Molecular constraints on CDR3 for thymic selection of MHC-restricted TCRs from a random pre-selection repertoire View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2019-12

AUTHORS

Jinghua Lu, François Van Laethem, Abhisek Bhattacharya, Marco Craveiro, Ingrid Saba, Jonathan Chu, Nicholas C. Love, Anastasia Tikhonova, Sergei Radaev, Xiaoping Sun, Annette Ko, Tomer Arnon, Eric Shifrut, Nir Friedman, Nan-Ping Weng, Alfred Singer, Peter D. Sun

ABSTRACT

The αβ T cell receptor (TCR) repertoire on mature T cells is selected in the thymus, but the basis for thymic selection of MHC-restricted TCRs from a randomly generated pre-selection repertoire is not known. Here we perform comparative repertoire sequence analyses of pre-selection and post-selection TCR from multiple MHC-sufficient and MHC-deficient mouse strains, and find that MHC-restricted and MHC-independent TCRs are primarily distinguished by features in their non-germline CDR3 regions, with many pre-selection CDR3 sequences not compatible with MHC-binding. Thymic selection of MHC-independent TCR is largely unconstrained, but the selection of MHC-specific TCR is restricted by both CDR3 length and specific amino acid usage. MHC-restriction disfavors TCR with CDR3 longer than 13 amino acids, limits positively charged and hydrophobic amino acids in CDR3β, and clonally deletes TCRs with cysteines in their CDR3 peptide-binding regions. Together, these MHC-imposed structural constraints form the basis to shape VDJ recombination sequences into MHC-restricted repertoires. More... »

PAGES

1019

References to SciGraph publications

  • 2009-04. Germline-encoded amino acids in the αβ T-cell receptor control thymic selection in NATURE
  • 2016-08. Hydrophobic CDR3 residues promote the development of self-reactive T cells in NATURE IMMUNOLOGY
  • 1949-01. National Museums and Galleries in Britain in NATURE
  • 2015-12. Thymoproteasomes produce unique peptide motifs for positive selection of CD8+ T cells in NATURE COMMUNICATIONS
  • 2009-02. The molecular basis of TCR germline bias for MHC is surprisingly simple in NATURE IMMUNOLOGY
  • 2014-12. Comparative analysis of human and mouse immunoglobulin variable heavy regions from IMGT/LIGM-DB with IMGT/HighV-QUEST in THEORETICAL BIOLOGY AND MEDICAL MODELLING
  • 2009-12. Naive T cell homeostasis: from awareness of space to a sense of place in NATURE REVIEWS IMMUNOLOGY
  • 1984-08. Genomic organization and sequence of T-cell receptor β-chain constant- and joining-region genes in NATURE
  • 2015-11. T cell receptor reversed polarity recognition of a self-antigen major histocompatibility complex in NATURE IMMUNOLOGY
  • 2012-06. Clonal deletion and the fate of autoreactive thymocytes that survive negative selection in NATURE IMMUNOLOGY
  • 2014-06. Towards error-free profiling of immune repertoires in NATURE METHODS
  • 2016-12. αβ T cell receptor germline CDR regions moderate contact with MHC ligands and regulate peptide cross-reactivity in SCIENTIFIC REPORTS
  • 2013-02. IL-7 signaling must be intermittent, not continuous, during CD8+ T cell homeostasis to promote cell survival instead of cell death in NATURE IMMUNOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41467-019-08906-7

