In Vivo Ligands of MDA5 and RIG-I in Measles Virus-Infected Cells
Publication Date
April 17, 2014
Journal
PLOS Pathogens
Authors
Simon Runge, Konstantin M. J. Sparrer, Charlotte Lässig, Katharina Hembach, et al
Volume
10
Issue
4
Pages
e1004081
DOI
https://dx.plos.org/10.1371/journal.ppat.1004081
Publisher URL
http://journals.plos.org/plospathogens/article?id=10.1371%2Fjournal.ppat.1004081
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24743923
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3990713
Europe PMC
http://europepmc.org/abstract/MED/24743923
Web of Science
000342033600037
Scopus
84901376043
Mendeley
http://www.mendeley.com/research/vivo-ligands-mda5-rigi-measles-virusinfected-cells
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Mendeley | Further Information

{"title"=>"In Vivo Ligands of MDA5 and RIG-I in Measles Virus-Infected Cells", "type"=>"journal", "authors"=>[{"first_name"=>"Simon", "last_name"=>"Runge", "scopus_author_id"=>"42962337800"}, {"first_name"=>"Konstantin M.J.", "last_name"=>"Sparrer", "scopus_author_id"=>"54973906800"}, {"first_name"=>"Charlotte", "last_name"=>"Lässig", "scopus_author_id"=>"55598598800"}, {"first_name"=>"Katharina", "last_name"=>"Hembach", "scopus_author_id"=>"56177984700"}, {"first_name"=>"Alina", "last_name"=>"Baum", "scopus_author_id"=>"35104303900"}, {"first_name"=>"Adolfo", "last_name"=>"García-Sastre", "scopus_author_id"=>"7006948562"}, {"first_name"=>"Johannes", "last_name"=>"Söding", "scopus_author_id"=>"6507385075"}, {"first_name"=>"Karl Klaus", "last_name"=>"Conzelmann", "scopus_author_id"=>"55890977500"}, {"first_name"=>"Karl Peter", "last_name"=>"Hopfner", "scopus_author_id"=>"7003594195"}], "year"=>2014, "source"=>"PLoS Pathogens", "identifiers"=>{"issn"=>"15537374", "scopus"=>"2-s2.0-84901376043", "sgr"=>"84901376043", "pui"=>"373162926", "isbn"=>"1553-7374 (Electronic)\\r1553-7366 (Linking)", "pmid"=>"24743923", "doi"=>"10.1371/journal.ppat.1004081"}, "id"=>"13703b52-1413-3800-9c6a-be6a87a912c4", "abstract"=>"RIG-I-like receptors (RLRs: RIG-I, MDA5 and LGP2) play a major role in the innate immune response against viral infections and detect patterns on viral RNA molecules that are typically absent from host RNA. Upon RNA binding, RLRs trigger a complex downstream signaling cascade resulting in the expression of type I interferons and proinflammatory cytokines. In the past decade extensive efforts were made to elucidate the nature of putative RLR ligands. In vitro and transfection studies identified 5'-triphosphate containing blunt-ended double-strand RNAs as potent RIG-I inducers and these findings were confirmed by next-generation sequencing of RIG-I associated RNAs from virus-infected cells. The nature of RNA ligands of MDA5 is less clear. Several studies suggest that double-stranded RNAs are the preferred agonists for the protein. However, the exact nature of physiological MDA5 ligands from virus-infected cells needs to be elucidated. In this work, we combine a crosslinking technique with next-generation sequencing in order to shed light on MDA5-associated RNAs from human cells infected with measles virus. Our findings suggest that RIG-I and MDA5 associate with AU-rich RNA species originating from the mRNA of the measles virus L gene. Corresponding sequences are poorer activators of ATP-hydrolysis by MDA5 in vitro, suggesting that they result in more stable MDA5 filaments. These data provide a possible model of how AU-rich sequences could activate type I interferon signaling.", "link"=>"http://www.mendeley.com/research/vivo-ligands-mda5-rigi-measles-virusinfected-cells", "reader_count"=>59, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>2, "Student > Doctoral Student"=>7, "Researcher"=>15, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>1, "Student > Master"=>5, "Student > Bachelor"=>3, "Professor"=>4}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>2, "Student > Doctoral Student"=>7, "Researcher"=>15, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>1, "Student > Master"=>5, "Student > Bachelor"=>3, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Biochemistry, Genetics and Molecular Biology"=>9, "Agricultural and Biological Sciences"=>27, "Medicine and Dentistry"=>9, "Computer Science"=>1, "Immunology and Microbiology"=>9, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>9}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>9}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>27}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>9}, "Unspecified"=>{"Unspecified"=>3}}, "reader_count_by_country"=>{"United States"=>3, "Norway"=>1, "United Kingdom"=>1, "Switzerland"=>1}, "group_count"=>1}

CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1469042"], "description"=>"<p>Validation of immunostimulatory activity of RNA from RIG-I, MDA5, and GFP immunoprecipitates upon transfection into 293T ISRE-FF reporter cells (n = 3, ** P<0.01).</p>", "links"=>[], "tags"=>["immunology", "Immune system", "Innate immune system", "immunity", "microbiology", "Pathology and laboratory medicine", "pathogenesis", "Host-pathogen interactions", "rlr-associated", "rna", "24", "mev"], "article_id"=>1002938, "categories"=>["Biological Sciences"], "users"=>["Simon Runge", "Konstantin M. J. Sparrer", "Charlotte Lässig", "Katharina Hembach", "Alina Baum", "Adolfo García-Sastre", "Johannes Söding", "Karl-Klaus Conzelmann", "Karl-Peter Hopfner"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004081.g002", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Immunoprecipitation_of_RLR_associated_RNA_from_24_h_MeV_infections_/1002938", "title"=>"Immunoprecipitation of RLR-associated RNA from 24 h MeV infections.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-17 03:32:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1469057"], "description"=>"<p>Sequences were generated according to deep sequencing data. The transcripts were either transfected into 293T ISRE-FF reporter cells in order to validate the immunostimulatory potential or ATPase hydrolysis experiments were performed in presence of recombinant <i>m</i>MDA5. <b>A:</b> Comparison of relative luciferase activities (black) and relative ATPase activities (grey) of <i>in vitro</i> transcribed RNAs (n = 3 and n = 2 respectively, values were normalized to the highest mean value of each replicate). <b>B:</b> Pearson correlation between (+) RNA maximal coverage and relative luciferase activity. <b>C:</b> Pearson correlation between (+) RNA maximal coverage and relative ATPase activity. <b>D:</b> Correlation analysis between AU content and luciferase or ATPase activity, and between ATPase and luciferase activity.</p>", "links"=>[], "tags"=>["immunology", "Immune system", "Innate immune system", "immunity", "microbiology", "Pathology and laboratory medicine", "pathogenesis", "Host-pathogen interactions", "transcribed", "rna", "measles"], "article_id"=>1002951, "categories"=>["Biological Sciences"], "users"=>["Simon Runge", "Konstantin M. J. Sparrer", "Charlotte Lässig", "Katharina Hembach", "Alina Baum", "Adolfo García-Sastre", "Johannes Söding", "Karl-Klaus Conzelmann", "Karl-Peter Hopfner"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004081.g007", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_in_vitro_transcribed_RNA_of_the_measles_virus_genome_/1002951", "title"=>"Analysis of <i>in vitro</i> transcribed RNA of the measles virus genome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-17 03:32:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1469056"], "description"=>"<p>The linear correlation is expressed via the Pearson coefficient. Every dot corresponds to one fragment with its respective AU content and mean coverage within an RLR library. The more yellow the plot, the more data points overlap. <b>A:</b> Correlation between AU composition and coverage of RIG-I-associated RNA of positive and negative RNA respectively. <b>B:</b> Correlation between AU composition and coverage of MDA5-associated RNA of positive and negative RNA respectively.</p>", "links"=>[], "tags"=>["immunology", "Immune system", "Innate immune system", "immunity", "microbiology", "Pathology and laboratory medicine", "pathogenesis", "Host-pathogen interactions", "au", "201", "nucleotide", "mev", "rna", "fragments"], "article_id"=>1002950, "categories"=>["Biological Sciences"], "users"=>["Simon Runge", "Konstantin M. J. Sparrer", "Charlotte Lässig", "Katharina Hembach", "Alina Baum", "Adolfo García-Sastre", "Johannes Söding", "Karl-Klaus Conzelmann", "Karl-Peter Hopfner"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004081.g006", "stats"=>{"downloads"=>1, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Heatscatter_plots_of_AU_content_of_201_nucleotide_MeV_RNA_fragments_and_the_fragment_s_mean_coverage_/1002950", "title"=>"Heatscatter plots of AU content of 201 nucleotide MeV RNA fragments and the fragment's mean coverage.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-17 03:32:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1469041"], "description"=>"<p><b>A:</b> Schematic representation of the experimental procedure for characterization of RLR-associated RNA molecules. <b>B:</b> Immunostimulatory activity of RNA from RIG-I and control (GFP) crosslinking samples in comparison to non-crosslinking immunoprecipitates. <b>C:</b> Western blot analysis of crosslinked and non-crosslinked RIG-I and control (GFP) pull-down experiments. <b>D:</b> Comparison of RNA recovery levels by quantitative PCR analysis of RIG-I-associated RNA from SeV-infected cells (n = 3). n.d. = not detectable.