1
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Oleynikov M, Jaffrey SR. RNA tertiary structure and conformational dynamics revealed by BASH MaP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.11.589009. [PMID: 38645201 PMCID: PMC11030352 DOI: 10.1101/2024.04.11.589009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The functional effects of an RNA can arise from complex three-dimensional folds known as tertiary structures. However, predicting the tertiary structure of an RNA and whether an RNA adopts distinct tertiary conformations remains challenging. To address this, we developed BASH MaP, a single-molecule dimethyl sulfate (DMS) footprinting method and DAGGER, a computational pipeline, to identify alternative tertiary structures adopted by different molecules of RNA. BASH MaP utilizes potassium borohydride to reveal the chemical accessibility of the N7 position of guanosine, a key mediator of tertiary structures. We used BASH MaP to identify diverse conformational states and dynamics of RNA G-quadruplexes, an important RNA tertiary motif, in vitro and in cells. BASH MaP and DAGGER analysis of the fluorogenic aptamer Spinach reveals that it adopts alternative tertiary conformations which determine its fluorescence states. BASH MaP thus provides an approach for structural analysis of RNA by revealing previously undetectable tertiary structures.
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2
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Arney JW, Laederach A, Weeks KM. Visualizing RNA structure ensembles by single-molecule correlated chemical probing. Curr Opin Struct Biol 2024; 88:102877. [PMID: 39024941 DOI: 10.1016/j.sbi.2024.102877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 07/20/2024]
Abstract
RNA molecules fold to form complex internal structures. Many of these RNA structures populate ensembles with rheostat-like properties, with each state having a distinct function. Until recently, analysis of RNA structures, especially within cells, was limited to modeling either a single averaged structure or computationally-modeled ensembles. These approaches obscure the intrinsic heterogeneity of many structured RNAs. Single-molecule correlated chemical probing (smCCP) strategies are now making it possible to measure and deconvolute RNA structure ensembles based on efficiently executed chemical probing experiments. Here, we provide an overview of fundamental single-molecule probing principles, review current ensemble deconvolution strategies, and discuss recent applications to diverse biological systems. smCCP is enabling a revolution in understanding how the plasticity of RNA structure is exploited in biological systems to respond to stimuli and alter gene function. The energetics of RNA ensembles are often subtle and a subset can likely be targeted to modulate disease-associated biological processes.
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Affiliation(s)
- J Winston Arney
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA.
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3
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Douds CA, Babitzke P, Bevilacqua PC. A new reagent for in vivo structure probing of RNA G and U residues that improves RNA structure prediction alone and combined with DMS. RNA (NEW YORK, N.Y.) 2024; 30:901-919. [PMID: 38670632 PMCID: PMC11182018 DOI: 10.1261/rna.079974.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024]
Abstract
A key to understanding the roles of RNA in regulating gene expression is knowing their structures in vivo. One way to obtain this information is through probing the structures of RNA with chemicals. To probe RNA structure directly in cells, membrane-permeable reagents that modify the Watson-Crick (WC) face of unpaired nucleotides can be used. Although dimethyl sulfate (DMS) has led to substantial insight into RNA structure, it has limited nucleotide specificity in vivo, with WC face reactivity only at adenine (A) and cytosine (C) at neutral pH. The reagent 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) was recently shown to modify the WC face of guanine (G) and uracil (U). Although useful at lower concentrations in experiments that measure chemical modifications by reverse transcription (RT) stops, at higher concentrations necessary for detection by mutational profiling (MaP), EDC treatment leads to degradation of RNA. Here, we demonstrate EDC-stimulated degradation of RNA in Gram-negative and Gram-positive bacteria. In an attempt to overcome these limitations, we developed a new carbodiimide reagent, 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide methiodide (ETC), which we show specifically modifies unpaired Gs and Us in vivo without substantial degradation of RNA. We establish ETC as a probe for MaP and optimize the RT conditions and computational analysis in Escherichia coli Importantly, we demonstrate the utility of ETC as a probe for improving RNA structure prediction both alone and with DMS.
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Affiliation(s)
- Catherine A Douds
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Philip C Bevilacqua
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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4
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Dey A, Yan S, Schlick T, Laederach A. Abolished frameshifting for predicted structure-stabilizing SARS-CoV-2 mutants: Implications to alternative conformations and their statistical structural analyses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.586935. [PMID: 38585719 PMCID: PMC10996636 DOI: 10.1101/2024.03.28.586935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The SARS-CoV-2 frameshifting element (FSE) has been intensely studied and explored as a therapeutic target for coronavirus diseases including COVID-19. Besides the intriguing virology, this small RNA is known to adopt many length-dependent conformations, as verified by multiple experimental and computational approaches. However, the role these alternative conformations play in the frameshifting mechanism and how to quantify this structural abundance has been an ongoing challenge. Here, we show by DMS and dual-luciferase functional assays that previously predicted FSE mutants (using the RAG graph theory approach) suppress structural transitions and abolish frameshifting. Furthermore, correlated mutation analysis of DMS data by three programs (DREEM, DRACO, and DANCE-MaP) reveals important differences in their estimation of specific RNA conformations, suggesting caution in the interpretation of such complex conformational landscapes. Overall, the abolished frameshifting in three different mutants confirms that all alternative conformations play a role in the pathways of ribosomal transition.
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5
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Irving PS, Weeks KM. RNAvigate: efficient exploration of RNA chemical probing datasets. Nucleic Acids Res 2024; 52:2231-2241. [PMID: 38348910 PMCID: PMC10954457 DOI: 10.1093/nar/gkae089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 02/27/2024] Open
Abstract
Chemical probing technologies enable high-throughput examination of diverse structural features of RNA, including local nucleotide flexibility, RNA secondary structure, protein and ligand binding, through-space interaction networks, and multistate structural ensembles. Deep understanding of RNA structure-function relationships typically requires evaluating a system under structure- and function-altering conditions, linking these data with additional information, and visualizing multilayered relationships. Current platforms lack the broad accessibility, flexibility and efficiency needed to iterate on integrative analyses of these diverse, complex data. Here, we share the RNA visualization and graphical analysis toolset RNAvigate, a straightforward and flexible Python library that automatically parses 21 standard file formats (primary sequence annotations, per- and internucleotide data, and secondary and tertiary structures) and outputs 18 plot types. RNAvigate enables efficient exploration of nuanced relationships between multiple layers of RNA structure information and across multiple experimental conditions. Compatibility with Jupyter notebooks enables nonburdensome, reproducible, transparent and organized sharing of multistep analyses and data visualization strategies. RNAvigate simplifies and accelerates discovery and characterization of RNA-centric functions in biology.
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Affiliation(s)
- Patrick S Irving
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
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6
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Aseev LV, Koledinskaya LS, Boni IV. Extraribosomal Functions of Bacterial Ribosomal Proteins-An Update, 2023. Int J Mol Sci 2024; 25:2957. [PMID: 38474204 DOI: 10.3390/ijms25052957] [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: 01/19/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Ribosomal proteins (r-proteins) are abundant, highly conserved, and multifaceted cellular proteins in all domains of life. Most r-proteins have RNA-binding properties and can form protein-protein contacts. Bacterial r-proteins govern the co-transcriptional rRNA folding during ribosome assembly and participate in the formation of the ribosome functional sites, such as the mRNA-binding site, tRNA-binding sites, the peptidyl transferase center, and the protein exit tunnel. In addition to their primary role in a cell as integral components of the protein synthesis machinery, many r-proteins can function beyond the ribosome (the phenomenon known as moonlighting), acting either as individual regulatory proteins or in complexes with various cellular components. The extraribosomal activities of r-proteins have been studied over the decades. In the past decade, our understanding of r-protein functions has advanced significantly due to intensive studies on ribosomes and gene expression mechanisms not only in model bacteria like Escherichia coli or Bacillus subtilis but also in little-explored bacterial species from various phyla. The aim of this review is to update information on the multiple functions of r-proteins in bacteria.
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Affiliation(s)
- Leonid V Aseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia
| | | | - Irina V Boni
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia
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7
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Irving PS, Weeks KM. RNAvigate: Efficient exploration of RNA chemical probing datasets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.538311. [PMID: 37162917 PMCID: PMC10168276 DOI: 10.1101/2023.04.25.538311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Chemical probing technologies enable high-throughput examination of diverse structural features of RNA including local nucleotide flexibility, RNA secondary structure, protein- and ligand-binding, through-space interaction networks, and multi-state structural ensembles. Performing these experiments, by themselves, does not directly lead to biological insight. Instead, deep understanding of RNA structure-function relationships typically requires evaluating a system under structure- and function-altering conditions, linking these data with additional information, and visualizing multi-layered relationships. Current platforms lack the broad accessibility, flexibility, and efficiency needed to iterate on integrative analyses of these diverse, complex data. Here, we share the RNA visualization and graphical analysis toolset RNAvigate, a straightforward and flexible Python library. RNAvigate currently automatically parses twenty-one standard file formats (primary sequence annotations, per- and internucleotide data, and secondary and tertiary structures) and outputs eighteen plot types. These features enable efficient exploration of nuanced relationships between chemical probing data, RNA structure, and motif annotations across multiple experimental samples. Compatibility with Jupyter Notebooks enables non-burdensome, reproducible, transparent and organized sharing of multi-step analyses and data visualization strategies. RNAvigate simplifies examination of multi-layered RNA structure information and accelerates discovery and characterization of RNA-centric functions in biology.