    DOI

    http://dx.doi.org/10.1038/s41467-019-08906-7

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1112507554

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/30833553


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/1107", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Immunology", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/11", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Medical and Health Sciences", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "National Institute of Allergy and Infectious Diseases", 
              "id": "https://www.grid.ac/institutes/grid.419681.3", 
              "name": [
                "Structural Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, 20852, Rockville, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Lu", 
            "givenName": "Jinghua", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Cancer Institute", 
              "id": "https://www.grid.ac/institutes/grid.48336.3a", 
              "name": [
                "Experimental Immunology Branch, National Cancer Institute, 20892, Bethesda, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Van Laethem", 
            "givenName": "Fran\u00e7ois", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Cancer Institute", 
              "id": "https://www.grid.ac/institutes/grid.48336.3a", 
              "name": [
                "Experimental Immunology Branch, National Cancer Institute, 20892, Bethesda, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Bhattacharya", 
            "givenName": "Abhisek", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Cancer Institute", 
              "id": "https://www.grid.ac/institutes/grid.48336.3a", 
              "name": [
                "Experimental Immunology Branch, National Cancer Institute, 20892, Bethesda, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Craveiro", 
            "givenName": "Marco", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Cancer Institute", 
              "id": "https://www.grid.ac/institutes/grid.48336.3a", 
              "name": [
                "Experimental Immunology Branch, National Cancer Institute, 20892, Bethesda, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Saba", 
            "givenName": "Ingrid", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Institute of Allergy and Infectious Diseases", 
              "id": "https://www.grid.ac/institutes/grid.419681.3", 
              "name": [
                "Structural Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, 20852, Rockville, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Chu", 
            "givenName": "Jonathan", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Cancer Institute", 
              "id": "https://www.grid.ac/institutes/grid.48336.3a", 
              "name": [
                "Experimental Immunology Branch, National Cancer Institute, 20892, Bethesda, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Love", 
            "givenName": "Nicholas C.", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Cancer Institute", 
              "id": "https://www.grid.ac/institutes/grid.48336.3a", 
              "name": [
                "Experimental Immunology Branch, National Cancer Institute, 20892, Bethesda, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Tikhonova", 
            "givenName": "Anastasia", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Institute of Allergy and Infectious Diseases", 
              "id": "https://www.grid.ac/institutes/grid.419681.3", 
              "name": [
                "Structural Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, 20852, Rockville, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Radaev", 
            "givenName": "Sergei", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Institute on Aging", 
              "id": "https://www.grid.ac/institutes/grid.419475.a", 
              "name": [
                "Lymphocyte Differentiation Section, Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institute of Health, 21224, Baltimore, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Sun", 
            "givenName": "Xiaoping", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Institute on Aging", 
              "id": "https://www.grid.ac/institutes/grid.419475.a", 
              "name": [
                "Lymphocyte Differentiation Section, Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institute of Health, 21224, Baltimore, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Ko", 
            "givenName": "Annette", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Alfred University", 
              "id": "https://www.grid.ac/institutes/grid.252018.c", 
              "name": [
                "Department of Immunology, Weizmann Institute of Science, 76100, Rehovot, Israel", 
                "Department of Physics and Astronomy, Alfred University, 1 Saxon Drive, 14802, Alfred, NY, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Arnon", 
            "givenName": "Tomer", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Weizmann Institute of Science", 
              "id": "https://www.grid.ac/institutes/grid.13992.30", 
              "name": [
                "Department of Immunology, Weizmann Institute of Science, 76100, Rehovot, Israel"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Shifrut", 
            "givenName": "Eric", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Weizmann Institute of Science", 
              "id": "https://www.grid.ac/institutes/grid.13992.30", 
              "name": [
                "Department of Immunology, Weizmann Institute of Science, 76100, Rehovot, Israel"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Friedman", 
            "givenName": "Nir", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Institute on Aging", 
              "id": "https://www.grid.ac/institutes/grid.419475.a", 
              "name": [
                "Lymphocyte Differentiation Section, Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institute of Health, 21224, Baltimore, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Weng", 
            "givenName": "Nan-Ping", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Cancer Institute", 
              "id": "https://www.grid.ac/institutes/grid.48336.3a", 
              "name": [
                "Experimental Immunology Branch, National Cancer Institute, 20892, Bethesda, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Singer", 
            "givenName": "Alfred", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Institute of Allergy and Infectious Diseases", 
              "id": "https://www.grid.ac/institutes/grid.419681.3", 
              "name": [
                "Structural Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, 20852, Rockville, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Sun", 
            "givenName": "Peter D.", 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "https://doi.org/10.1016/j.immuni.2007.10.007", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000139030"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1101/gr.170753.113", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1001588090"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ncomms8484", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1003682647", 
              "https://doi.org/10.1038/ncomms8484"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1146/annurev.immunol.26.021607.090421", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1004718812"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1146/annurev.immunol.21.120601.141107", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007566154"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.it.2012.05.005", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011793128"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.cell.2005.05.013", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1012919320"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/310387a0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013108288", 
