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Duran E, Schmidt A, Welty R, Jalihal AP, Pitchiaya S, Walter NG. Utilizing functional cell-free extracts to dissect ribonucleoprotein complex biology at single-molecule resolution. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1787. [PMID: 37042458 PMCID: PMC10524090 DOI: 10.1002/wrna.1787] [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: 11/12/2022] [Revised: 03/06/2023] [Accepted: 03/21/2023] [Indexed: 04/13/2023]
Abstract
Cellular machineries that drive and regulate gene expression often rely on the coordinated assembly and interaction of a multitude of proteins and RNA together called ribonucleoprotein complexes (RNPs). As such, it is challenging to fully reconstitute these cellular machines recombinantly and gain mechanistic understanding of how they operate and are regulated within the complex environment that is the cell. One strategy for overcoming this challenge is to perform single molecule fluorescence microscopy studies within crude or recombinantly supplemented cell extracts. This strategy enables elucidation of the interaction and kinetic behavior of specific fluorescently labeled biomolecules within RNPs under conditions that approximate native cellular environments. In this review, we describe single molecule fluorescence microcopy approaches that dissect RNP-driven processes within cellular extracts, highlighting general strategies used in these methods. We further survey biological advances in the areas of pre-mRNA splicing and transcription regulation that have been facilitated through this approach. Finally, we conclude with a summary of practical considerations for the implementation of the featured approaches to facilitate their broader future implementation in dissecting the mechanisms of RNP-driven cellular processes. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Elizabeth Duran
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Andreas Schmidt
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Robb Welty
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Ameya P Jalihal
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Sethuramasundaram Pitchiaya
- Michigan Center for Translational Pathology, Department of Pathology, Department of Urology, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
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2
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Ray S, Pal N, Walter NG. Single bacterial resolvases first exploit, then constrain intrinsic dynamics of the Holliday junction to direct recombination. Nucleic Acids Res 2021; 49:2803-2815. [PMID: 33619520 PMCID: PMC7969024 DOI: 10.1093/nar/gkab096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 01/30/2021] [Accepted: 02/06/2021] [Indexed: 11/13/2022] Open
Abstract
Homologous recombination forms and resolves an entangled DNA Holliday Junction (HJ) crucial for achieving genetic reshuffling and genome repair. To maintain genomic integrity, specialized resolvase enzymes cleave the entangled DNA into two discrete DNA molecules. However, it is unclear how two similar stacking isomers are distinguished, and how a cognate sequence is found and recognized to achieve accurate recombination. We here use single-molecule fluorescence observation and cluster analysis to examine how prototypic bacterial resolvase RuvC singles out two of the four HJ strands and achieves sequence-specific cleavage. We find that RuvC first exploits, then constrains the dynamics of intrinsic HJ isomer exchange at a sampled branch position to direct cleavage toward the catalytically competent HJ conformation and sequence, thus controlling recombination output at minimal energetic cost. Our model of rapid DNA scanning followed by ‘snap-locking’ of a cognate sequence is strikingly consistent with the conformational proofreading of other DNA-modifying enzymes.
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Affiliation(s)
- Sujay Ray
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan Ann Arbor, MI 48109, USA
| | - Nibedita Pal
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan Ann Arbor, MI 48109, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan Ann Arbor, MI 48109, USA
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3
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Li J, Zhang L, Johnson-Buck A, Walter NG. Automatic classification and segmentation of single-molecule fluorescence time traces with deep learning. Nat Commun 2020; 11:5833. [PMID: 33203879 PMCID: PMC7673028 DOI: 10.1038/s41467-020-19673-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 10/20/2020] [Indexed: 01/19/2023] Open
Abstract
Traces from single-molecule fluorescence microscopy (SMFM) experiments exhibit photophysical artifacts that typically necessitate human expert screening, which is time-consuming and introduces potential for user-dependent expectation bias. Here, we use deep learning to develop a rapid, automatic SMFM trace selector, termed AutoSiM, that improves the sensitivity and specificity of an assay for a DNA point mutation based on single-molecule recognition through equilibrium Poisson sampling (SiMREPS). The improved performance of AutoSiM is based on accepting both more true positives and fewer false positives than the conventional approach of hidden Markov modeling (HMM) followed by hard thresholding. As a second application, the selector is used for automated screening of single-molecule Förster resonance energy transfer (smFRET) data to identify high-quality traces for further analysis, and achieves ~90% concordance with manual selection while requiring less processing time. Finally, we show that AutoSiM can be adapted readily to novel datasets, requiring only modest Transfer Learning.
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Affiliation(s)
- Jieming Li
- Single Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, The University of Michigan, Ann Arbor, MI, USA
- Bristol-Myers Squibb Company, New Brunswick, NJ, USA
| | - Leyou Zhang
- Department of Physics, The University of Michigan, Ann Arbor, MI, USA
- Google, Pittsburgh, PA, USA
| | - Alexander Johnson-Buck
- Single Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, The University of Michigan, Ann Arbor, MI, USA.