</p>", "links"=>[], "tags"=>["immunology", "Immune system", "Innate immune system", "immunity", "microbiology", "Pathology and laboratory medicine", "pathogenesis", "Host-pathogen interactions", "crosslinking", "immunoprecipitation", "complexes", "24", "virus-infected"], "article_id"=>1002937, "categories"=>["Biological Sciences"], "users"=>["Simon Runge", "Konstantin M. J. Sparrer", "Charlotte Lässig", "Katharina Hembach", "Alina Baum", "Adolfo García-Sastre", "Johannes Söding", "Karl-Klaus Conzelmann", "Karl-Peter Hopfner"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004081.g001", "stats"=>{"downloads"=>1, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Validation_of_crosslinking_and_immunoprecipitation_of_RLR_RNA_complexes_from_24_h_virus_infected_cells_/1002937", "title"=>"Validation of crosslinking and immunoprecipitation of RLR/RNA complexes from 24 h virus-infected cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-17 03:32:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1469078", "https://ndownloader.figshare.com/files/1469079", "https://ndownloader.figshare.com/files/1469080", "https://ndownloader.figshare.com/files/1469081", "https://ndownloader.figshare.com/files/1469082", "https://ndownloader.figshare.com/files/1469084", "https://ndownloader.figshare.com/files/1469085", "https://ndownloader.figshare.com/files/1469086", "https://ndownloader.figshare.com/files/1469088", "https://ndownloader.figshare.com/files/1469089", "https://ndownloader.figshare.com/files/1469090", "https://ndownloader.figshare.com/files/1469091", "https://ndownloader.figshare.com/files/1469092"], "description"=>"<div><p>RIG-I-like receptors (RLRs: RIG-I, MDA5 and LGP2) play a major role in the innate immune response against viral infections and detect patterns on viral RNA molecules that are typically absent from host RNA. Upon RNA binding, RLRs trigger a complex downstream signaling cascade resulting in the expression of type I interferons and proinflammatory cytokines. In the past decade extensive efforts were made to elucidate the nature of putative RLR ligands. <i>In vitro</i> and transfection studies identified 5′-triphosphate containing blunt-ended double-strand RNAs as potent RIG-I inducers and these findings were confirmed by next-generation sequencing of RIG-I associated RNAs from virus-infected cells. The nature of RNA ligands of MDA5 is less clear. Several studies suggest that double-stranded RNAs are the preferred agonists for the protein. However, the exact nature of physiological MDA5 ligands from virus-infected cells needs to be elucidated. In this work, we combine a crosslinking technique with next-generation sequencing in order to shed light on MDA5-associated RNAs from human cells infected with measles virus. Our findings suggest that RIG-I and MDA5 associate with AU-rich RNA species originating from the mRNA of the measles virus L gene. Corresponding sequences are poorer activators of ATP-hydrolysis by MDA5 <i>in vitro</i>, suggesting that they result in more stable MDA5 filaments. These data provide a possible model of how AU-rich sequences could activate type I interferon signaling.</p></div>", "links"=>[], "tags"=>["immunology", "Immune system", "Innate immune system", "immunity", "microbiology", "Pathology and laboratory medicine", "pathogenesis", "Host-pathogen interactions", "ligands", "mda5", "rig-i", "measles", "virus-infected", "cells"], "article_id"=>1002966, "categories"=>["Biological Sciences"], "users"=>["Simon Runge", "Konstantin M. J. Sparrer", "Charlotte Lässig", "Katharina Hembach", "Alina Baum", "Adolfo García-Sastre", "Johannes Söding", "Karl-Klaus Conzelmann", "Karl-Peter Hopfner"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1004081.s001", "https://dx.doi.org/10.1371/journal.ppat.1004081.s002", "https://dx.doi.org/10.1371/journal.ppat.1004081.s003", "https://dx.doi.org/10.1371/journal.ppat.1004081.s004", "https://dx.doi.org/10.1371/journal.ppat.1004081.s005", "https://dx.doi.org/10.1371/journal.ppat.1004081.s006", "https://dx.doi.org/10.1371/journal.ppat.1004081.s007", "https://dx.doi.org/10.1371/journal.ppat.1004081.s008", "https://dx.doi.org/10.1371/journal.ppat.1004081.s009", "https://dx.doi.org/10.1371/journal.ppat.1004081.s010", "https://dx.doi.org/10.1371/journal.ppat.1004081.s011", "https://dx.doi.org/10.1371/journal.ppat.1004081.s012", "https://dx.doi.org/10.1371/journal.ppat.1004081.s013"], "stats"=>{"downloads"=>41, "page_views"=>41, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_In_Vivo_Ligands_of_MDA5_and_RIG_I_in_Measles_Virus_Infected_Cells/1002966", "title"=>"<i>In Vivo</i> Ligands of MDA5 and RIG-I in Measles Virus-Infected Cells", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-04-17 03:32:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1469052"], "description"=>"<p><b>A:</b> Comparison of RNA levels between RIG-I and MDA5 immunoprecipitates for each genomic segment at 24 hpi. Relative RNA ratios were normalized against the control (GFP) library (mean values, n = 2). <b>B:</b> Western blot analysis of RLR pull-down experiments in comparison to the GFP pull-down. <b>C:</b> Immunostimulatory activity of RLR-associated RNA at 24 hpi.