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Affiliation(s)
- Patrick S. Irving
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290
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8
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Sieg JP, Jolley EA, Huot MJ, Babitzke P, Bevilacqua P. In vivo-like nearest neighbor parameters improve prediction of fractional RNA base-pairing in cells. Nucleic Acids Res 2023; 51:11298-11317. [PMID: 37855684 PMCID: PMC10639048 DOI: 10.1093/nar/gkad807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/11/2023] [Accepted: 09/27/2023] [Indexed: 10/20/2023] Open
Abstract
We conducted a thermodynamic analysis of RNA stability in Eco80 artificial cytoplasm, which mimics in vivo conditions, and compared it to transcriptome-wide probing of mRNA. Eco80 contains 80% of Escherichia coli metabolites, with biological concentrations of metal ions, including 2 mM free Mg2+ and 29 mM metabolite-chelated Mg2+. Fluorescence-detected binding isotherms (FDBI) were used to conduct a thermodynamic analysis of 24 RNA helices and found that these helices, which have an average stability of -12.3 kcal/mol, are less stable by ΔΔGo37 ∼1 kcal/mol. The FDBI data was used to determine a set of Watson-Crick free energy nearest neighbor parameters (NNPs), which revealed that Eco80 reduces the stability of three NNPs. This information was used to adjust the NN model using the RNAstructure package. The in vivo-like adjustments have minimal effects on the prediction of RNA secondary structures determined in vitro and in silico, but markedly improve prediction of fractional RNA base pairing in E. coli, as benchmarked with our in vivo DMS and EDC RNA chemical probing data. In summary, our thermodynamic and chemical probing analyses of RNA helices indicate that RNA secondary structures are less stable in cells than in artificially stable in vitro buffer conditions.
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Affiliation(s)
- Jacob P Sieg
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Elizabeth A Jolley
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Melanie J Huot
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Paul Babitzke
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular 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 and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
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9
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Conor Moran J, Brivanlou A, Brischigliaro M, Fontanesi F, Rouskin S, Barrientos A. The human mitochondrial mRNA structurome reveals mechanisms of gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.564750. [PMID: 37961485 PMCID: PMC10635011 DOI: 10.1101/2023.10.31.564750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The mammalian mitochondrial genome encodes thirteen oxidative phosphorylation system proteins, crucial in aerobic energy transduction. These proteins are translated from 9 monocistronic and 2 bicistronic transcripts, whose native structures remain unexplored, leaving fundamental molecular determinants of mitochondrial gene expression unknown. To address this gap, we developed a mitoDMS-MaPseq approach and used DREEM clustering to resolve the native human mitochondrial mt-mRNA structurome. We gained insights into mt-mRNA biology and translation regulatory mechanisms, including a unique programmed ribosomal frameshifting for the ATP8/ATP6 transcript. Furthermore, absence of the mt-mRNA maintenance factor LRPPRC led to a mitochondrial transcriptome structured differently, with specific mRNA regions exhibiting increased or decreased structuredness. This highlights the role of LRPPRC in maintaining mRNA folding to promote mt-mRNA stabilization and efficient translation. In conclusion, our mt-mRNA folding maps reveal novel mitochondrial gene expression mechanisms, serving as a detailed reference and tool for studying them in different physiological and pathological contexts.
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10
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Mitchell D, Cotter J, Saleem I, Mustoe AM. Mutation signature filtering enables high-fidelity RNA structure probing at all four nucleobases with DMS. Nucleic Acids Res 2023; 51:8744-8757. [PMID: 37334863 PMCID: PMC10484685 DOI: 10.1093/nar/gkad522] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/30/2023] [Accepted: 06/02/2023] [Indexed: 06/21/2023] Open
Abstract
Chemical probing experiments have transformed RNA structure analysis, enabling high-throughput measurement of base-pairing in living cells. Dimethyl sulfate (DMS) is one of the most widely used structure probing reagents and has played a pivotal role in enabling next-generation single-molecule probing analyses. However, DMS has traditionally only been able to probe adenine and cytosine nucleobases. We previously showed that, using appropriate conditions, DMS can also be used to interrogate base-pairing of uracil and guanines in vitro at reduced accuracy. However, DMS remained unable to informatively probe guanines in cells. Here, we develop an improved DMS mutational profiling (MaP) strategy that leverages the unique mutational signature of N1-methylguanine DMS modifications to enable high-fidelity structure probing at all four nucleotides, including in cells. Using information theory, we show that four-base DMS reactivities convey greater structural information than current two-base DMS and SHAPE probing strategies. Four-base DMS experiments further enable improved direct base-pair detection by single-molecule PAIR analysis, and ultimately support RNA structure modeling at superior accuracy. Four-base DMS probing experiments are straightforward to perform and will broadly facilitate improved RNA structural analysis in living cells.
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Affiliation(s)
- David Mitchell
- Therapeutic Innovation Center, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer Cotter
- Therapeutic Innovation Center, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Irfana Saleem
- Therapeutic Innovation Center, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Anthony M Mustoe
- Therapeutic Innovation Center, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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11
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Faison EM, Nallathambi A, Zhang Q. Characterizing Protonation-Coupled Conformational Ensembles in RNA via pH-Differential Mutational Profiling with DMS Probing. J Am Chem Soc 2023; 145:18773-18777. [PMID: 37582279 DOI: 10.1021/jacs.3c07736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
RNA molecules undergo conformational transitions in response to cellular and environmental stimuli. Site-specific protonation, a fundamental chemical property, can alter the conformational landscape of RNA to regulate their functions. However, characterizing protonation-coupled RNA conformational ensembles on a large scale remains challenging. Here, we present pH-differential mutational profiling (PD-MaP) with dimethyl sulfate probing for high-throughput detection of protonation-coupled conformational ensembles in RNA. We demonstrated this approach on microRNA-21 precursor (pre-miR-21) and recapitulated a previously discovered A+-G-coupled conformational ensemble. Additionally, we identified a secondary protonation event involving an A+-C mismatch. We validated the occurrence of both protonation-coupled ensembles in pre-miR-21 using NMR relaxation dispersion spectroscopy. Furthermore, the application of PD-MaP on a library of well-annotated human primary microRNAs uncovered widespread protonation-coupled conformational ensembles, suggesting their potentially broad functions in biology.
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12
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Bohn P, Gribling-Burrer AS, Ambi UB, Smyth RP. Nano-DMS-MaP allows isoform-specific RNA structure determination. Nat Methods 2023; 20:849-859. [PMID: 37106231 PMCID: PMC10250195 DOI: 10.1038/s41592-023-01862-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 03/21/2023] [Indexed: 04/29/2023]
Abstract
Genome-wide measurements of RNA structure can be obtained using reagents that react with unpaired bases, leading to adducts that can be identified by mutational profiling on next-generation sequencing machines. One drawback of these experiments is that short sequencing reads can rarely be mapped to specific transcript isoforms. Consequently, information is acquired as a population average in regions that are shared between transcripts, thus blurring the underlying structural landscape. Here, we present nanopore dimethylsulfate mutational profiling (Nano-DMS-MaP)-a method that exploits long-read sequencing to provide isoform-resolved structural information of highly similar RNA molecules. We demonstrate the value of Nano-DMS-MaP by resolving the complex structural landscape of human immunodeficiency virus-1 transcripts in infected cells. We show that unspliced and spliced transcripts have distinct structures at the packaging site within the common 5' untranslated region, likely explaining why spliced viral RNAs are excluded from viral particles. Thus, Nano-DMS-MaP is a straightforward method to resolve biologically important transcript-specific RNA structures that were previously hidden in short-read ensemble analyses.
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Affiliation(s)
- Patrick Bohn
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Anne-Sophie Gribling-Burrer
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Uddhav B Ambi
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.
- Julius-Maximilians-Universität Würzburg, Faculty of Medicine, Würzburg, Germany.
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13
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Mitchell D, Cotter J, Saleem I, Mustoe AM. Mutation signature filtering enables high-fidelity RNA structure probing at all four nucleobases with DMS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.10.536308. [PMID: 37090560 PMCID: PMC10120657 DOI: 10.1101/2023.04.10.536308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Chemical probing experiments have transformed RNA structure analysis, enabling high-throughput measurement of base-pairing in living cells. Dimethyl sulfate (DMS) is one of the most widely used structure probing reagents and has played a prominent role in enabling next-generation single-molecule probing analyses. However, DMS has traditionally only been able to probe adenine and cytosine nucleobases. We previously showed that, using appropriate conditions, DMS can also be used to interrogate base-pairing of uracil and guanines in vitro at reduced accuracy. However, DMS remained unable to informatively probe guanines in cells. Here, we develop an improved DMS mutational profiling (MaP) strategy that leverages the unique mutational signature of N 1 -methylguanine DMS modifications to enable robust, high-fidelity structure probing at all four nucleotides, including in cells. Using information theory, we show that four-base DMS reactivities convey greater structural information than comparable two-base DMS and SHAPE probing strategies. Four-base DMS experiments further enable improved direct base-pair detection by single-molecule PAIR analysis, and ultimately support RNA structure modeling at superior accuracy. Four-base DMS probing experiments are easily performed and will broadly facilitate improved RNA structural analysis in living cells.