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI, USA.
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry and Center for RNA Biomedicine, The University of Michigan, Ann Arbor, MI, USA.
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4
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Cooperative Analysis of Structural Dynamics in RNA-Protein Complexes by Single-Molecule Förster Resonance Energy Transfer Spectroscopy. Molecules 2020; 25:molecules25092057. [PMID: 32354083 PMCID: PMC7248720 DOI: 10.3390/molecules25092057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/31/2020] [Accepted: 04/13/2020] [Indexed: 12/24/2022] Open
Abstract
RNA-protein complexes (RNPs) are essential components in a variety of cellular processes, and oftentimes exhibit complex structures and show mechanisms that are highly dynamic in conformation and structure. However, biochemical and structural biology approaches are mostly not able to fully elucidate the structurally and especially conformationally dynamic and heterogeneous nature of these RNPs, to which end single molecule Förster resonance energy transfer (smFRET) spectroscopy can be harnessed to fill this gap. Here we summarize the advantages of strategic smFRET studies to investigate RNP dynamics, complemented by structural and biochemical data. Focusing on recent smFRET studies of three essential biological systems, we demonstrate that investigation of RNPs on a single molecule level can answer important functional questions that remained elusive with structural or biochemical approaches alone: The complex structural rearrangements throughout the splicing cycle, unwinding dynamics of the G-quadruplex (G4) helicase RHAU, and aspects in telomere maintenance regulation and synthesis.
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5
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Lund PE, Chatterjee S, Daher M, Walter NG. Protein unties the pseudoknot: S1-mediated unfolding of RNA higher order structure. Nucleic Acids Res 2020; 48:2107-2125. [PMID: 31832686 PMCID: PMC7038950 DOI: 10.1093/nar/gkz1166] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/26/2019] [Accepted: 12/02/2019] [Indexed: 11/13/2022] Open
Abstract
Ribosomal protein S1 plays important roles in the translation initiation step of many Escherichia coli mRNAs, particularly those with weak Shine-Dalgarno sequences or structured 5′ UTRs, in addition to a variety of cellular processes beyond the ribosome. In all cases, the RNA-binding activity of S1 is a central feature of its function. While sequence determinants of S1 affinity and many elements of the interactions of S1 with simple secondary structures are known, mechanistic details of the protein's interactions with RNAs of more complex secondary and tertiary structure are less understood. Here, we investigate the interaction of S1 with the well-characterized H-type pseudoknot of a class-I translational preQ1 riboswitch as a highly structured RNA model whose conformation and structural dynamics can be tuned by the addition of ligands of varying binding affinity, particularly preQ1, guanine, and 2,6-diaminopurine. Combining biochemical and single molecule fluorescence approaches, we show that S1 preferentially interacts with the less folded form of the pseudoknot and promotes a dynamic, partially unfolded conformation. The ability of S1 to unfold the RNA is inversely correlated with the structural stability of the pseudoknot. These mechanistic insights delineate the scope and limitations of S1-chaperoned unfolding of structured RNAs.
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Affiliation(s)
- Paul E Lund
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Surajit Chatterjee
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - May Daher
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.,Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA
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6
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Ganser LR, Kelly ML, Herschlag D, Al-Hashimi HM. The roles of structural dynamics in the cellular functions of RNAs. Nat Rev Mol Cell Biol 2020; 20:474-489. [PMID: 31182864 DOI: 10.1038/s41580-019-0136-0] [Citation(s) in RCA: 254] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RNAs fold into 3D structures that range from simple helical elements to complex tertiary structures and quaternary ribonucleoprotein assemblies. The functions of many regulatory RNAs depend on how their 3D structure changes in response to a diverse array of cellular conditions. In this Review, we examine how the structural characterization of RNA as dynamic ensembles of conformations, which form with different probabilities and at different timescales, is improving our understanding of RNA function in cells. We discuss the mechanisms of gene regulation by microRNAs, riboswitches, ribozymes, post-transcriptional RNA modifications and RNA-binding proteins, and how the cellular environment and processes such as liquid-liquid phase separation may affect RNA folding and activity. The emerging RNA-ensemble-function paradigm is changing our perspective and understanding of RNA regulation, from in vitro to in vivo and from descriptive to predictive.
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Affiliation(s)
- Laura R Ganser
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Megan L Kelly
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford ChEM-H Chemistry, Engineering, and Medicine for Human Health, Stanford University, Stanford, CA, USA.,Department of Chemical Engineering, Stanford ChEM-H Chemistry, Engineering, and Medicine for Human Health, Stanford University, Stanford, CA, USA.,Department of Chemistry, Stanford ChEM-H Chemistry, Engineering, and Medicine for Human Health, Stanford University, Stanford, CA, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA. .,Department of Chemistry, Duke University, Durham, NC, USA.
