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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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Raymond WS, Ghaffari S, Aguilera LU, Ron E, Morisaki T, Fox ZR, May MP, Stasevich TJ, Munsky B. Using mechanistic models and machine learning to design single-color multiplexed nascent chain tracking experiments. Front Cell Dev Biol 2023; 11:1151318. [PMID: 37325568 PMCID: PMC10267835 DOI: 10.3389/fcell.2023.1151318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
mRNA translation is the ubiquitous cellular process of reading messenger-RNA strands into functional proteins. Over the past decade, large strides in microscopy techniques have allowed observation of mRNA translation at a single-molecule resolution for self-consistent time-series measurements in live cells. Dubbed Nascent chain tracking (NCT), these methods have explored many temporal dynamics in mRNA translation uncaptured by other experimental methods such as ribosomal profiling, smFISH, pSILAC, BONCAT, or FUNCAT-PLA. However, NCT is currently restricted to the observation of one or two mRNA species at a time due to limits in the number of resolvable fluorescent tags. In this work, we propose a hybrid computational pipeline, where detailed mechanistic simulations produce realistic NCT videos, and machine learning is used to assess potential experimental designs for their ability to resolve multiple mRNA species using a single fluorescent color for all species. Our simulation results show that with careful application this hybrid design strategy could in principle be used to extend the number of mRNA species that could be watched simultaneously within the same cell. We present a simulated example NCT experiment with seven different mRNA species within the same simulated cell and use our ML labeling to identify these spots with 90% accuracy using only two distinct fluorescent tags. We conclude that the proposed extension to the NCT color palette should allow experimentalists to access a plethora of new experimental design possibilities, especially for cell Signaling applications requiring simultaneous study of multiple mRNAs.
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Affiliation(s)
- William S Raymond
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, United States
| | - Sadaf Ghaffari
- Department of Computer Science, Colorado State University, Fort Collins, CO, United States
| | - Luis U Aguilera
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States
| | - Eric Ron
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, United States
| | - Tatsuya Morisaki
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Zachary R Fox
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, United States
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Michael P May
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, United States
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
- World Research Hub Initiative and Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Brian Munsky
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, United States
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States
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3
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Single-molecule visualization of mRNA circularization during translation. Exp Mol Med 2023; 55:283-289. [PMID: 36720916 PMCID: PMC9981743 DOI: 10.1038/s12276-023-00933-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/04/2022] [Accepted: 12/04/2022] [Indexed: 02/02/2023] Open
Abstract
Translation is mediated by precisely orchestrated sequential interactions among translation initiation components, mRNA, and ribosomes. Biochemical, structural, and genetic techniques have revealed the fundamental mechanism that determines what occurs and when, where and in what order. Most mRNAs are circularized via the eIF4E-eIF4G-PABP interaction, which stabilizes mRNAs and enhances translation by recycling ribosomes. However, studies using single-molecule fluorescence imaging have allowed for the visualization of complex data that opposes the traditional "functional circularization" theory. Here, we briefly introduce single-molecule techniques applied to studies on mRNA circularization and describe the results of in vitro and live-cell imaging. Finally, we discuss relevant insights and questions gained from single-molecule research related to translation.
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Kilic Z, Schweiger M, Moyer C, Shepherd D, Pressé S. Gene expression model inference from snapshot RNA data using Bayesian non-parametrics. NATURE COMPUTATIONAL SCIENCE 2023; 3:174-183. [PMID: 38125199 PMCID: PMC10732567 DOI: 10.1038/s43588-022-00392-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2023]
Abstract
Gene expression models, which are key towards understanding cellular regulatory response, underlie observations of single-cell transcriptional dynamics. Although RNA expression data encode information on gene expression models, existing computational frameworks do not perform simultaneous Bayesian inference of gene expression models and parameters from such data. Rather, gene expression models-composed of gene states, their connectivities and associated parameters-are currently deduced by pre-specifying gene state numbers and connectivity before learning associated rate parameters. Here we propose a method to learn full distributions over gene states, state connectivities and associated rate parameters, simultaneously and self-consistently from single-molecule RNA counts. We propagate noise from fluctuating RNA counts over models by treating models themselves as random variables. We achieve this within a Bayesian non-parametric paradigm. We demonstrate our method on the Escherichia coli lacZ pathway and the Saccharomyces cerevisiae STL1 pathway, and verify its robustness on synthetic data.