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Affiliation(s)
- David Mitchell
- Therapeutic Innovation Center, and Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Jennifer Cotter
- Therapeutic Innovation Center, and Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Irfana Saleem
- Therapeutic Innovation Center, and Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Anthony M. Mustoe
- Therapeutic Innovation Center, and Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
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14
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Mustoe AM, Weidmann CA, Weeks KM. Single-Molecule Correlated Chemical Probing: A Revolution in RNA Structure Analysis. Acc Chem Res 2023; 56:763-775. [PMID: 36917683 PMCID: PMC10078950 DOI: 10.1021/acs.accounts.2c00782] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
RNA molecules convey biological information both in their linear sequence and in their base-paired secondary and tertiary structures. Chemical probing experiments, which involve treating an RNA with a reagent that modifies conformationally dynamic nucleotides, have broadly enabled examination of short- and long-range RNA structure in diverse contexts, including in living cells. For decades, chemical probing experiments have been interpreted in a per-nucleotide way, such that the reactivity measured at each nucleotide reports the average structure at a position over all RNA molecules within a sample. However, there are numerous important cases where per-nucleotide chemical probing falls short, including for RNAs that are bound by proteins, RNAs that form complex higher order structures, and RNAs that sample multiple conformations.Recent experimental and computational innovations have started a revolution in RNA structure analysis by transforming chemical probing into a massively parallel, single-molecule experiment. Enabled by a specialized reverse transcription strategy called mutational profiling (MaP), multiple chemical modification events can be measured within individual RNA molecules. Nucleotides that communicate structurally through direct base pairing or large-scale folding-unfolding transitions will react with chemical probes in a correlated manner, thereby revealing structural complexity hidden to conventional approaches. These single-molecule correlated chemical probing (smCCP) experiments can be interpreted to directly identify nucleotides that base pair (the PAIR-MaP strategy) and to reveal long-range, through-space structural communication (RING-MaP). Correlated probing can also define the thermodynamic populations of complex RNA ensembles (DANCE-MaP). Complex RNA-protein networks can be interrogated by cross-linking proteins to RNA and measuring correlations between cross-linked positions (RNP-MaP).smCCP thus visualizes RNA secondary and higher-order structure with unprecedented accuracy, defining novel structures, RNA-protein interaction networks, time-resolved dynamics, and allosteric structural switches. These strategies are not mutually exclusive; in favorable cases, multiple levels of RNA structure ─ base pairing, through-space structural communication, and equilibrium ensembles ─ can be resolved concurrently. The physical experimentation required for smCCP is profoundly simple, and experiments are readily performed in cells on RNAs of any size, including large noncoding RNAs and mRNAs. Single-molecule correlated chemical probing is paving the way for a new generation of biophysical studies on RNA in living systems.
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Affiliation(s)
- Anthony M. Mustoe
- Verna and Marrs McClean Department of Biochemistry and Molecular Biology, Department of Molecular and Human Genetics, and Therapeutic Innovation Center (THINC), One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030
| | - Chase A. Weidmann
- Department of Biological Chemistry, Center for RNA Biomedicine, 1150 W. Medical Center Drive, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill NC 27599-3290
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15
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Kavita K, Breaker RR. Discovering riboswitches: the past and the future. Trends Biochem Sci 2023; 48:119-141. [PMID: 36150954 PMCID: PMC10043782 DOI: 10.1016/j.tibs.2022.08.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/18/2022] [Accepted: 08/26/2022] [Indexed: 01/25/2023]
Abstract
Riboswitches are structured noncoding RNA domains used by many bacteria to monitor the concentrations of target ligands and regulate gene expression accordingly. In the past 20 years over 55 distinct classes of natural riboswitches have been discovered that selectively sense small molecules or elemental ions, and thousands more are predicted to exist. Evidence suggests that some riboswitches might be direct descendants of the RNA-based sensors and switches that were likely present in ancient organisms before the evolutionary emergence of proteins. We provide an overview of the current state of riboswitch research, focusing primarily on the discovery of riboswitches, and speculate on the major challenges facing researchers in the field.
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Affiliation(s)
- Kumari Kavita
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8103, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8103, USA.
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16
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Saha K, Ghosh G. Chemical Probing of RNA Structure In Vivo Using SHAPE-MaP and DMS-MaP. Methods Mol Biol 2023; 2666:81-93. [PMID: 37166658 DOI: 10.1007/978-1-0716-3191-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The functional roles of RNAs are often regulated by their structure. Selective 2' hydroxyl acylation analyzed by primer extension (SHAPE) and dimethyl sulfate (DMS) base reactivity can be employed to investigate the flexibility of nucleotides and correlate it to the constraints imparted by base-pairing and/or protein-binding. In vivo, a multitude of proteins could bind an RNA molecule, regulating its structure and function. Hence, to obtain a more comprehensive view of the RNA structure-function relationship in vivo, it may be required to characterize both the RNA structure and the RNA-protein interaction network. In this chapter, we describe methods for characterizing the in vivo nucleotide flexibility of RNA in cells by SHAPE-MaP (SHAPE by Mutational Profiling) and DMS-MaP. In another chapter, we will discuss the characterization of RNA-protein interaction network by RNP-MaP.
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Affiliation(s)
- Kaushik Saha
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
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17
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Saha K, Ghosh G. Analysis of RNA-Protein Interaction Networks Using RNP-MaP. Methods Mol Biol 2023; 2666:95-105. [PMID: 37166659 DOI: 10.1007/978-1-0716-3191-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
RNA-protein interactions regulate a myriad of biological functions through formation of ribonucleoprotein complexes. These complexes may consist of one or more RNA-protein interaction network(s) providing additional layers of regulatory potential to the RNA. Moreover, since the protein-binding also regulates local and global structure of the RNA by structurally remodeling the latter, it is important to correlate RNA nucleotide flexibility with the site of protein-binding. We have discussed methods for chemical probing of structure of the RNA in the protein-free and protein-bound states in the preceding chapters. In this chapter, we describe a ribonucleoprotein mutational profiling (RNP-MaP) method for probing RNA-protein interaction networks.
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Affiliation(s)
- Kaushik Saha
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
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18
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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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19
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Grayeski PJ, Weidmann CA, Kumar J, Lackey L, Mustoe A, Busan S, Laederach A, Weeks KM. Global 5'-UTR RNA structure regulates translation of a SERPINA1 mRNA. Nucleic Acids Res 2022; 50:9689-9704. [PMID: 36107773 PMCID: PMC9508835 DOI: 10.1093/nar/gkac739] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 08/11/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
SERPINA1 mRNAs encode the protease inhibitor α-1-antitrypsin and are regulated through post-transcriptional mechanisms. α-1-antitrypsin deficiency leads to chronic obstructive pulmonary disease (COPD) and liver cirrhosis, and specific variants in the 5'-untranslated region (5'-UTR) are associated with COPD. The NM_000295.4 transcript is well expressed and translated in lung and blood and features an extended 5'-UTR that does not contain a competing upstream open reading frame (uORF). We show that the 5'-UTR of NM_000295.4 folds into a well-defined multi-helix structural domain. We systematically destabilized mRNA structure across the NM_000295.4 5'-UTR, and measured changes in (SHAPE quantified) RNA structure and cap-dependent translation relative to a native-sequence reporter. Surprisingly, despite destabilizing local RNA structure, most mutations either had no effect on or decreased translation. Most structure-destabilizing mutations retained native, global 5'-UTR structure. However, those mutations that disrupted the helix that anchors the 5'-UTR domain yielded three groups of non-native structures. Two of these non-native structure groups refolded to create a stable helix near the translation initiation site that decreases translation. Thus, in contrast to the conventional model that RNA structure in 5'-UTRs primarily inhibits translation, complex folding of the NM_000295.4 5'-UTR creates a translation-optimized message by promoting accessibility at the translation initiation site.
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Affiliation(s)
- Philip J Grayeski
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Chase A Weidmann
- Department of Biological Chemistry, Center for RNA Biomedicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jayashree Kumar
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Lela Lackey
- Department of Genetics and Biochemistry, Center for Human Genetics, Clemson University, Greenwood, SC 29646, USA
| | - Anthony M Mustoe
- Verna and Marrs McClean Department of Biochemistry and Molecular Biology, Department of Molecular and Human Genetics, and Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, TX 77030, USA
| | - Steven Busan
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
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20
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Sheng C, Zhao J, Di Z, Huang Y, Zhao Y, Li L. Spatially resolved in vivo imaging of inflammation-associated mRNA via enzymatic fluorescence amplification in a molecular beacon. Nat Biomed Eng 2022; 6:1074-1084. [PMID: 36050523 DOI: 10.1038/s41551-022-00932-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 07/26/2022] [Indexed: 11/09/2022]
Abstract
The in vivo optical imaging of RNA biomarkers of inflammation is hindered by low signal-to-background ratios, owing to non-specific signal amplification in healthy tissues. Here we report the design and in vivo applicability, for the imaging of inflammation-associated messenger RNAs (mRNAs), of a molecular beacon bearing apurinic/apyrimidinic sites, whose amplification of fluorescence is triggered by human apurinic/apyrimidinic endonuclease 1 on translocation from the nucleus into the cytoplasm specifically in inflammatory cells. We assessed the sensitivity and tissue specificity of an engineered molecular beacon targeting interleukin-6 (IL-6) mRNA in live mice, by detecting acute inflammation in their paws and drug-induced inflammation in their livers. This enzymatic-amplification strategy may enable the specific and sensitive imaging of other disease-relevant RNAs in vivo.