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7
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8
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Jia X, Sun C. Structural dynamics of the N-terminal domain and the Switch loop of Prp8 during spliceosome assembly and activation. Nucleic Acids Res 2019; 46:3833-3840. [PMID: 29635373 PMCID: PMC5934631 DOI: 10.1093/nar/gky242] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/03/2018] [Indexed: 11/13/2022] Open
Abstract
Precursor message RNA (pre-mRNA) splicing is executed by the spliceosome, a large ribonucleoprotein (RNP) machinery that is comparable to the ribosome. Driven by the rapid progress of cryo-electron microscopy (cryo-EM) technology, high resolution structures of the spliceosome in its different splicing stages have proliferated over the past three years, which has greatly facilitated the mechanistic understanding of pre-mRNA splicing. As the largest and most conserved protein in the spliceosome, Prp8 plays a pivotal role within this protein-directed ribozyme. Structure determination of different spliceosomal complexes has revealed intimate and dynamic interactions between Prp8 and catalytic RNAs as well as with other protein factors during splicing. Here we review the structural dynamics of two elements of Prp8, the N-terminal domain (N-domain) and the Switch loop, and delineate the dynamic organisation and underlying functional significance of these two elements during spliceosome assembly and activation. Further biochemical and structural dissections of idiographic splicing stages are much needed for a complete understanding of the spliceosome and pre-mRNA splicing.
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Affiliation(s)
- Xu Jia
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu 610500, China
| | - Chengfu Sun
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu 610500, China
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9
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Giannetti CA, Busan S, Weidmann CA, Weeks KM. SHAPE Probing Reveals Human rRNAs Are Largely Unfolded in Solution. Biochemistry 2019; 58:3377-3385. [PMID: 31305988 DOI: 10.1021/acs.biochem.9b00076] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Chemical probing experiments, coupled with empirically determined free energy change relationships, can enable accurate modeling of the secondary structures of diverse and complex RNAs. A current frontier lies in modeling large and structurally heterogeneous transcripts, including complex eukaryotic RNAs. To validate and improve on experimentally driven approaches for modeling large transcripts, we obtained high-quality SHAPE data for the protein-free human 18S and 28S ribosomal RNAs (rRNAs). To our surprise, SHAPE-directed structure models for the human rRNAs poorly matched accepted structures. Analysis of predicted rRNA structures based on low-SHAPE and low-entropy (lowSS) metrics revealed that, whereas ∼75% of Escherichia coli rRNA sequences form well-determined lowSS secondary structure, only ∼40% of the human rRNAs do. Critically, regions of the human rRNAs that specifically fold into well-determined lowSS structures were modeled to high accuracy using SHAPE data. This work reveals that eukaryotic rRNAs are more unfolded than are those of prokaryotic rRNAs and indeed are largely unfolded overall, likely reflecting increased protein dependence for eukaryotic ribosome structure. In addition, those regions and substructures that are well-determined can be identified de novo and successfully modeled by SHAPE-directed folding.
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Affiliation(s)
- Catherine A Giannetti
- Department of Chemistry , The University of North Carolina , Chapel Hill , North Carolina 27599-3290 , United States
| | - Steven Busan
- Department of Chemistry , The University of North Carolina , Chapel Hill , North Carolina 27599-3290 , United States
| | - Chase A Weidmann
- Department of Chemistry , The University of North Carolina , Chapel Hill , North Carolina 27599-3290 , United States
| | - Kevin M Weeks
- Department of Chemistry , The University of North Carolina , Chapel Hill , North Carolina 27599-3290 , United States
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10
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Hon J, Gonzalez RL. Bayesian-Estimated Hierarchical HMMs Enable Robust Analysis of Single-Molecule Kinetic Heterogeneity. Biophys J 2019; 116:1790-1802. [PMID: 31010664 DOI: 10.1016/j.bpj.2019.02.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 01/27/2019] [Accepted: 02/13/2019] [Indexed: 10/27/2022] Open
Abstract
Single-molecule kinetic experiments allow the reaction trajectories of individual biomolecules to be directly observed, eliminating the effects of population averaging and providing a powerful approach for elucidating the kinetic mechanisms of biomolecular processes. A major challenge to the analysis and interpretation of these experiments, however, is the kinetic heterogeneity that almost universally complicates the recorded single-molecule signal versus time trajectories (i.e., signal trajectories). Such heterogeneity manifests as changes and/or differences in the transition rates that are observed within individual signal trajectories or across a population of signal trajectories. Because characterizing kinetic heterogeneity can provide critical mechanistic information, we have developed a computational method that effectively and comprehensively enables such analysis. To this end, we have developed a computational algorithm and software program, hFRET, that uses the variational approximation for Bayesian inference to estimate the parameters of a hierarchical hidden Markov model, thereby enabling robust identification and characterization of kinetic heterogeneity. Using simulated signal trajectories, we demonstrate the ability of hFRET to accurately and precisely characterize kinetic heterogeneity. In addition, we use hFRET to analyze experimentally recorded signal trajectories reporting on the conformational dynamics of ribosomal pre-translocation (PRE) complexes. The results of our analyses demonstrate that PRE complexes exhibit kinetic heterogeneity, reveal the physical origins of this heterogeneity, and allow us to expand the current model of PRE complex dynamics. The methods described here can be applied to signal trajectories generated using any type of signal and can be easily extended to the analysis of signal trajectories exhibiting more complex kinetic behaviors. Moreover, variations of our approach can be easily developed to integrate kinetic data obtained from different experimental constructs and/or from molecular dynamics simulations of a biomolecule of interest.
