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We are analyzing https://www.nature.com/articles/s41592-018-0121-0.

Title:
COMRADES determines in vivo RNA structures and interactions | Nature Methods
Description:
The structural flexibility of RNA underlies fundamental biological processes, but there are no methods for exploring the multiple conformations adopted by RNAs in vivo. We developed cross-linking of matched RNAs and deep sequencing (COMRADES) for in-depth RNA conformation capture, and a pipeline for the retrieval of RNA structural ensembles. Using COMRADES, we determined the architecture of the Zika virus RNA genome inside cells, and identified multiple site-specific interactions with human noncoding RNAs. In vivo probing of RNA structures with COMRADES yields insight into RNA folding of the ZIKA virus genome and its interaction with host RNAs.
Website Age:
30 years and 10 months (reg. 1994-08-11).

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  • Education
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Custom-built

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🌆 Monumental Traffic: 20M - 50M visitors per month


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$536,300 per month
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Keywords {🔍}

pubmed, article, google, scholar, cas, rna, supplementary, zikv, nature, central, data, structures, interactions, figure, genome, comrades, virus, cambridge, structure, predicted, access, methods, university, shown, fragment, cells, number, research, control, supporting, cell, content, vivo, ziv, miska, authors, mol, bioinformatics, institute, rnarna, cookies, analysis, information, lun, liu, human, basepairing, clustering, nat, biol,

Topics {✒️}

nature portfolio journals permissions reprints privacy policy nature portfolio cancer research uk crispr/cas9 mir21 deletion-clones crispr-cas9 mir21 deletion-clones long-range rna–rna interactions long-range rna-rna interactions advertising scripps research institute nature biotechnology social media virus research open resource zhong-yu liu chun kit kwok zikv rna-rna interactions cheng-feng qin renilla/firefly luminescence signals vitro mir-21-binding experiments zikv enriched libraries sun yat-sen university nature+ nature 519 nature 460 nature 505 nature site specific base-pairing t-test p-values highest chimeric-reads support rna-rna interactions accession number e-mtab-6427 supplementary data files jessica sheu-gruttadauria & ian rna base-pairing permissions rna-folding strategy china crosslinked libraries control libraries springerlink instant access rna structural ensembles capped circular rna human noncoding rnas crispr–cas9 knockout bioanalyzer rna profiles long-distance interactions figure 3b rights t-test p

Schema {🗺️}

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         headline:COMRADES determines in vivo RNA structures and interactions
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      headline:COMRADES determines in vivo RNA structures and interactions
      description:The structural flexibility of RNA underlies fundamental biological processes, but there are no methods for exploring the multiple conformations adopted by RNAs in vivo. We developed cross-linking of matched RNAs and deep sequencing (COMRADES) for in-depth RNA conformation capture, and a pipeline for the retrieval of RNA structural ensembles. Using COMRADES, we determined the architecture of the Zika virus RNA genome inside cells, and identified multiple site-specific interactions with human noncoding RNAs. In vivo probing of RNA structures with COMRADES yields insight into RNA folding of the ZIKA virus genome and its interaction with host RNAs.
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               name:Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
               type:PostalAddress
            type:Organization
      name:Luca F. R. Gebert
      affiliation:
            name:the Scripps Research Institute
            address:
               name:Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, USA
               type:PostalAddress
            type:Organization
      name:Jessica Sheu-Gruttadauria
      affiliation:
            name:the Scripps Research Institute
            address:
               name:Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, USA
               type:PostalAddress
            type:Organization
      name:Luke W. Meredith
      affiliation:
            name:University of Cambridge
            address:
               name:Department of Pathology, University of Cambridge, Cambridge, UK
               type:PostalAddress
            type:Organization
      name:Zhong-Yu Liu
      url:http://orcid.org/0000-0001-7385-5681
      affiliation:
            name:Beijing Institute of Microbiology and Epidemiology
            address:
               name:State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
               type:PostalAddress
            type:Organization
            name:Sun Yat-sen University
            address:
               name:School of Medicine (Shenzhen), Sun Yat-sen University, Guangzhou, China
               type:PostalAddress
            type:Organization
      name:Chun Kit Kwok
      url:http://orcid.org/0000-0001-9175-8543
      affiliation:
            name:City University of Hong Kong
            address:
               name:Department of Chemistry, City University of Hong Kong, Hong Kong, China
               type:PostalAddress
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      name:Cheng-Feng Qin
      url:http://orcid.org/0000-0002-0632-2807
      affiliation:
            name:Beijing Institute of Microbiology and Epidemiology
            address:
               name:State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
               type:PostalAddress
            type:Organization
      name:Ian J. MacRae
      affiliation:
            name:the Scripps Research Institute
            address:
               name:Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, USA
               type:PostalAddress
            type:Organization
      name:Ian Goodfellow
      affiliation:
            name:University of Cambridge
            address:
               name:Department of Pathology, University of Cambridge, Cambridge, UK
               type:PostalAddress
            type:Organization
      name:John C. Marioni
      affiliation:
            name:University of Cambridge
            address:
               name:Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
               type:PostalAddress
            type:Organization
            name:European Bioinformatics Institute (EMBL-EBI)
            address:
               name:European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
               type:PostalAddress
            type:Organization
            name:Wellcome Sanger Institute
            address:
               name:Wellcome Sanger Institute, Cambridge, UK
               type:PostalAddress
            type:Organization
      name:Grzegorz Kudla
      url:http://orcid.org/0000-0002-7924-2744
      affiliation:
            name:University of Edinburgh
            address:
               name:MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
               type:PostalAddress
            type:Organization
      email:[email protected]
      name:Eric A. Miska
      url:http://orcid.org/0000-0002-4450-576X
      affiliation:
            name:University of Cambridge
            address:
               name:Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
               type:PostalAddress
            type:Organization
            name:University of Cambridge
            address:
               name:Department of Genetics, University of Cambridge, Cambridge, UK
               type:PostalAddress
            type:Organization
            name:Wellcome Sanger Institute
            address:
               name:Wellcome Sanger Institute, Cambridge, UK
               type:PostalAddress
            type:Organization
      email:[email protected]
PostalAddress:
      name:Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
      name:Department of Genetics, University of Cambridge, Cambridge, UK
      name:MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
      name:Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
      name:Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, USA
      name:Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, USA
      name:Department of Pathology, University of Cambridge, Cambridge, UK
      name:State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
      name:School of Medicine (Shenzhen), Sun Yat-sen University, Guangzhou, China
      name:Department of Chemistry, City University of Hong Kong, Hong Kong, China
      name:State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
      name:Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, USA
      name:Department of Pathology, University of Cambridge, Cambridge, UK
      name:Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
      name:European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
      name:Wellcome Sanger Institute, Cambridge, UK
      name:MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
      name:Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
      name:Department of Genetics, University of Cambridge, Cambridge, UK
      name:Wellcome Sanger Institute, Cambridge, UK
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