              "https://doi.org/10.1038/310387a0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.2960", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016186405", 
              "https://doi.org/10.1038/nmeth.2960"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ni.f.219", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016211641", 
              "https://doi.org/10.1038/ni.f.219"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1084/jem.179.1.323", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016985351"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature07812", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017171182", 
              "https://doi.org/10.1038/nature07812"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/s0145-305x(02)00039-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023004273"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.immuni.2016.09.007", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1025504678"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1101/gr.092924.109", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1025925546"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/s0065-2776(01)78004-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030458628"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/srep35006", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1031025433", 
              "https://doi.org/10.1038/srep35006"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ni.2292", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032395563", 
              "https://doi.org/10.1038/ni.2292"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.cell.2013.08.009", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1033189184"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1128/jvi.00460-11", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035215399"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1742-4682-11-30", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1037611761", 
              "https://doi.org/10.1186/1742-4682-11-30"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ni.3271", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040464787", 
              "https://doi.org/10.1038/ni.3271"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1073/pnas.1525510113", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040682341"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nri2657", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1041558860", 
              "https://doi.org/10.1038/nri2657"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nri2657", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1041558860", 
              "https://doi.org/10.1038/nri2657"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1073/pnas.90.9.3913", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1044250198"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ni.3491", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1046358698", 
              "https://doi.org/10.1038/ni.3491"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/163001a0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1049864460", 
              "https://doi.org/10.1038/163001a0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/163001a0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1049864460", 
              "https://doi.org/10.1038/163001a0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.immuni.2011.11.013", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051662692"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ni.2494", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1052081172", 
              "https://doi.org/10.1038/ni.2494"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.it.2012.05.006", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1052394955"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.279.5354.1166", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1062559670"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.celrep.2017.03.072", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1084925911"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.7554/elife.22057", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1090828309"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1111/imcb.12047", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1103783173"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1111/imcb.12047", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1103783173"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2019-12", 
        "datePublishedReg": "2019-12-01", 
        "description": "The \u03b1\u03b2 T cell receptor (TCR) repertoire on mature T cells is selected in the thymus, but the basis for thymic selection of MHC-restricted TCRs from a randomly generated pre-selection repertoire is not known. Here we perform comparative repertoire sequence analyses of pre-selection and post-selection TCR from multiple MHC-sufficient and MHC-deficient mouse strains, and find that MHC-restricted and MHC-independent TCRs are primarily distinguished by features in their non-germline CDR3 regions, with many pre-selection CDR3 sequences not compatible with MHC-binding. Thymic selection of MHC-independent TCR is largely unconstrained, but the selection of MHC-specific TCR is restricted by both CDR3 length and specific amino acid usage. MHC-restriction disfavors TCR with CDR3 longer than 13 amino acids, limits positively charged and hydrophobic amino acids in CDR3\u03b2, and clonally deletes TCRs with cysteines in their CDR3 peptide-binding regions. Together, these MHC-imposed structural constraints form the basis to shape VDJ recombination sequences into MHC-restricted repertoires.", 
        "genre": "research_article", 
        "id": "sg:pub.10.1038/s41467-019-08906-7", 
        "inLanguage": [
          "en"
        ], 
        "isAccessibleForFree": true, 
        "isPartOf": [
          {
            "id": "sg:journal.1043282", 
            "issn": [
              "2041-1723"
            ], 
            "name": "Nature Communications", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "10"
          }
        ], 
        "name": "Molecular constraints on CDR3 for thymic selection of MHC-restricted TCRs from a random pre-selection repertoire", 
        "pagination": "1019", 
        "productId": [
          {
            "name": "readcube_id", 
            "type": "PropertyValue", 
            "value": [
              "4d7edeb4b57231c9eb70467ecb06fa4bbdffc52acf531f88978a99ccc6bb8561"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "30833553"
            ]
          }, 
          {
            "name": "nlm_unique_id", 
            "type": "PropertyValue", 
            "value": [
              "101528555"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1038/s41467-019-08906-7"
            ]
          }, 
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1112507554"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1038/s41467-019-08906-7", 
          "https://app.dimensions.ai/details/publication/pub.1112507554"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2019-04-11T13:00", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000365_0000000365/records_71701_00000002.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://www.nature.com/articles/s41467-019-08906-7"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/s41467-019-08906-7'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/s41467-019-08906-7'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s41467-019-08906-7'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/s41467-019-08906-7'