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Affiliation(s)
- Jason Hon
- Department of Chemistry, Columbia University, New York, New York
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, New York, New York.
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11
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Jalihal AP, Lund PE, Walter NG. Coming Together: RNAs and Proteins Assemble under the Single-Molecule Fluorescence Microscope. Cold Spring Harb Perspect Biol 2019; 11:11/4/a032441. [PMID: 30936188 DOI: 10.1101/cshperspect.a032441] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
RNAs, across their numerous classes, often work in concert with proteins in RNA-protein complexes (RNPs) to execute critical cellular functions. Ensemble-averaging methods have been instrumental in revealing many important aspects of these RNA-protein interactions, yet are insufficiently sensitive to much of the dynamics at the heart of RNP function. Single-molecule fluorescence microscopy (SMFM) offers complementary, versatile tools to probe RNP conformational and compositional changes in detail. In this review, we first outline the basic principles of SMFM as applied to RNPs, describing key considerations for labeling, imaging, and quantitative analysis. We then sample applications of in vitro and in vivo single-molecule visualization using the case studies of pre-messenger RNA (mRNA) splicing and RNA silencing, respectively. After discussing specific insights single-molecule fluorescence methods have yielded, we briefly review recent developments in the field and highlight areas of anticipated growth.
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Affiliation(s)
- Ameya P Jalihal
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, Michigan 48109.,Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Paul E Lund
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109.,Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109
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12
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Frankiw L, Majumdar D, Burns C, Vlach L, Moradian A, Sweredoski MJ, Baltimore D. BUD13 Promotes a Type I Interferon Response by Countering Intron Retention in Irf7. Mol Cell 2019; 73:803-814.e6. [DOI: 10.1016/j.molcel.2018.11.038] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/20/2018] [Accepted: 11/29/2018] [Indexed: 01/12/2023]
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13
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Smith CS, Jouravleva K, Huisman M, Jolly SM, Zamore PD, Grunwald D. An automated Bayesian pipeline for rapid analysis of single-molecule binding data. Nat Commun 2019; 10:272. [PMID: 30655518 PMCID: PMC6336789 DOI: 10.1038/s41467-018-08045-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 12/13/2018] [Indexed: 11/29/2022] Open
Abstract
Single-molecule binding assays enable the study of how molecular machines assemble and function. Current algorithms can identify and locate individual molecules, but require tedious manual validation of each spot. Moreover, no solution for high-throughput analysis of single-molecule binding data exists. Here, we describe an automated pipeline to analyze single-molecule data over a wide range of experimental conditions. In addition, our method enables state estimation on multivariate Gaussian signals. We validate our approach using simulated data, and benchmark the pipeline by measuring the binding properties of the well-studied, DNA-guided DNA endonuclease, TtAgo, an Argonaute protein from the Eubacterium Thermus thermophilus. We also use the pipeline to extend our understanding of TtAgo by measuring the protein’s binding kinetics at physiological temperatures and for target DNAs containing multiple, adjacent binding sites. Analysis of single-molecule binding assays still requires substantial manual user intervention. Here, the authors present a pipeline for rapid, automated analysis of co-localization single-molecule spectroscopy images, with a modular user interface that can be adjusted to a range of experimental conditions.
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Affiliation(s)
- Carlas S Smith
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA. .,Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
| | - Karina Jouravleva
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Maximiliaan Huisman
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Samson M Jolly
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Phillip D Zamore
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA. .,Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA.
| | - David Grunwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA.
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14
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Yu Y, Ma L, Li L, Deng Y, Xu L, Liu H, Xiao L, Su X. Digestion of Dynamic Substrate by Exonuclease Reveals High Single-Mismatch Selectivity. Anal Chem 2018; 90:13655-13662. [DOI: 10.1021/acs.analchem.8b03963] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yingjie Yu
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Liang Ma
- Clinical laboratory, China-Japan Friendship Hospital, Beijing 100029, China
| | - Lidan Li
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yingnan Deng
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lida Xu
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hua Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Lehui Xiao
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xin Su
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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15
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Ray S, Widom JR, Walter NG. Life under the Microscope: Single-Molecule Fluorescence Highlights the RNA World. Chem Rev 2018; 118:4120-4155. [PMID: 29363314 PMCID: PMC5918467 DOI: 10.1021/acs.chemrev.7b00519] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The emergence of single-molecule (SM) fluorescence techniques has opened up a vast new toolbox for exploring the molecular basis of life. The ability to monitor individual biomolecules in real time enables complex, dynamic folding pathways to be interrogated without the averaging effect of ensemble measurements. In parallel, modern biology has been revolutionized by our emerging understanding of the many functions of RNA. In this comprehensive review, we survey SM fluorescence approaches and discuss how the application of these tools to RNA and RNA-containing macromolecular complexes in vitro has yielded significant insights into the underlying biology. Topics covered include the three-dimensional folding landscapes of a plethora of isolated RNA molecules, their assembly and interactions in RNA-protein complexes, and the relation of these properties to their biological functions. In all of these examples, the use of SM fluorescence methods has revealed critical information beyond the reach of ensemble averages.