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Affiliation(s)
- Chuangui Sheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China.,College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Jian Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China.,College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Zhenghan Di
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China.,College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Yuanyu Huang
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China.,College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, China.,GBA Research Innovation Institute for Nanotechnology, Guangdong, China
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China. .,College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, China. .,GBA Research Innovation Institute for Nanotechnology, Guangdong, China.
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21
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Genome-wide analysis of the in vivo tRNA structurome reveals RNA structural and modification dynamics under heat stress. Proc Natl Acad Sci U S A 2022; 119:e2201237119. [PMID: 35696576 PMCID: PMC9231505 DOI: 10.1073/pnas.2201237119] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
RNA structure plays roles in myriad cellular events including transcription, translation, and RNA processing. Genome-wide analyses of RNA secondary structure in vivo by chemical probing have revealed critical structural features of mRNAs and long ncRNAs. Here, we examine the in vivo secondary structure of a small RNA class, tRNAs. Study of tRNA structure is challenging because tRNAs are heavily modified and strongly structured. We introduce "tRNA structure-seq," a new workflow that accurately determines in vivo secondary structures of tRNA. The workflow combines dimethyl sulfate (DMS) probing, ultra-processive RT, and mutational profiling (MaP), which provides mutations opposite DMS and natural modifications thereby allowing multiple modifications to be identified in a single read. We applied tRNA structure-seq to E. coli under control and stress conditions. A leading folding algorithm predicts E. coli tRNA structures with only ∼80% average accuracy from sequence alone. Strikingly, tRNA structure-seq, by providing experimental restraints, improves structure prediction under in vivo conditions to ∼95% accuracy, with more than 14 tRNAs predicted completely correctly. tRNA structure-seq also quantifies the relative levels of tRNAs and their natural modifications at single nucleotide resolution, as validated by LC-MS/MS. Our application of tRNA structure-seq yields insights into tRNA structure in living cells, revealing that it is not immutable but has dynamics, with partial unfolding of secondary and tertiary tRNA structure under heat stress that is correlated with a loss of tRNA abundance. This method is applicable to other small RNAs, including those with natural modifications and highly structured regions.
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22
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Measuring thermodynamic preferences to form non-native conformations in nucleic acids using ultraviolet melting. Proc Natl Acad Sci U S A 2022; 119:e2112496119. [PMID: 35671421 PMCID: PMC9214542 DOI: 10.1073/pnas.2112496119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Thermodynamic preferences to form non-native conformations are crucial for understanding how nucleic acids fold and function. However, they are difficult to measure experimentally because this requires accurately determining the population of minor low-abundance (<10%) conformations in a sea of other conformations. Here, we show that melting experiments enable facile measurements of thermodynamic preferences to adopt nonnative conformations in DNA and RNA. The key to this "delta-melt" approach is to use chemical modifications to render specific minor non-native conformations the major state. The validity and robustness of delta-melt is established for four different non-native conformations under various physiological conditions and sequence contexts through independent measurements of thermodynamic preferences using NMR. Delta-melt is faster relative to NMR, simple, and cost-effective and enables thermodynamic preferences to be measured for exceptionally low-populated conformations. Using delta-melt, we obtained rare insights into conformational cooperativity, obtaining evidence for significant cooperativity (1.0 to 2.5 kcal/mol) when simultaneously forming two adjacent Hoogsteen base pairs. We also measured the thermodynamic preferences to form G-C+ and A-T Hoogsteen and A-T base open states for nearly all 16 trinucleotide sequence contexts and found distinct sequence-specific variations on the order of 2 to 3 kcal/mol. This rich landscape of sequence-specific non-native minor conformations in the DNA double helix may help shape the sequence specificity of DNA biochemistry. Thus, melting experiments can now be used to access thermodynamic information regarding regions of the free energy landscape of biomolecules beyond the native folded and unfolded conformations.
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23
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Kumar J, Lackey L, Waldern JM, Dey A, Mustoe AM, Weeks KM, Mathews DH, Laederach A. Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing. eLife 2022; 11:73888. [PMID: 35695373 PMCID: PMC9236610 DOI: 10.7554/elife.73888] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 06/12/2022] [Indexed: 11/29/2022] Open
Abstract
Splicing is highly regulated and is modulated by numerous factors. Quantitative predictions for how a mutation will affect precursor mRNA (pre-mRNA) structure and downstream function are particularly challenging. Here, we use a novel chemical probing strategy to visualize endogenous precursor and mature MAPT mRNA structures in cells. We used these data to estimate Boltzmann suboptimal structural ensembles, which were then analyzed to predict consequences of mutations on pre-mRNA structure. Further analysis of recent cryo-EM structures of the spliceosome at different stages of the splicing cycle revealed that the footprint of the Bact complex with pre-mRNA best predicted alternative splicing outcomes for exon 10 inclusion of the alternatively spliced MAPT gene, achieving 74% accuracy. We further developed a β-regression weighting framework that incorporates splice site strength, RNA structure, and exonic/intronic splicing regulatory elements capable of predicting, with 90% accuracy, the effects of 47 known and 6 newly discovered mutations on inclusion of exon 10 of MAPT. This combined experimental and computational framework represents a path forward for accurate prediction of splicing-related disease-causing variants.
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Affiliation(s)
- Jayashree Kumar
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Lela Lackey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Genetics and Biochemistry, Center for Human Genetics, Clemson University, Greenwood, United States
| | - Justin M Waldern
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Abhishek Dey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Anthony M Mustoe
- Verna and Marrs McClean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center (THINC), and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - David H Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, United States
| | - Alain Laederach
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
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24
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Aviran S, Incarnato D. Computational approaches for RNA structure ensemble deconvolution from structure probing data. J Mol Biol 2022; 434:167635. [PMID: 35595163 DOI: 10.1016/j.jmb.2022.167635] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 12/15/2022]
Abstract
RNA structure probing experiments have emerged over the last decade as a straightforward way to determine the structure of RNA molecules in a number of different contexts. Although powerful, the ability of RNA to dynamically interconvert between, and to simultaneously populate, alternative structural configurations, poses a nontrivial challenge to the interpretation of data derived from these experiments. Recent efforts aimed at developing computational methods for the reconstruction of coexisting alternative RNA conformations from structure probing data are paving the way to the study of RNA structure ensembles, even in the context of living cells. In this review, we critically discuss these methods, their limitations and possible future improvements.
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Affiliation(s)
- Sharon Aviran
- Biomedical Engineering Department and Genome Center, University of California, Davis, 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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25
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Abstract
Recent events have pushed RNA research into the spotlight. Continued discoveries of RNA with unexpected diverse functions in healthy and diseased cells, such as the role of RNA as both the source and countermeasure to a severe acute respiratory syndrome coronavirus 2 infection, are igniting a new passion for understanding this functionally and structurally versatile molecule. Although RNA structure is key to function, many foundational characteristics of RNA structure are misunderstood, and the default state of RNA is often thought of and depicted as a single floppy strand. The purpose of this perspective is to help adjust mental models, equipping the community to better use the fundamental aspects of RNA structural information in new mechanistic models, enhance experimental design to test these models, and refine data interpretation. We discuss six core observations focused on the inherent nature of RNA structure and how to incorporate these characteristics to better understand RNA structure. We also offer some ideas for future efforts to make validated RNA structural information available and readily used by all researchers.
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Affiliation(s)
- Quentin Vicens
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO 80045
- RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045
| | - Jeffrey S. Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO 80045
- RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045
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26
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Dykstra PB, Kaplan M, Smolke CD. Engineering synthetic RNA devices for cell control. Nat Rev Genet 2022; 23:215-228. [PMID: 34983970 PMCID: PMC9554294 DOI: 10.1038/s41576-021-00436-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2021] [Indexed: 12/16/2022]
Abstract
The versatility of RNA in sensing and interacting with small molecules, proteins and other nucleic acids while encoding genetic instructions for protein translation makes it a powerful substrate for engineering biological systems. RNA devices integrate cellular information sensing, processing and actuation of specific signals into defined functions and have yielded programmable biological systems and novel therapeutics of increasing sophistication. However, challenges centred on expanding the range of analytes that can be sensed and adding new mechanisms of action have hindered the full realization of the field's promise. Here, we describe recent advances that address these limitations and point to a significant maturation of synthetic RNA-based devices.
