosphate of the GUA triple, and suggested that this hydrogen bond contributes to backbone rigidity. Substituting deoxyguanosine for G, to eliminate this hydrogen bond, results in a substantial decrease in cleavage at G and U of the triple. We conclude that this hydrogen bond is a linchpin of backbone structure around the triple.
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Affiliation(s)
- Shakti Ingle
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Robert N Azad
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Swapan S Jain
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Thomas D Tullius
- Department of Chemistry, Boston University, Boston, MA 02215, USA Program in Bioinformatics, Boston University, Boston, MA 02215, USA
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Abstract
A comprehensive understanding of RNA structure will provide fundamental insights into the cellular function of both coding and non-coding RNAs. Although many RNA structures have been analysed by traditional biophysical and biochemical methods, the low-throughput nature of these approaches has prevented investigation of the vast majority of cellular transcripts. Triggered by advances in sequencing technology, genome-wide approaches for probing the transcriptome are beginning to reveal how RNA structure affects each step of protein expression and RNA stability. In this Review, we discuss the emerging relationships between RNA structure and the regulation of gene expression.
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