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Affiliation(s)
| | | | - Nils G. Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA
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16
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Tartari F, Conti A, Cerqueti R. Assessing the relationship between toxicity and economic cost of oncological target agents: A systematic review of clinical trials. PLoS One 2017; 12:e0183639. [PMID: 28829823 PMCID: PMC5567914 DOI: 10.1371/journal.pone.0183639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 07/29/2017] [Indexed: 12/19/2022] Open
Abstract
Target agents are peculiar oncological drugs which differ from the traditional therapies in their ability of recognizing specific molecules expressed by tumor cells and microenvironment. Thus, their toxicity is generally lower than that associated to chemotherapy, and they represent nowadays a new standard of care in a number of tumors. This paper deals with the relationship between economic costs and toxicity of target agents. At this aim, a cluster analysis-based exploration of the main features of a large collection of them is carried out, with a specific focus on the variables leading to the identification of their toxicity and related costs. The analysis of the toxicity is based on the Severe Adverse Events (SAE) and Discontinuation (D) rates of each target agent considering data published on PubMed from 1965 to 2016 in the phase II and III studies that have led to the approval of these drugs for cancer patients by US Food and Drug Administration. The construction of the dataset represents a key step of the research, and is grounded on the critical analysis of a wide set of clinical studies. In order to capture different evaluation strategies of the toxicity, clustering is performed according to three different criteria (including Voronoi tessellation). Our procedure allows us to identify 5 different groups of target agents pooled by similar SAE and D rates and, at the same time, 3 groups based on target agents' costs for 1 month and for the median whole duration of therapy. Results highlight several specific regularities for toxicity and costs. This study present several limitations, being realized starting from clinical trials and not from individual patients' data. However, a macroscopic perspective suggests that costs are rather heterogeneous, and they do not clearly follow the clustering based on SAE and D rates.
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Affiliation(s)
- Francesca Tartari
- Department of Economics and Law, University of Macerata. Via Crescimbeni, Macerata, Italy
| | - Alessandro Conti
- Azienda Ospedaliera dell’Alto Adige, Bressanone/Brissen Hospital. Via Dante, Bressanone/Brissen, Italy
| | - Roy Cerqueti
- Department of Economics and Law, University of Macerata. Via Crescimbeni, Macerata, Italy
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17
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Sgouralis I, Pressé S. ICON: An Adaptation of Infinite HMMs for Time Traces with Drift. Biophys J 2017; 112:2117-2126. [PMID: 28538149 DOI: 10.1016/j.bpj.2017.04.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 04/01/2017] [Accepted: 04/11/2017] [Indexed: 11/19/2022] Open
Abstract
Bayesian nonparametric methods have recently transformed emerging areas within data science. One such promising method, the infinite hidden Markov model (iHMM), generalizes the HMM that itself has become a workhorse in single molecule data analysis. The iHMM goes beyond the HMM by self-consistently learning all parameters learned by the HMM in addition to learning the number of states without recourse to any model selection steps. Despite its generality, simple features (such as drift), common to single molecule time traces, result in an overinterpretation of drift and the introduction of artifact states. Here we present an adaptation of the iHMM that can treat data with drift originating from one or many traces (e.g., Förster resonance energy transfer). Our fully Bayesian method couples the iHMM to a continuous control process (drift) self-consistently learned while learning all other quantities determined by the iHMM (including state numbers). A key advantage of this method is that all traces-regardless of drift or states visited across traces-may now be treated on an equal footing, thereby eliminating user-dependent trace selection (based on drift levels), preprocessing to remove drift, and postprocessing model selection based on state number.
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Affiliation(s)
| | - Steve Pressé
- Department of Physics, Arizona State University, Tempe, Arizona; School of Molecular Sciences, Arizona State University, Tempe, Arizona.