     

    This table displays all metadata directly associated to this object as RDF triples.

    291 TRIPLES      21 PREDICATES      63 URIs      21 LITERALS      9 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1038/s41467-019-08906-7 schema:about anzsrc-for:11
    2 anzsrc-for:1107
    3 schema:author Nf52d8f3dbf09486abe3a9c41bcd4820a
    4 schema:citation sg:pub.10.1038/163001a0
    5 sg:pub.10.1038/310387a0
    6 sg:pub.10.1038/nature07812
    7 sg:pub.10.1038/ncomms8484
    8 sg:pub.10.1038/ni.2292
    9 sg:pub.10.1038/ni.2494
    10 sg:pub.10.1038/ni.3271
    11 sg:pub.10.1038/ni.3491
    12 sg:pub.10.1038/ni.f.219
    13 sg:pub.10.1038/nmeth.2960
    14 sg:pub.10.1038/nri2657
    15 sg:pub.10.1038/srep35006
    16 sg:pub.10.1186/1742-4682-11-30
    17 https://doi.org/10.1016/j.cell.2005.05.013
    18 https://doi.org/10.1016/j.cell.2013.08.009
    19 https://doi.org/10.1016/j.celrep.2017.03.072
    20 https://doi.org/10.1016/j.immuni.2007.10.007
    21 https://doi.org/10.1016/j.immuni.2011.11.013
    22 https://doi.org/10.1016/j.immuni.2016.09.007
    23 https://doi.org/10.1016/j.it.2012.05.005
    24 https://doi.org/10.1016/j.it.2012.05.006
    25 https://doi.org/10.1016/s0065-2776(01)78004-2
    26 https://doi.org/10.1016/s0145-305x(02)00039-3
    27 https://doi.org/10.1073/pnas.1525510113
    28 https://doi.org/10.1073/pnas.90.9.3913
    29 https://doi.org/10.1084/jem.179.1.323
    30 https://doi.org/10.1101/gr.092924.109
    31 https://doi.org/10.1101/gr.170753.113
    32 https://doi.org/10.1111/imcb.12047
    33 https://doi.org/10.1126/science.279.5354.1166
    34 https://doi.org/10.1128/jvi.00460-11
    35 https://doi.org/10.1146/annurev.immunol.21.120601.141107
    36 https://doi.org/10.1146/annurev.immunol.26.021607.090421
    37 https://doi.org/10.7554/elife.22057
    38 schema:datePublished 2019-12
    39 schema:datePublishedReg 2019-12-01
    40 schema:description The αβ T cell receptor (TCR) repertoire on mature T cells is selected in the thymus, but the basis for thymic selection of MHC-restricted TCRs from a randomly generated pre-selection repertoire is not known. Here we perform comparative repertoire sequence analyses of pre-selection and post-selection TCR from multiple MHC-sufficient and MHC-deficient mouse strains, and find that MHC-restricted and MHC-independent TCRs are primarily distinguished by features in their non-germline CDR3 regions, with many pre-selection CDR3 sequences not compatible with MHC-binding. Thymic selection of MHC-independent TCR is largely unconstrained, but the selection of MHC-specific TCR is restricted by both CDR3 length and specific amino acid usage. MHC-restriction disfavors TCR with CDR3 longer than 13 amino acids, limits positively charged and hydrophobic amino acids in CDR3β, and clonally deletes TCRs with cysteines in their CDR3 peptide-binding regions. Together, these MHC-imposed structural constraints form the basis to shape VDJ recombination sequences into MHC-restricted repertoires.
    41 schema:genre research_article
    42 schema:inLanguage en
    43 schema:isAccessibleForFree true
    44 schema:isPartOf Ne9481f6146e64febabb0945475ba613f
    45 Nfa297bfe8bba42d5a75f2e336d8edf84
    46 sg:journal.1043282
    47 schema:name Molecular constraints on CDR3 for thymic selection of MHC-restricted TCRs from a random pre-selection repertoire
    48 schema:pagination 1019
    49 schema:productId N070ecf052eb642ff88f03f01f016aef7
    50 N6f734a3ddcbe423f972cf8833732d2f5
    51 N9c884bc89d914072839790b75b4571fa
    52 N9f48fafcaf4c4c02b83aabb4d21918f7
    53 Ndaa079689ccc4f36b7b7d0f37ef78eeb
    54 schema:sameAs https://app.dimensions.ai/details/publication/pub.1112507554
    55 https://doi.org/10.1038/s41467-019-08906-7
    56 schema:sdDatePublished 2019-04-11T13:00
    57 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    58 schema:sdPublisher Na686e9c08a20472db9954faf5ba320c9