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Affiliation(s)
- Zeliha Kilic
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
- These authors contributed equally: Zeliha Kilic, Max Schweiger
| | - Max Schweiger
- Center for Biological Physics, ASU, Tempe, AZ, USA
- Department of Physics, ASU, Tempe, AZ, USA
- These authors contributed equally: Zeliha Kilic, Max Schweiger
| | - Camille Moyer
- Center for Biological Physics, ASU, Tempe, AZ, USA
- School of Mathematics and Statistical Sciences, ASU, Tempe, AZ, USA
| | - Douglas Shepherd
- Center for Biological Physics, ASU, Tempe, AZ, USA
- Department of Physics, ASU, Tempe, AZ, USA
| | - Steve Pressé
- Center for Biological Physics, ASU, Tempe, AZ, USA
- Department of Physics, ASU, Tempe, AZ, USA
- School of Molecular Sciences, ASU, Tempe, AZ, USA
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5
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Raymond WS, Ghaffari S, Aguilera LU, Ron E, Morisaki T, Fox ZR, May MP, Stasevich TJ, Munsky B. Using Mechanistic Models and Machine Learning to Design Single-Color Multiplexed Nascent Chain Tracking Experiments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525583. [PMID: 36747627 PMCID: PMC9900927 DOI: 10.1101/2023.01.25.525583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
mRNA translation is the ubiquitous cellular process of reading messenger-RNA strands into functional proteins. Over the past decade, large strides in microscopy techniques have allowed observation of mRNA translation at a single-molecule resolution for self-consistent time-series measurements in live cells. Dubbed Nascent chain tracking (NCT), these methods have explored many temporal dynamics in mRNA translation uncaptured by other experimental methods such as ribosomal profiling, smFISH, pSILAC, BONCAT, or FUNCAT-PLA. However, NCT is currently restricted to the observation of one or two mRNA species at a time due to limits in the number of resolvable fluorescent tags. In this work, we propose a hybrid computational pipeline, where detailed mechanistic simulations produce realistic NCT videos, and machine learning is used to assess potential experimental designs for their ability to resolve multiple mRNA species using a single fluorescent color for all species. Through simulation, we show that with careful application, this hybrid design strategy could in principle be used to extend the number of mRNA species that could be watched simultaneously within the same cell. We present a simulated example NCT experiment with seven different mRNA species within the same simulated cell and use our ML labeling to identify these spots with 90% accuracy using only two distinct fluorescent tags. The proposed extension to the NCT color palette should allow experimentalists to access a plethora of new experimental design possibilities, especially for cell signalling applications requiring simultaneous study of multiple mRNAs.
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Affiliation(s)
- William S. Raymond
- School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA
| | - Sadaf Ghaffari
- Department of Computer Science, Colorado State University, Fort Collins, Colorado, USA
| | - Luis U. Aguilera
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado, USA
| | - Eric Ron
- School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA
| | - Tatsuya Morisaki
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Zachary R. Fox
- School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA,Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Michael P. May
- School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA
| | - Timothy J. Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA,Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Brian Munsky
- School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA,Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado, USA,Corresponding Author: Brian Munsky -
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6
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Cialek CA, Galindo G, Morisaki T, Zhao N, Montgomery TA, Stasevich TJ. Imaging translational control by Argonaute with single-molecule resolution in live cells. Nat Commun 2022; 13:3345. [PMID: 35688806 PMCID: PMC9187665 DOI: 10.1038/s41467-022-30976-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/24/2022] [Indexed: 11/29/2022] Open
Abstract
A major challenge to our understanding of translational control has been deconvolving the individual impact specific regulatory factors have on the complex dynamics of mRNA translation. MicroRNAs (miRNAs), for example, guide Argonaute and associated proteins to target mRNAs, where they direct gene silencing in multiple ways that are not well understood. To better deconvolve these dynamics, we have developed technology to directly visualize and quantify the impact of human Argonaute2 (Ago2) on the translation and subcellular localization of individual reporter mRNAs in living cells. We show that our combined translation and Ago2 tethering sensor reflects endogenous miRNA-mediated gene silencing. Using the sensor, we find that Ago2 association leads to progressive silencing of translation at individual mRNA. Silencing was occasionally interrupted by brief bursts of translational activity and took 3–4 times longer than a single round of translation, consistent with a gradual increase in the inhibition of translation initiation. At later time points, Ago2-tethered mRNAs cluster and coalesce with P-bodies, where a translationally silent state is maintained. These results provide a framework for exploring miRNA-mediated gene regulation in live cells at the single-molecule level. Furthermore, our tethering-based, single-molecule reporter system will likely have wide-ranging application in studying RNA-protein interactions. Guided by miRNA, Argonaute proteins silence mRNA in multiple ways that are not well understood. Here, the authors develop live-cell biosensors to image the impact tethered regulatory factors, such as Argonaute, have on single-mRNA translation dynamics.
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Affiliation(s)
- Charlotte A Cialek
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Gabriel Galindo
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Tatsuya Morisaki
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Ning Zhao
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Taiowa A Montgomery
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Timothy J Stasevich
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA. .,Cell Biology Center and World Research Hub Initiative, Tokyo Institute of Technology, Yokohama, Japan.