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18
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An Introduction to Infinite HMMs for Single-Molecule Data Analysis. Biophys J 2017; 112:2021-2029. [PMID: 28538142 DOI: 10.1016/j.bpj.2017.04.027] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 04/01/2017] [Accepted: 04/20/2017] [Indexed: 12/19/2022] Open
Abstract
The hidden Markov model (HMM) has been a workhorse of single-molecule data analysis and is now commonly used as a stand-alone tool in time series analysis or in conjunction with other analysis methods such as tracking. Here, we provide a conceptual introduction to an important generalization of the HMM, which is poised to have a deep impact across the field of biophysics: the infinite HMM (iHMM). As a modeling tool, iHMMs can analyze sequential data without a priori setting a specific number of states as required for the traditional (finite) HMM. Although the current literature on the iHMM is primarily intended for audiences in statistics, the idea is powerful and the iHMM's breadth in applicability outside machine learning and data science warrants a careful exposition. Here, we explain the key ideas underlying the iHMM, with a special emphasis on implementation, and provide a description of a code we are making freely available. In a companion article, we provide an important extension of the iHMM to accommodate complications such as drift.
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19
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Single-Molecule Analysis beyond Dwell Times: Demonstration and Assessment in and out of Equilibrium. Biophys J 2017; 111:1375-1384. [PMID: 27705761 DOI: 10.1016/j.bpj.2016.08.023] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/01/2016] [Accepted: 08/09/2016] [Indexed: 11/21/2022] Open
Abstract
We present a simple and robust technique for extracting kinetic rate models and thermodynamic quantities from single-molecule time traces. Single-molecule analysis of complex kinetic sequences (SMACKS) is a maximum-likelihood approach that resolves all statistically relevant rates and also their uncertainties. This is achieved by optimizing one global kinetic model based on the complete data set while allowing for experimental variations between individual trajectories. In contrast to dwell-time analysis, which is the current standard method, SMACKS includes every experimental data point, not only dwell times. As a result, it works as well for long trajectories as for an equivalent set of short ones. In addition, the previous systematic overestimation of fast over slow rates is solved. We demonstrate the power of SMACKS on the kinetics of the multidomain protein Hsp90 measured by single-molecule Förster resonance energy transfer. Experiments in and out of equilibrium are analyzed and compared to simulations, shedding new light on the role of Hsp90's ATPase function. SMACKS resolves accurate rate models even if states cause indistinguishable signals. Thereby, it pushes the boundaries of single-molecule kinetics beyond those of current methods.
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20
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Ren X, Deng R, Wang L, Zhang K, Li J. RNA splicing process analysis for identifying antisense oligonucleotide inhibitors with padlock probe-based isothermal amplification. Chem Sci 2017; 8:5692-5698. [PMID: 28989608 PMCID: PMC5621167 DOI: 10.1039/c7sc01336a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 06/07/2017] [Indexed: 12/24/2022] Open
Abstract
We report a highly sensitive method for quantifying the splicing products in different steps, enabling us to analyze the splicing process and identify ASO inhibitors.
RNA splicing, which mainly involves two transesterification steps, is a fundamental process of gene expression and its abnormal regulation contributes to serious genetic diseases. Antisense oligonucleotides (ASOs) are genetic control tools that can be used to specifically control genes through alteration of the RNA splicing pathway. Despite intensive research, how ASOs or various other factors influence the multiple processes of RNA splicing still remains obscure. This is largely due to an inability to analyze the splicing efficiency of each step in the RNA splicing process with high sensitivity. We addressed this limitation by introducing a padlock probe-based isothermal amplification assay to achieve quantification of the specific products in different splicing steps. With this amplified assay, the roles that ASOs play in RNA splicing inhibition in the first and second steps could be distinguished. We identified that 5′-ASO could block RNA splicing by inhibiting the first step, while 3′-ASO could block RNA splicing by inhibiting the second step. This method provides a versatile tool for assisting efficient ASO design and discovering new splicing modulators and therapeutic drugs.
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Affiliation(s)
- Xiaojun Ren
- School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , China.,Department of Chemistry , Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China .
| | - Ruijie Deng
- Department of Chemistry , Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China .
| | - Lida Wang
- Department of Chemistry , Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China .
| | - Kaixiang Zhang
- Department of Chemistry , Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China .
| | - Jinghong Li
- Department of Chemistry , Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China .
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21
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van der Feltz C, Hoskins AA. Methodologies for studying the spliceosome's RNA dynamics with single-molecule FRET. Methods 2017; 125:45-54. [PMID: 28529063 DOI: 10.1016/j.ymeth.2017.05.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 05/13/2017] [Accepted: 05/16/2017] [Indexed: 11/30/2022] Open
Abstract
The spliceosome is an extraordinarily dynamic molecular machine in which significant changes in composition as well as protein and RNA conformation are required for carrying out pre-mRNA splicing. Single-molecule fluorescence resonance energy transfer (smFRET) can be used to elucidate these dynamics both in well-characterized model systems and in entire spliceosomes. These types of single-molecule data provide novel information about spliceosome components and can be used to identify sub-populations of molecules with unique behaviors. When smFRET is combined with single-molecule fluorescence colocalization, conformational dynamics can be further linked to the presence or absence of a given spliceosome component. Here, we provide a description of experimental considerations, approaches, and workflows for smFRET with an emphasis on applications for the splicing machinery.