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Affiliation(s)
- Peter B. Dykstra
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Matias Kaplan
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Christina D. Smolke
- Department of Bioengineering, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA.,
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27
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Olson SW, Turner AMW, Arney JW, Saleem I, Weidmann CA, Margolis DM, Weeks KM, Mustoe AM. Discovery of a large-scale, cell-state-responsive allosteric switch in the 7SK RNA using DANCE-MaP. Mol Cell 2022; 82:1708-1723.e10. [PMID: 35320755 PMCID: PMC9081252 DOI: 10.1016/j.molcel.2022.02.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/29/2021] [Accepted: 02/02/2022] [Indexed: 12/17/2022]
Abstract
7SK is a conserved noncoding RNA that regulates transcription by sequestering the transcription factor P-TEFb. 7SK function entails complex changes in RNA structure, but characterizing RNA dynamics in cells remains an unsolved challenge. We developed a single-molecule chemical probing strategy, DANCE-MaP (deconvolution and annotation of ribonucleic conformational ensembles), that defines per-nucleotide reactivity, direct base pairing interactions, tertiary interactions, and thermodynamic populations for each state in RNA structural ensembles from a single experiment. DANCE-MaP reveals that 7SK RNA encodes a large-scale structural switch that couples dissolution of the P-TEFb binding site to structural remodeling at distal release factor binding sites. The 7SK structural equilibrium shifts in response to cell growth and stress and can be targeted to modulate expression of P-TEFbresponsive genes. Our study reveals that RNA structural dynamics underlie 7SK function as an integrator of diverse cellular signals to control transcription and establishes the power of DANCE-MaP to define RNA dynamics in cells.
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Affiliation(s)
- Samuel W Olson
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Anne-Marie W Turner
- Department of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; UNC HIV Cure Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - J Winston Arney
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Irfana Saleem
- Verna and Marrs McClean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, TX 77030, USA
| | - Chase A Weidmann
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - David M Margolis
- Department of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; UNC HIV Cure Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA.
| | - Anthony M Mustoe
- Verna and Marrs McClean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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28
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Zeller MJ, Nuthanakanti A, Li K, Aubé J, Serganov A, Weeks KM. Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery. ACS Chem Biol 2022; 17:438-448. [PMID: 35060698 PMCID: PMC8938680 DOI: 10.1021/acschembio.1c00880] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA molecules can show high levels of cooperativity in their global folding and interactions with divalent ions. However, cooperativity at individual ligand-RNA interaction sites remains poorly understood. Here, we investigated the binding of thiamine and methylene diphosphonic acid (MDP, a soluble structural analogue of pyrophosphate) to the thiamine pyrophosphate riboswitch. These ligands each bind weakly at proximal subsites, with 10 μM and 1 mM affinities, respectively. The affinity of MDP moderately improves when thiamine or thiamine-like fragments are pre-bound to the RNA. Covalent linking of thiamine and MDP substantially increases riboswitch binding to a notable high affinity of 20 nM. Crystal structures and single-molecule correlated chemical probing revealed favorable induced fit effects upon binding of individual ligands and, unexpectedly, a substantial thermodynamically unfavorable RNA structural rearrangement upon binding of the linked thiamine-MDP ligand. Thus, linking of two ligands of modest affinity, accompanied by an unfavorable structural rearrangement, still yields a potent linked RNA-binding compound. Since complex ligands often bind riboswitches and other RNAs at proximal subsites, principles derived from this work inform and support fragment-linking strategies for identifying small molecules that interact with RNA specifically and with high affinity.
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Affiliation(s)
- Meredith J. Zeller
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290
| | - Ashok Nuthanakanti
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016
| | - Kelin Li
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7363
| | - Jeffrey Aubé
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290,Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7363
| | - Alexander Serganov
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290,correspondence,
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29
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Przanowska RK, Weidmann CA, Saha S, Cichewicz MA, Jensen KN, Przanowski P, Irving PS, Janes KA, Guertin MJ, Weeks KM, Dutta A. Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors. Cell Rep 2022; 38:110361. [PMID: 35172143 PMCID: PMC8937029 DOI: 10.1016/j.celrep.2022.110361] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/03/2021] [Accepted: 01/19/2022] [Indexed: 12/27/2022] Open
Abstract
Many lncRNAs have been discovered using transcriptomic data; however, it is unclear what fraction of lncRNAs is functional and what structural properties affect their phenotype. MUNC lncRNA (also known as DRReRNA) acts as an enhancer RNA for the Myod1 gene in cis and stimulates the expression of other promyogenic genes in trans by recruiting the cohesin complex. Here, experimental probing of the RNA structure revealed that MUNC contains multiple structural domains not detected by prediction algorithms in the absence of experimental information. We show that these specific and structurally distinct domains are required for induction of promyogenic genes, for binding genomic sites and gene expression regulation, and for binding the cohesin complex. Myod1 induction and cohesin interaction comprise only a subset of MUNC phenotype. Our study reveals unexpectedly complex, structure-driven functions for the MUNC lncRNA and emphasizes the importance of experimentally determined structures for understanding structure-function relationships in lncRNAs.
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Affiliation(s)
- Roza K Przanowska
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Biomedical Engineering, University of Virginia School of Engineering, Charlottesville, VA 22908, USA
| | - Chase A Weidmann
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biological Chemistry and Center for RNA Biomedicine, University of Michigan Medical School, Ann Arbor, MI 48103, USA
| | - Shekhar Saha
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Magdalena A Cichewicz
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Kate N Jensen
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Piotr Przanowski
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Biomedical Engineering, University of Virginia School of Engineering, Charlottesville, VA 22908, USA
| | - Patrick S Irving
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kevin A Janes
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Biomedical Engineering, University of Virginia School of Engineering, Charlottesville, VA 22908, USA
| | - Michael J Guertin
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut, Farmington, CT 06030, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Genetics, University of Alabama, Birmingham, AL 35233, USA.
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30
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Robertson N, Shchepachev V, Wright D, Turowski TW, Spanos C, Helwak A, Zamoyska R, Tollervey D. A disease-linked lncRNA mutation in RNase MRP inhibits ribosome synthesis. Nat Commun 2022; 13:649. [PMID: 35115551 PMCID: PMC8814244 DOI: 10.1038/s41467-022-28295-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 01/14/2022] [Indexed: 01/02/2023] Open
Abstract
RMRP encodes a non-coding RNA forming the core of the RNase MRP ribonucleoprotein complex. Mutations cause Cartilage Hair Hypoplasia (CHH), characterized by skeletal abnormalities and impaired T cell activation. Yeast RNase MRP cleaves a specific site in the pre-ribosomal RNA (pre-rRNA) during ribosome synthesis. CRISPR-mediated disruption of RMRP in human cells lines caused growth arrest, with pre-rRNA accumulation. Here, we analyzed disease-relevant primary cells, showing that mutations in RMRP impair mouse T cell activation and delay pre-rRNA processing. Patient-derived human fibroblasts with CHH-linked mutations showed similar pre-rRNA processing delay. Human cells engineered with the most common CHH mutation (70AG in RMRP) show specifically impaired pre-rRNA processing, resulting in reduced mature rRNA and a reduced ratio of cytosolic to mitochondrial ribosomes. Moreover, the 70AG mutation caused a reduction in intact RNase MRP complexes. Together, these results indicate that CHH is a ribosomopathy.
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Affiliation(s)
- Nic Robertson
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Vadim Shchepachev
- The Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK
| | - David Wright
- Ashworth Laboratories, Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - Tomasz W Turowski
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Christos Spanos
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Aleksandra Helwak
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Rose Zamoyska
- Ashworth Laboratories, Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - David Tollervey
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
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31
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Abstract
Cotranscriptional folding is a fundamental step in RNA biogenesis and the basis for many RNA-mediated gene regulation systems. Understanding how RNA folds as it is synthesized requires experimental methods that can systematically identify intermediate RNA structures that form during transcription. Cotranscriptional RNA chemical probing experiments achieve this by applying high-throughput RNA structure probing to an in vitro transcribed array of cotranscriptionally folded intermediate transcripts. In this chapter, we present guidelines and procedures for integrating single-round in vitro transcription using E. coli RNA polymerase with high-throughput RNA chemical probing workflows. We provide an overview of key concepts including DNA template design, transcription roadblocking strategies, single-round in vitro transcription with E. coli RNA polymerase, and RNA chemical probing and describe procedures for DNA template preparation, cotranscriptional RNA chemical probing, RNA purification, and 3' adapter ligation. The end result of these procedures is a purified RNA library that can be prepared for Illumina sequencing using established high-throughput RNA structure probing library construction strategies.
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Affiliation(s)
- Courtney E Szyjka
- Department of Biological Sciences, The University at Buffalo, Buffalo, NY, USA
| | - Eric J Strobel
- Department of Biological Sciences, The University at Buffalo, Buffalo, NY, USA.