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Koch AL, Morisaki T, Stasevich TJ. A Multi-color Bicistronic Biosensor to Compare the Translation Dynamics of Different Open Reading Frames at Single-molecule Resolution in Live Cells. Bio Protoc 2021; 11:e4096. [PMID: 34395732 DOI: 10.21769/bioprotoc.4096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/29/2021] [Accepted: 05/16/2021] [Indexed: 11/02/2022] Open
Abstract
Here, we describe how to image and quantitate the translation dynamics of a bicistronic biosensor that we recently created to fairly compare cap-dependent and IRES-mediated translation at single-molecule resolution in live human cells. This technique employs a pair of complementary intrabodies loaded into living cells that co-translationally bind complementary epitopes in the two separate ORFs of the bicistronic biosensor. This causes the biosensor to fluoresce in different colors depending on which ORF/epitopes are translated. Using the biosensor together with high-resolution fluorescence microscopy and single-molecule tracking analysis allows for the quantitative comparison of translation dynamics between the two ORFs at a resolution of tens-of-nanometers in space and sub-seconds in time, which is not possible with more traditional GFP or luciferase reporters. Since both ORFs are on the same biosensor, they experience the same microenvironment, allowing a fair comparison of their relative translational activities. In this protocol, we describe how to get this assay up and running in cultured human cells so that translation dynamics can be studied under both normal and stressful cellular conditions. We also provide a number of useful tips and notes to help express components at appropriate levels inside cells for optimal live cell imaging. Graphical abstract: Steps required for 3-color single-molecule translation imaging and analysis.
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Affiliation(s)
- Amanda L Koch
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Tatsuya Morisaki
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA.,Cell Biology Center and World Research Hub Initiative, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
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8
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Single-Molecule Imaging in Living Plant Cells: A Methodological Review. Int J Mol Sci 2021; 22:ijms22105071. [PMID: 34064786 PMCID: PMC8151321 DOI: 10.3390/ijms22105071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/06/2021] [Accepted: 05/09/2021] [Indexed: 12/23/2022] Open
Abstract
Single-molecule imaging is emerging as a revolutionary approach to studying fundamental questions in plants. However, compared with its use in animals, the application of single-molecule imaging in plants is still underexplored. Here, we review the applications, advantages, and challenges of single-molecule fluorescence imaging in plant systems from the perspective of methodology. Firstly, we provide a general overview of single-molecule imaging methods and their principles. Next, we summarize the unprecedented quantitative details that can be obtained using single-molecule techniques compared to bulk assays. Finally, we discuss the main problems encountered at this stage and provide possible solutions.
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9
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Shannon MJ, Mace EM. Natural Killer Cell Integrins and Their Functions in Tissue Residency. Front Immunol 2021; 12:647358. [PMID: 33777044 PMCID: PMC7987804 DOI: 10.3389/fimmu.2021.647358] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/16/2021] [Indexed: 12/12/2022] Open
Abstract
Integrins are transmembrane receptors associated with adhesion and migration and are often highly differentially expressed receptors amongst natural killer cell subsets in microenvironments. Tissue resident natural killer cells are frequently defined by their differential integrin expression compared to other NK cell subsets, and integrins can further localize tissue resident NK cells to tissue microenvironments. As such, integrins play important roles in both the phenotypic and functional identity of NK cell subsets. Here we review the expression of integrin subtypes on NK cells and NK cell subsets with the goal of better understanding how integrin selection can dictate tissue residency and mediate function from the nanoscale to the tissue environment.
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Affiliation(s)
| | - Emily M. Mace
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
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Minehart JA, Speer CM. A Picture Worth a Thousand Molecules-Integrative Technologies for Mapping Subcellular Molecular Organization and Plasticity in Developing Circuits. Front Synaptic Neurosci 2021; 12:615059. [PMID: 33469427 PMCID: PMC7813761 DOI: 10.3389/fnsyn.2020.615059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/07/2020] [Indexed: 12/23/2022] Open
Abstract
A key challenge in developmental neuroscience is identifying the local regulatory mechanisms that control neurite and synaptic refinement over large brain volumes. Innovative molecular techniques and high-resolution imaging tools are beginning to reshape our view of how local protein translation in subcellular compartments drives axonal, dendritic, and synaptic development and plasticity. Here we review recent progress in three areas of neurite and synaptic study in situ-compartment-specific transcriptomics/translatomics, targeted proteomics, and super-resolution imaging analysis of synaptic organization and development. We discuss synergies between sequencing and imaging techniques for the discovery and validation of local molecular signaling mechanisms regulating synaptic development, plasticity, and maintenance in circuits.
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Affiliation(s)
| | - Colenso M. Speer
- Department of Biology, University of Maryland, College Park, MD, United States
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11
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Editorial overview: Diving into the Genome. Curr Opin Genet Dev 2020; 61:iii-vi. [PMID: 32950132 DOI: 10.1016/j.gde.2020.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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