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Affiliation(s)
- Clarisse van der Feltz
- Department of Biochemistry, 433 Babcock Dr., University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Aaron A Hoskins
- Department of Biochemistry, 433 Babcock Dr., University of Wisconsin-Madison, Madison, WI 53706, USA.
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22
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Li L, Xiao X, Ge J, Han M, Zhou X, Wang L, Su X, Yu C. Discrimination Cascade Enabled Selective Detection of Single-Nucleotide Mutation. ACS Sens 2017; 2:419-425. [PMID: 28723215 DOI: 10.1021/acssensors.7b00005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Owing to the significance of single nucleotide mutation (SNM) for personalized medicine, the detection of SNM with high accuracy has recently attracted considerable interest. Here, we present a kinetic method for selective detection of SNM based on a discrimination cascade constructed by combining the toehold strand displacement (TSD) and endonuclease IV (Endo IV) catalyzed hydrolysis. The single-nucleotide specificity of the two DNA reactions allows highly selective detection of all types of single nucleotide changes (including single-nucleotide insertion and deletion), achieving a high discrimination factor with a median of 491 which is comparable with recently reported methods. For the first time, the enzyme assisted nucleic acid assay was characterized by single molecule analysis on total internal reflection fluorescence microscope (TIRFM) suggesting that the two steps do not work independently and the rate of TSD can be tuned by Endo IV facilitated conformation selection. The effective discrimination of the point mutation of BRAF gene in cancer and normal cell line suggests that this method can be a prominent post-PCR genotyping assay.
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Affiliation(s)
- Lidan Li
- College
of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xianjin Xiao
- Family
Planning Research Institute/Center of Reproductive Medicine, Tongji
Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Jingyang Ge
- College
of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Manli Han
- College
of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xu Zhou
- College
of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lei Wang
- College
of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xin Su
- College
of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Changyuan Yu
- College
of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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23
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Wu BH, Ivie JA, Johnson TK, Monti OLA. Uncovering hierarchical data structure in single molecule transport. J Chem Phys 2017. [DOI: 10.1063/1.4974937] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Ben H. Wu
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721, USA
| | - Jeffrey A. Ivie
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721, USA
| | - Tyler K. Johnson
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721, USA
| | - Oliver L. A. Monti
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721, USA
- Department of Physics, University of Arizona, 1118 E. Fourth Street, Tucson, Arizona 85721, USA
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24
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Rohlman CE, Blanco MR, Walter NG. Putting Humpty-Dumpty Together: Clustering the Functional Dynamics of Single Biomolecular Machines Such as the Spliceosome. Methods Enzymol 2016; 581:257-283. [PMID: 27793282 DOI: 10.1016/bs.mie.2016.08.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The spliceosome is a biomolecular machine that, in all eukaryotes, accomplishes site-specific splicing of introns from precursor messenger RNAs (pre-mRNAs) with high fidelity. Operating at the nanometer scale, where inertia and friction have lost the dominant role they play in the macroscopic realm, the spliceosome is highly dynamic and assembles its active site around each pre-mRNA anew. To understand the structural dynamics underlying the molecular motors, clocks, and ratchets that achieve functional accuracy in the yeast spliceosome (a long-standing model system), we have developed single-molecule fluorescence resonance energy transfer (smFRET) approaches that report changes in intra- and intermolecular interactions in real time. Building on our work using hidden Markov models (HMMs) to extract kinetic and conformational state information from smFRET time trajectories, we recognized that HMM analysis of individual state transitions as independent stochastic events is insufficient for a biomolecular machine as complex as the spliceosome. In this chapter, we elaborate on the recently developed smFRET-based Single-Molecule Cluster Analysis (SiMCAn) that dissects the intricate conformational dynamics of a pre-mRNA through the splicing cycle in a model-free fashion. By leveraging hierarchical clustering techniques developed for Bioinformatics, SiMCAn efficiently analyzes large datasets to first identify common molecular behaviors. Through a second level of clustering based on the abundance of dynamic behaviors exhibited by defined functional intermediates that have been stalled by biochemical or genetic tools, SiMCAn then efficiently assigns pre-mRNA FRET states and transitions to specific splicing complexes, with the potential to find heretofore undescribed conformations. SiMCAn thus arises as a general tool to analyze dynamic cellular machines more broadly.
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Affiliation(s)
| | - M R Blanco
- Single Molecule Analysis Group and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, United States
| | - N G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, United States.