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32
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Identifying proximal RNA interactions from cDNA-encoded crosslinks with ShapeJumper. PLoS Comput Biol 2021; 17:e1009632. [PMID: 34905538 PMCID: PMC8670686 DOI: 10.1371/journal.pcbi.1009632] [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: 01/22/2021] [Accepted: 11/11/2021] [Indexed: 01/07/2023] Open
Abstract
SHAPE-JuMP is a concise strategy for identifying close-in-space interactions in RNA molecules. Nucleotides in close three-dimensional proximity are crosslinked with a bi-reactive reagent that covalently links the 2'-hydroxyl groups of the ribose moieties. The identities of crosslinked nucleotides are determined using an engineered reverse transcriptase that jumps across crosslinked sites, resulting in a deletion in the cDNA that is detected using massively parallel sequencing. Here we introduce ShapeJumper, a bioinformatics pipeline to process SHAPE-JuMP sequencing data and to accurately identify through-space interactions, as observed in complex JuMP datasets. ShapeJumper identifies proximal interactions with near-nucleotide resolution using an alignment strategy that is optimized to tolerate the unique non-templated reverse-transcription profile of the engineered crosslink-traversing reverse-transcriptase. JuMP-inspired strategies are now poised to replace adapter-ligation for detecting RNA-RNA interactions in most crosslinking experiments.
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33
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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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34
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Helm M, Schmidt-Dengler MC, Weber M, Motorin Y. General Principles for the Detection of Modified Nucleotides in RNA by Specific Reagents. Adv Biol (Weinh) 2021; 5:e2100866. [PMID: 34535986 DOI: 10.1002/adbi.202100866] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/09/2021] [Indexed: 12/16/2022]
Abstract
Epitranscriptomics heavily rely on chemical reagents for the detection, quantification, and localization of modified nucleotides in transcriptomes. Recent years have seen a surge in mapping methods that use innovative and rediscovered organic chemistry in high throughput approaches. While this has brought about a leap of progress in this young field, it has also become clear that the different chemistries feature variegated specificity and selectivity. The associated error rates, e.g., in terms of false positives and false negatives, are in large part inherent to the chemistry employed. This means that even assuming technically perfect execution, the interpretation of mapping results issuing from the application of such chemistries are limited by intrinsic features of chemical reactivity. An important but often ignored fact is that the huge stochiometric excess of unmodified over-modified nucleotides is not inert to any of the reagents employed. Consequently, any reaction aimed at chemical discrimination of modified versus unmodified nucleotides has optimal conditions for selectivity that are ultimately anchored in relative reaction rates, whose ratio imposes intrinsic limits to selectivity. Here chemical reactivities of canonical and modified ribonucleosides are revisited as a basis for an understanding of the limits of selectivity achievable with chemical methods.
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Affiliation(s)
- Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudingerweg 5, D-55128, Mainz, Germany
| | - Martina C Schmidt-Dengler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudingerweg 5, D-55128, Mainz, Germany
| | - Marlies Weber
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudingerweg 5, D-55128, Mainz, Germany
| | - Yuri Motorin
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core facility, Nancy, F-54000, France.,Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, F-54000, France
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35
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Poblete S, Guzman HV. Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models. Viruses 2021; 13:1555. [PMID: 34452420 PMCID: PMC8402887 DOI: 10.3390/v13081555] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
Three-dimensional RNA domain reconstruction is important for the assembly, disassembly and delivery functionalities of a packed proteinaceus capsid. However, to date, the self-association of RNA molecules is still an open problem. Recent chemical probing reports provide, with high reliability, the secondary structure of diverse RNA ensembles, such as those of viral genomes. Here, we present a method for reconstructing the complete 3D structure of RNA genomes, which combines a coarse-grained model with a subdomain composition scheme to obtain the entire genome inside proteinaceus capsids based on secondary structures from experimental techniques. Despite the amount of sampling involved in the folded and also unfolded RNA molecules, advanced microscope techniques can provide points of anchoring, which enhance our model to include interactions between capsid pentamers and RNA subdomains. To test our method, we tackle the satellite tobacco mosaic virus (STMV) genome, which has been widely studied by both experimental and computational communities. We provide not only a methodology to structurally analyze the tertiary conformations of the RNA genome inside capsids, but a flexible platform that allows the easy implementation of features/descriptors coming from both theoretical and experimental approaches.
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Affiliation(s)
- Simón Poblete
- Instituto de Ciencias Físicas y Matemáticas, Universidad Austral de Chile, Valdivia 5091000, Chile
- Chile and Computational Biology Lab, Fundación Ciencia & Vida, Santiago 7780272, Chile
| | - Horacio V. Guzman
- Department of Theoretical Physics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
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36
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Schlick T, Zhu Q, Dey A, Jain S, Yan S, Laederach A. To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element. J Am Chem Soc 2021; 143:11404-11422. [PMID: 34283611 PMCID: PMC8315264 DOI: 10.1021/jacs.1c03003] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The SARS-CoV-2 frameshifting RNA element (FSE) is an excellent target for therapeutic intervention against Covid-19. This small gene element employs a shifting mechanism to pause and backtrack the ribosome during translation between Open Reading Frames 1a and 1b, which code for viral polyproteins. Any interference with this process has a profound effect on viral replication and propagation. Pinpointing the structures adapted by the FSE and associated structural transformations involved in frameshifting has been a challenge. Using our graph-theory-based modeling tools for representing RNA secondary structures, "RAG" (RNA-As-Graphs), and chemical structure probing experiments, we show that the 3-stem H-type pseudoknot (3_6 dual graph), long assumed to be the dominant structure, has a viable alternative, an HL-type 3-stem pseudoknot (3_3) for longer constructs. In addition, an unknotted 3-way junction RNA (3_5) emerges as a minor conformation. These three conformations share Stems 1 and 3, while the different Stem 2 may be involved in a conformational switch and possibly associations with the ribosome during translation. For full-length genomes, a stem-loop motif (2_2) may compete with these forms. These structural and mechanistic insights advance our understanding of the SARS-CoV-2 frameshifting process and concomitant virus life cycle, and point to three avenues of therapeutic intervention.
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Affiliation(s)
- Tamar Schlick
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, New York 10003, United States
- Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, New York 10012, United States
- New York University-East China Normal University Center for Computational Chemistry, New York University-Shanghai, Shanghai 200062, P. R. China
| | - Qiyao Zhu
- Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, New York 10012, United States
| | - Abhishek Dey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Swati Jain
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, New York 10003, United States
| | - Shuting Yan
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, New York 10003, United States
| | - Alain Laederach
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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37
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Schlick T, Zhu Q, Dey A, Jain S, Yan S, Laederach A. To knot or not to knot: Multiple conformations of the SARS-CoV-2 frameshifting RNA element. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.31.437955. [PMID: 33821274 PMCID: PMC8020974 DOI: 10.1101/2021.03.31.437955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The SARS-CoV-2 frameshifting RNA element (FSE) is an excellent target for therapeutic intervention against Covid-19. This small gene element employs a shifting mechanism to pause and backtrack the ribosome during translation between Open Reading Frames 1a and 1b, which code for viral polyproteins. Any interference with this process has profound effect on viral replication and propagation. Pinpointing the structures adapted by the FSE and associated structural transformations involved in frameshifting has been a challenge. Using our graph-theory-based modeling tools for representing RNA secondary structures, "RAG" (RNA-As-Graphs), and chemical structure probing experiments, we show that the 3-stem H-type pseudoknot (3_6 dual graph), long assumed to be the dominant structure has a viable alternative, an HL-type 3-stem pseudoknot (3_3) for longer constructs. In addition, an unknotted 3-way junction RNA (3_5) emerges as a minor conformation. These three conformations share Stems 1 and 3, while the different Stem 2 may be involved in a conformational switch and possibly associations with the ribosome during translation. For full-length genomes, a stem-loop motif (2_2) may compete with these forms. These structural and mechanistic insights advance our understanding of the SARS-CoV-2 frameshifting process and concomitant virus life cycle, and point to three avenues of therapeutic intervention.
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Affiliation(s)
- Tamar Schlick
- Department of Chemistry, 100 Washington Square East, Silver Building, New York University, New York, NY 10003 U.S.A
- Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, NY 10012 U.S.A
- NYU-ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200062, P.R. China
| | - Qiyao Zhu
- Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, NY 10012 U.S.A
| | - Abhishek Dey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Swati Jain
- Department of Chemistry, 100 Washington Square East, Silver Building, New York University, New York, NY 10003 U.S.A
| | - Shuting Yan
- Department of Chemistry, 100 Washington Square East, Silver Building, New York University, New York, NY 10003 U.S.A
| | - Alain Laederach
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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38
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Christy TW, Giannetti CA, Houlihan G, Smola MJ, Rice GM, Wang J, Dokholyan NV, Laederach A, Holliger P, Weeks KM. Direct Mapping of Higher-Order RNA Interactions by SHAPE-JuMP. Biochemistry 2021; 60:1971-1982. [PMID: 34121404 PMCID: PMC8256721 DOI: 10.1021/acs.biochem.1c00270] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Higher-order structure governs function for many RNAs. However, discerning this structure for large RNA molecules in solution is an unresolved challenge. Here, we present SHAPE-JuMP (selective 2'-hydroxyl acylation analyzed by primer extension and juxtaposed merged pairs) to interrogate through-space RNA tertiary interactions. A bifunctional small molecule is used to chemically link proximal nucleotides in an RNA structure. The RNA cross-link site is then encoded into complementary DNA (cDNA) in a single, direct step using an engineered reverse transcriptase that "jumps" across cross-linked nucleotides. The resulting cDNAs contain a deletion relative to the native RNA sequence, which can be detected by sequencing, that indicates the sites of cross-linked nucleotides. SHAPE-JuMP measures RNA tertiary structure proximity concisely across large RNA molecules at nanometer resolution. SHAPE-JuMP is especially effective at measuring interactions in multihelix junctions and loop-to-helix packing, enables modeling of the global fold for RNAs up to several hundred nucleotides in length, facilitates ranking of structural models by consistency with through-space restraints, and is poised to enable solution-phase structural interrogation and modeling of complex RNAs.