</p>", "links"=>[], "tags"=>["immunology", "Immune system", "Innate immune system", "immunity", "microbiology", "Pathology and laboratory medicine", "pathogenesis", "Host-pathogen interactions", "pcr", "rlr-associated", "rna", "mev-infected"], "article_id"=>1002948, "categories"=>["Biological Sciences"], "users"=>["Simon Runge", "Konstantin M. J. Sparrer", "Charlotte Lässig", "Katharina Hembach", "Alina Baum", "Adolfo García-Sastre", "Johannes Söding", "Karl-Klaus Conzelmann", "Karl-Peter Hopfner"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004081.g005", "stats"=>{"downloads"=>0, "page_views"=>26, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Quantitative_PCR_analysis_of_RLR_associated_RNA_from_MeV_infected_cells_/1002948", "title"=>"Quantitative PCR analysis of RLR-associated RNA from MeV-infected cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-17 03:32:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1469049"], "description"=>"<p>RNA deep sequencing libraries were generated based on the strand-specific mRNA sample preparation protocol from Epicentre. The Epicentre protocol encompasses sequential ligation of 5′ and 3′ adapters to RNA molecules, thus preserving strandness information. <b>A:</b> RIG-I-associated sequences in comparison to the control mapped to the viral antigenome. (+) RNA is shown in red; (−) RNA is shown in magenta; the control library is shown in black and grey. <b>B:</b> MDA5-associated sequences in comparison to the control mapped to the viral antigenome. (+) RNA is shown in blue, (−) RNA is shown in cyan; the control library is shown in black and grey.</p>", "links"=>[], "tags"=>["immunology", "Immune system", "Innate immune system", "immunity", "microbiology", "Pathology and laboratory medicine", "pathogenesis", "Host-pathogen interactions", "sequencing", "libraries", "mev"], "article_id"=>1002945, "categories"=>["Biological Sciences"], "users"=>["Simon Runge", "Konstantin M. J. Sparrer", "Charlotte Lässig", "Katharina Hembach", "Alina Baum", "Adolfo García-Sastre", "Johannes Söding", "Karl-Klaus Conzelmann", "Karl-Peter Hopfner"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004081.g004", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Strand_separation_of_sequencing_libraries_into_and_8722_MeV_RNA_/1002945", "title"=>"Strand separation of sequencing libraries into (+) and (−) MeV RNA.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-17 03:32:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1469047"], "description"=>"<p><b>A–C:</b> RNA from RIG-I pull-down (red), MDA5 pull-down (blue), and control (GFP) pull-down (black) from MeV-infected cells were subjected to Illumina deep sequencing analysis. Obtained sequencing reads are mapped to their position on the viral antigenome. The x-axis corresponds to all possible 15,894 positions in the MeV antigenome and the y-axis shows the number of reads at the respective position. (<i>A</i>) RIG-I-associated sequences in comparison to the control mapped to the viral antigenome. (<i>B</i>) MDA5-associated sequences in comparison to the control mapped to the viral antigenome. (<i>C</i>) Overlay of RIG-I associated and MDA5-associated sequences. <b>D:</b> Western blot analysis of RIG-I and MDA5 immunopurification in comparison to the GFP pull-down. <b>E:</b> Validation of immunostimulatory activity of RNA from RIG-I, MDA5, and GFP immunoprecipitates upon transfection into 293T ISRE-FF reporter cells.</p>", "links"=>[], "tags"=>["immunology", "Immune system", "Innate immune system", "immunity", "microbiology", "Pathology and laboratory medicine", "pathogenesis", "Host-pathogen interactions", "sequencing", "rlr-associated", "rna", "mev-infected"], "article_id"=>1002943, "categories"=>["Biological Sciences"], "users"=>["Simon Runge", "Konstantin M. J. Sparrer", "Charlotte Lässig", "Katharina Hembach", "Alina Baum", "Adolfo García-Sastre", "Johannes Söding", "Karl-Klaus Conzelmann", "Karl-Peter Hopfner"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1004081.g003", "stats"=>{"downloads"=>1, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Deep_sequencing_analysis_of_RLR_associated_RNA_from_MeV_infected_cells_/1002943", "title"=>"Deep sequencing analysis of RLR-associated RNA from MeV-infected cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-17 03:32:03"}

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