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25
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DeHaven AC, Norden IS, Hoskins AA. Lights, camera, action! Capturing the spliceosome and pre-mRNA splicing with single-molecule fluorescence microscopy. WILEY INTERDISCIPLINARY REVIEWS. RNA 2016; 7:683-701. [PMID: 27198613 PMCID: PMC4990488 DOI: 10.1002/wrna.1358] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/20/2016] [Accepted: 04/04/2016] [Indexed: 11/06/2022]
Abstract
The process of removing intronic sequences from a precursor to messenger RNA (pre-mRNA) to yield a mature mRNA transcript via splicing is an integral step in eukaryotic gene expression. Splicing is carried out by a cellular nanomachine called the spliceosome that is composed of RNA components and dozens of proteins. Despite decades of study, many fundamentals of spliceosome function have remained elusive. Recent developments in single-molecule fluorescence microscopy have afforded new tools to better probe the spliceosome and the complex, dynamic process of splicing by direct observation of single molecules. These cutting-edge technologies enable investigators to monitor the dynamics of specific splicing components, whole spliceosomes, and even cotranscriptional splicing within living cells. WIREs RNA 2016, 7:683-701. doi: 10.1002/wrna.1358 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Alexander C. DeHaven
- Integrated Program in Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
- Department of Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
| | - Ian S. Norden
- Integrated Program in Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
- Department of Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
| | - Aaron A. Hoskins
- Department of Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
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26
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Semlow DR, Blanco MR, Walter NG, Staley JP. Spliceosomal DEAH-Box ATPases Remodel Pre-mRNA to Activate Alternative Splice Sites. Cell 2016; 164:985-98. [PMID: 26919433 DOI: 10.1016/j.cell.2016.01.025] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 01/08/2016] [Accepted: 01/15/2016] [Indexed: 12/19/2022]
Abstract
During pre-mRNA splicing, a central step in the expression and regulation of eukaryotic genes, the spliceosome selects splice sites for intron excision and exon ligation. In doing so, the spliceosome must distinguish optimal from suboptimal splice sites. At the catalytic stage of splicing, suboptimal splice sites are repressed by the DEAH-box ATPases Prp16 and Prp22. Here, using budding yeast, we show that these ATPases function further by enabling the spliceosome to search for and utilize alternative branch sites and 3' splice sites. The ATPases facilitate this search by remodeling the splicing substrate to disengage candidate splice sites. Our data support a mechanism involving 3' to 5' translocation of the ATPases along substrate RNA and toward a candidate site, but, surprisingly, not across the site. Thus, our data implicate DEAH-box ATPases in acting at a distance by pulling substrate RNA from the catalytic core of the spliceosome.
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Affiliation(s)
- Daniel R Semlow
- Graduate Program in Cell and Molecular Biology, University of Chicago, 920 East 58(th) Street, Chicago, IL 60637, USA
| | - Mario R Blanco
- Cellular and Molecular Biology, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109, USA; Single Molecule Analysis Group, Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109, USA
| | - Jonathan P Staley
- Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58(th) Street, Chicago, IL 60637, USA.
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27
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Wang X, Yang Y, Zuo Y, Yang F, Shen H, Wu D. Facile creation of FRET systems from a pH-responsive AIE fluorescent vesicle. Chem Commun (Camb) 2016; 52:5320-3. [DOI: 10.1039/c6cc01706a] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We demonstrate a facile approach to constructing aggregation induced emission (AIE) fluorescent vesicles for creation of FRET systems.
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Affiliation(s)
- Xing Wang
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory of Polymer Physics & Chemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Yanyu Yang
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory of Polymer Physics & Chemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Yunfei Zuo
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory of Polymer Physics & Chemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Fei Yang
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory of Polymer Physics & Chemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Hong Shen
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory of Polymer Physics & Chemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Decheng Wu
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory of Polymer Physics & Chemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
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28
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Kahlscheuer ML, Widom J, Walter NG. Single-Molecule Pull-Down FRET to Dissect the Mechanisms of Biomolecular Machines. Methods Enzymol 2015; 558:539-570. [PMID: 26068753 PMCID: PMC4886477 DOI: 10.1016/bs.mie.2015.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Spliceosomes are multimegadalton RNA-protein complexes responsible for the faithful removal of noncoding segments (introns) from pre-messenger RNAs (pre-mRNAs), a process critical for the maturation of eukaryotic mRNAs for subsequent translation by the ribosome. Both the spliceosome and ribosome, as well as many other RNA and DNA processing machineries, contain central RNA components that endow biomolecular complexes with precise, sequence-specific nucleic acid recognition, and versatile structural dynamics. Single-molecule fluorescence (or Förster) resonance energy transfer (smFRET) microscopy is a powerful tool for the study of local and global conformational changes of both simple and complex biomolecular systems involving RNA. The integration of biochemical tools such as immunoprecipitation with advanced methods in smFRET microscopy and data analysis has opened up entirely new avenues toward studying the mechanisms of biomolecular machines isolated directly from complex biological specimens, such as cell extracts. Here, we detail the general steps for using prism-based total internal reflection fluorescence microscopy in exemplary single-molecule pull-down FRET studies of the yeast spliceosome and discuss the broad application potential of this technique.
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Affiliation(s)
- Matthew L Kahlscheuer
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Julia Widom
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
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