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Affiliation(s)
- Thomas W. Christy
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Catherine A. Giannetti
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - Gillian Houlihan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Matthew J. Smola
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - Greggory M. Rice
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - Jian Wang
- Departments of Pharmacology, and Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Nikolay V. Dokholyan
- Departments of Pharmacology, and Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, PA 17033, USA
- Departments of Chemistry, and Biomedical Engineering, Pennsylvania State University, University Park, PA 16802
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
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39
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Gupta A, Beaudoin JD. Extreme conservation encodes the structural dynamics and function of 5' UTRs. Nat Genet 2021; 53:591-592. [PMID: 33888910 DOI: 10.1038/s41588-021-00869-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Amit Gupta
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, USA
| | - Jean-Denis Beaudoin
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, USA.
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40
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Cao J, Xue Y. Characteristic chemical probing patterns of loop motifs improve prediction accuracy of RNA secondary structures. Nucleic Acids Res 2021; 49:4294-4307. [PMID: 33849076 PMCID: PMC8096282 DOI: 10.1093/nar/gkab250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 03/24/2021] [Accepted: 04/10/2021] [Indexed: 12/14/2022] Open
Abstract
RNA structures play a fundamental role in nearly every aspect of cellular physiology and pathology. Gaining insights into the functions of RNA molecules requires accurate predictions of RNA secondary structures. However, the existing thermodynamic folding models remain less accurate than desired, even when chemical probing data, such as selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) reactivities, are used as restraints. Unlike most SHAPE-directed algorithms that only consider SHAPE restraints for base pairing, we extract two-dimensional structural features encoded in SHAPE data and establish robust relationships between characteristic SHAPE patterns and loop motifs of various types (hairpin, internal, and bulge) and lengths (2-11 nucleotides). Such characteristic SHAPE patterns are closely related to the sugar pucker conformations of loop residues. Based on these patterns, we propose a computational method, SHAPELoop, which refines the predicted results of the existing methods, thereby further improving their prediction accuracy. In addition, SHAPELoop can provide information about local or global structural rearrangements (including pseudoknots) and help researchers to easily test their hypothesized secondary structures.
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Affiliation(s)
- Jingyi Cao
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Yi Xue
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
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41
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Abstract
RNA lies upstream of nearly all biology and functions as the central conduit of information exchange in all cells. RNA molecules encode information both in their primary sequences and in complex structures that form when an RNA folds back on itself. From the time of discovery of mRNA in the late 1950s until quite recently, we had only a rudimentary understanding of RNA structure across vast regions of most messenger and noncoding RNAs. This deficit is now rapidly being addressed, especially by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry, mutational profiling (MaP), and closely related platform technologies that, collectively, create chemical microscopes for RNA. These technologies make it possible to interrogate RNA structure, quantitatively, at nucleotide resolution, and at large scales, for entire mRNAs, noncoding RNAs, and viral RNA genomes. By applying comprehensive structure probing to diverse problems, we and others are showing that control of biological function mediated by RNA structure is ubiquitous across prokaryotic and eukaryotic organisms.Work over the past decade using SHAPE-based analyses has clarified key principles. First, the method of RNA structure probing matters. SHAPE-MaP, with its direct and one-step readout that probes nearly every nucleotide by reaction at the 2'-hydroxyl, gives a more detailed and accurate readout than alternatives. Second, comprehensive chemical probing is essential. Focusing on fragments of large RNAs or using meta-gene or statistical analyses to compensate for sparse data sets misses critical features and often yields structure models with poor predictive power. Finally, every RNA has its own internal structural personality. There are myriad ways in which RNA structure modulates sequence accessibility, protein binding, translation, splice-site choice, phase separation, and other fundamental biological processes. In essentially every instance where we have applied rigorous and quantitative SHAPE technologies to study RNA structure-function interrelationships, new insights regarding biological regulatory mechanisms have emerged. RNA elements with more complex higher-order structures appear more likely to contain high-information-content clefts and pockets that bind small molecules, broadly informing a vigorous field of RNA-targeted drug discovery.The broad implications of this collective work are twofold. First, it is long past time to abandon depiction of large RNAs as simple noodle-like or gently flowing molecules. Instead, we need to emphasize that nearly all RNAs are punctuated with distinctive internal structures, a subset of which modulate function in profound ways. Second, structure probing should be an integral component of any effort that seeks to understand the functional nexuses and biological roles of large RNAs.
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Affiliation(s)
- Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, United States
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42
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Zafferani M, Hargrove AE. Small molecule targeting of biologically relevant RNA tertiary and quaternary structures. Cell Chem Biol 2021; 28:594-609. [PMID: 33823146 DOI: 10.1016/j.chembiol.2021.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/03/2021] [Accepted: 03/10/2021] [Indexed: 02/06/2023]
Abstract
Initial successes in developing small molecule ligands for non-coding RNAs have underscored their potential as therapeutic targets. More recently, these successes have been aided by advances in biophysical and structural techniques for identification and characterization of more complex RNA structures; these higher-level folds present protein-like binding pockets that offer opportunities to design small molecules that could achieve a degree of selectivity often hard to obtain at the primary and secondary structure level. More specifically, identification and small molecule targeting of RNA tertiary and quaternary structures have allowed researchers to probe several human diseases and have resulted in promising clinical candidates. In this review we highlight a selection of diverse and exciting successes and the experimental approaches that led to their discovery. These studies include examples of recent developments in RNA-centric assays and ligands that provide insight into the features responsible for the affinity and biological outcome of RNA-targeted chemical probes. This report highlights the potential and emerging opportunities to selectively target RNA tertiary and quaternary structures as a route to better understand and, ultimately, treat many diseases.
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43
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Functional and structural basis of extreme conservation in vertebrate 5' untranslated regions. Nat Genet 2021; 53:729-741. [PMID: 33821006 PMCID: PMC8825242 DOI: 10.1038/s41588-021-00830-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 02/26/2021] [Indexed: 01/07/2023]
Abstract
The lack of knowledge about extreme conservation in genomes remains a major gap in our understanding of the evolution of gene regulation. Here, we reveal an unexpected role of extremely conserved 5' untranslated regions (UTRs) in noncanonical translational regulation that is linked to the emergence of essential developmental features in vertebrate species. Endogenous deletion of conserved elements within these 5' UTRs decreased gene expression, and extremely conserved 5' UTRs possess cis-regulatory elements that promote cell-type-specific regulation of translation. We further developed in-cell mutate-and-map (icM2), a new methodology that maps RNA structure inside cells. Using icM2, we determined that an extremely conserved 5' UTR encodes multiple alternative structures and that each single nucleotide within the conserved element maintains the balance of alternative structures important to control the dynamic range of protein expression. These results explain how extreme sequence conservation can lead to RNA-level biological functions encoded in the untranslated regions of vertebrate genomes.
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44
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Schärfen L, Neugebauer KM. Transcription Regulation Through Nascent RNA Folding. J Mol Biol 2021; 433:166975. [PMID: 33811916 DOI: 10.1016/j.jmb.2021.166975] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/14/2022]
Abstract
Folding of RNA into secondary structures through intramolecular base pairing determines an RNA's three-dimensional architecture and associated function. Simple RNA structures like stem loops can provide specialized functions independent of coding capacity, such as protein binding, regulation of RNA processing and stability, stimulation or inhibition of translation. RNA catalysis is dependent on tertiary structures found in the ribosome, tRNAs and group I and II introns. While the extent to which non-coding RNAs contribute to cellular maintenance is generally appreciated, the fact that both non-coding and coding RNA can assume relevant structural states has only recently gained attention. In particular, the co-transcriptional folding of nascent RNA of all classes has the potential to regulate co-transcriptional processing, RNP (ribonucleoprotein particle) formation, and transcription itself. Riboswitches are established examples of co-transcriptionally folded coding RNAs that directly regulate transcription, mainly in prokaryotes. Here we discuss recent studies in both prokaryotes and eukaryotes showing that structure formation may carry a more widespread regulatory logic during RNA synthesis. Local structures forming close to the catalytic center of RNA polymerases have the potential to regulate transcription by reducing backtracking. In addition, stem loops or more complex structures may alter co-transcriptional RNA processing or its efficiency. Several examples of functional structures have been identified to date, and this review provides an overview of physiologically distinct processes where co-transcriptionally folded RNA plays a role. Experimental approaches such as single-molecule FRET and in vivo structural probing to further advance our insight into the significance of co-transcriptional structure formation are discussed.
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Affiliation(s)
- Leonard Schärfen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
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Rivas E. Evolutionary conservation of RNA sequence and structure. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1649. [PMID: 33754485 PMCID: PMC8250186 DOI: 10.1002/wrna.1649] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 12/22/2022]
Abstract
An RNA structure prediction from a single‐sequence RNA folding program is not evidence for an RNA whose structure is important for function. Random sequences have plausible and complex predicted structures not easily distinguishable from those of structural RNAs. How to tell when an RNA has a conserved structure is a question that requires looking at the evolutionary signature left by the conserved RNA. This question is important not just for long noncoding RNAs which usually lack an identified function, but also for RNA binding protein motifs which can be single stranded RNAs or structures. Here we review recent advances using sequence and structural analysis to determine when RNA structure is conserved or not. Although covariation measures assess structural RNA conservation, one must distinguish covariation due to RNA structure from covariation due to independent phylogenetic substitutions. We review a statistical test to measure false positives expected under the null hypothesis of phylogenetic covariation alone (specificity). We also review a complementary test that measures power, that is, expected covariation derived from sequence variation alone (sensitivity). Power in the absence of covariation signals the absence of a conserved RNA structure. We analyze artifacts that falsely identify conserved RNA structure such as the misuse of programs that do not assess significance, the use of inappropriate statistics confounded by signals other than covariation, or misalignments that induce spurious covariation. Among artifacts that obscure the signal of a conserved RNA structure, we discuss the inclusion of pseudogenes in alignments which increase power but destroy covariation. This article is categorized under:RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Evolution and Genomics > Computational Analyses of RNA RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution
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Affiliation(s)
- Elena Rivas
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
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Compendium of Methods to Uncover RNA-Protein Interactions In Vivo. Methods Protoc 2021; 4:mps4010022. [PMID: 33808611 PMCID: PMC8006020 DOI: 10.3390/mps4010022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 01/01/2023] Open
Abstract
Control of gene expression is critical in shaping the pro-and eukaryotic organisms’ genotype and phenotype. The gene expression regulatory pathways solely rely on protein–protein and protein–nucleic acid interactions, which determine the fate of the nucleic acids. RNA–protein interactions play a significant role in co- and post-transcriptional regulation to control gene expression. RNA-binding proteins (RBPs) are a diverse group of macromolecules that bind to RNA and play an essential role in RNA biology by regulating pre-mRNA processing, maturation, nuclear transport, stability, and translation. Hence, the studies aimed at investigating RNA–protein interactions are essential to advance our knowledge in gene expression patterns associated with health and disease. Here we discuss the long-established and current technologies that are widely used to study RNA–protein interactions in vivo. We also present the advantages and disadvantages of each method discussed in the review.
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Weidmann CA, Mustoe AM, Jariwala PB, Calabrese JM, Weeks KM. Analysis of RNA-protein networks with RNP-MaP defines functional hubs on RNA. Nat Biotechnol 2021; 39:347-356. [PMID: 33077962 PMCID: PMC7956044 DOI: 10.1038/s41587-020-0709-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 09/16/2020] [Indexed: 12/29/2022]
Abstract
RNA-protein interaction networks govern many biological processes but are difficult to examine comprehensively. We devised ribonucleoprotein networks analyzed by mutational profiling (RNP-MaP), a live-cell chemical probing strategy that maps cooperative interactions among multiple proteins bound to single RNA molecules at nucleotide resolution. RNP-MaP uses a hetero-bifunctional crosslinker to freeze interacting proteins in place on RNA and then maps multiple bound proteins on single RNA strands by read-through reverse transcription and DNA sequencing. RNP-MaP revealed that RNase P and RMRP, two sequence-divergent but structurally related non-coding RNAs, share RNP networks and that network hubs define functional sites in these RNAs. RNP-MaP also identified protein interaction networks conserved between mouse and human XIST long non-coding RNAs and defined protein communities whose binding sites colocalize and form networks in functional regions of XIST. RNP-MaP enables discovery and efficient validation of functional protein interaction networks on long RNAs in living cells.
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Affiliation(s)
- Chase A Weidmann
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Anthony M Mustoe
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Parth B Jariwala
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - J Mauro Calabrese
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA.
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Roden C, Gladfelter AS. RNA contributions to the form and function of biomolecular condensates. Nat Rev Mol Cell Biol 2021; 22:183-195. [PMID: 32632317 PMCID: PMC7785677 DOI: 10.1038/s41580-020-0264-6] [Citation(s) in RCA: 294] [Impact Index Per Article: 98.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2020] [Indexed: 01/08/2023]
Abstract
Biomolecular condensation partitions cellular contents and has important roles in stress responses, maintaining homeostasis, development and disease. Many nuclear and cytoplasmic condensates are rich in RNA and RNA-binding proteins (RBPs), which undergo liquid-liquid phase separation (LLPS). Whereas the role of RBPs in condensates has been well studied, less attention has been paid to the contribution of RNA to LLPS. In this Review, we discuss the role of RNA in biomolecular condensation and highlight considerations for designing condensate reconstitution experiments. We focus on RNA properties such as composition, length, structure, modifications and expression level. These properties can modulate the biophysical features of native condensates, including their size, shape, viscosity, liquidity, surface tension and composition. We also discuss the role of RNA-protein condensates in development, disease and homeostasis, emphasizing how their properties and function can be determined by RNA. Finally, we discuss the multifaceted cellular functions of biomolecular condensates, including cell compartmentalization through RNA transport and localization, supporting catalytic processes, storage and inheritance of specific molecules, and buffering noise and responding to stress.
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Affiliation(s)
- Christine Roden
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- The Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Amy S Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- The Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
- Whitman Center, Marine Biology Laboratory, Woods Hole, MA, USA.
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Saldi T, Riemondy K, Erickson B, Bentley DL. Alternative RNA structures formed during transcription depend on elongation rate and modify RNA processing. Mol Cell 2021; 81:1789-1801.e5. [PMID: 33631106 DOI: 10.1016/j.molcel.2021.01.040] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 12/24/2022]
Abstract
Most RNA processing occurs co-transcriptionally. We interrogated nascent pol II transcripts by chemical and enzymatic probing and determined how the "nascent RNA structureome" relates to splicing, A-I editing and transcription speed. RNA folding within introns and steep structural transitions at splice sites are associated with efficient co-transcriptional splicing. A slow pol II mutant elicits extensive remodeling into more folded conformations with increased A-I editing. Introns that become more structured at their 3' splice sites get co-transcriptionally excised more efficiently. Slow pol II altered folding of intronic Alu elements where cryptic splicing and intron retention are stimulated, an outcome mimicked by UV, which decelerates transcription. Slow transcription also remodeled RNA folding around alternative exons in distinct ways that predict whether skipping or inclusion is favored, even though it occurs post-transcriptionally. Hence, co-transcriptional RNA folding modulates post-transcriptional alternative splicing. In summary, the plasticity of nascent transcripts has widespread effects on RNA processing.
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Affiliation(s)
- Tassa Saldi
- RNA Bioscience Initiative, Department Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - Kent Riemondy
- RNA Bioscience Initiative, Department Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - Benjamin Erickson
- RNA Bioscience Initiative, Department Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - David L Bentley
- RNA Bioscience Initiative, Department Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA.
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50
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Gawroński P, Enroth C, Kindgren P, Marquardt S, Karpiński S, Leister D, Jensen PE, Vinther J, Scharff LB. Light-Dependent Translation Change of Arabidopsis psbA Correlates with RNA Structure Alterations at the Translation Initiation Region. Cells 2021; 10:322. [PMID: 33557293 PMCID: PMC7914831 DOI: 10.3390/cells10020322] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 01/21/2023] Open
Abstract
mRNA secondary structure influences translation. Proteins that modulate the mRNA secondary structure around the translation initiation region may regulate translation in plastids. To test this hypothesis, we exposed Arabidopsis thaliana to high light, which induces translation of psbA mRNA encoding the D1 subunit of photosystem II. We assayed translation by ribosome profiling and applied two complementary methods to analyze in vivo RNA secondary structure: DMS-MaPseq and SHAPE-seq. We detected increased accessibility of the translation initiation region of psbA after high light treatment, likely contributing to the observed increase in translation by facilitating translation initiation. Furthermore, we identified the footprint of a putative regulatory protein in the 5' UTR of psbA at a position where occlusion of the nucleotide sequence would cause the structure of the translation initiation region to open up, thereby facilitating ribosome access. Moreover, we show that other plastid genes with weak Shine-Dalgarno sequences (SD) are likely to exhibit psbA-like regulation, while those with strong SDs do not. This supports the idea that changes in mRNA secondary structure might represent a general mechanism for translational regulation of psbA and other plastid genes.
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Affiliation(s)
- Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland; (P.G.); (S.K.)
| | - Christel Enroth
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 København N, Denmark; (C.E.); (J.V.)
| | - Peter Kindgren
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; (P.K.); (S.M.)
| | - Sebastian Marquardt
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; (P.K.); (S.M.)
| | - Stanisław Karpiński
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland; (P.G.); (S.K.)
| | - Dario Leister
- Plant Molecular Biology, Department Biology I, Ludwig-Maximilians-University Munich, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany;
| | - Poul Erik Jensen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark;
| | - Jeppe Vinther
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 København N, Denmark; (C.E.); (J.V.)
| | - Lars B. Scharff
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; (P.K.); (S.M.)
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