    59 schema:url https://www.nature.com/articles/s41467-019-08906-7
    60 sgo:license sg:explorer/license/
    61 sgo:sdDataset articles
    62 rdf:type schema:ScholarlyArticle
    63 N0476a49511824f61bb0efdbe02773aca rdf:first N8d9f58109fd249a29bbae478bd6dc1c7
    64 rdf:rest N717993e2f5ba4357830b3c77e3548f31
    65 N070ecf052eb642ff88f03f01f016aef7 schema:name nlm_unique_id
    66 schema:value 101528555
    67 rdf:type schema:PropertyValue
    68 N187a351b1c8a4f16902d0027d9655b49 schema:affiliation https://www.grid.ac/institutes/grid.419475.a
    69 schema:familyName Weng
    70 schema:givenName Nan-Ping
    71 rdf:type schema:Person
    72 N1a3b49a0c7fa4e4bba5b96695542c5db rdf:first N550b307b93d84c729f6440b25f28e78e
    73 rdf:rest Ne7015ac2d50d4bdbbb36226a8648390c
    74 N2c77bf38482040279457bb26964caa02 schema:affiliation https://www.grid.ac/institutes/grid.48336.3a
    75 schema:familyName Craveiro
    76 schema:givenName Marco
    77 rdf:type schema:Person
    78 N34977c4674a8400bbc4153d1027a9fa4 schema:affiliation https://www.grid.ac/institutes/grid.419475.a
    79 schema:familyName Sun
    80 schema:givenName Xiaoping
    81 rdf:type schema:Person
    82 N3841cf3605f540ec89ebbd1db1ccdd44 rdf:first N7e150c249ffb4f23bf64fed868b74c43
    83 rdf:rest Nbadf667869bb40cfa53b843bea26e781
    84 N4a8fb663d272495895a4ab2366dd930b rdf:first N34977c4674a8400bbc4153d1027a9fa4
    85 rdf:rest Nd6cf041bc5e74f869d4b6f47dafb1a75
    86 N4aa0dd33329d4d86b5347cc31030433e schema:affiliation https://www.grid.ac/institutes/grid.419681.3
    87 schema:familyName Radaev
    88 schema:givenName Sergei
    89 rdf:type schema:Person
    90 N4d0ec5c09680468bac0b722a19888963 rdf:first Ne42222d702ed4fbbad81d48f9a30283f
    91 rdf:rest N6501c86b3f5c4e0fbe163fa90fbfa576
    92 N550b307b93d84c729f6440b25f28e78e schema:affiliation https://www.grid.ac/institutes/grid.252018.c
    93 schema:familyName Arnon
    94 schema:givenName Tomer
    95 rdf:type schema:Person
    96 N5889cad464464d419c3d7cbb6db5b9a8 schema:affiliation https://www.grid.ac/institutes/grid.419475.a
    97 schema:familyName Ko
    98 schema:givenName Annette
    99 rdf:type schema:Person
    100 N628a6fbde2884efe8faf5df1504f4db2 rdf:first N4aa0dd33329d4d86b5347cc31030433e
    101 rdf:rest N4a8fb663d272495895a4ab2366dd930b
    102 N6501c86b3f5c4e0fbe163fa90fbfa576 rdf:first N88ae42a86f544a5b9d52e7b662d42117
    103 rdf:rest Na9c275962b49486b80ee7b98ba61d29a
    104 N6e2cfb8943a849d1810db66643bfc978 schema:affiliation https://www.grid.ac/institutes/grid.48336.3a
    105 schema:familyName Tikhonova
    106 schema:givenName Anastasia
    107 rdf:type schema:Person
    108 N6efdad14e5aa4e0e940bdba9eac4a2ed schema:affiliation https://www.grid.ac/institutes/grid.48336.3a
    109 schema:familyName Singer
    110 schema:givenName Alfred
    111 rdf:type schema:Person
    112 N6f734a3ddcbe423f972cf8833732d2f5 schema:name dimensions_id
    113 schema:value pub.1112507554
    114 rdf:type schema:PropertyValue
    115 N717993e2f5ba4357830b3c77e3548f31 rdf:first N6e2cfb8943a849d1810db66643bfc978
    116 rdf:rest N628a6fbde2884efe8faf5df1504f4db2
    117 N7e150c249ffb4f23bf64fed868b74c43 schema:affiliation https://www.grid.ac/institutes/grid.13992.30
    118 schema:familyName Friedman
    119 schema:givenName Nir
    120 rdf:type schema:Person
    121 N88ae42a86f544a5b9d52e7b662d42117 schema:affiliation https://www.grid.ac/institutes/grid.48336.3a
    122 schema:familyName Bhattacharya
    123 schema:givenName Abhisek
    124 rdf:type schema:Person
    125 N8c29313ac88948b2a0d7b737e62ca2d8 schema:affiliation https://www.grid.ac/institutes/grid.13992.30
    126 schema:familyName Shifrut
    127 schema:givenName Eric
    128 rdf:type schema:Person
    129 N8d9f58109fd249a29bbae478bd6dc1c7 schema:affiliation https://www.grid.ac/institutes/grid.48336.3a
    130 schema:familyName Love
    131 schema:givenName Nicholas C.
    132 rdf:type schema:Person
    133 N9c884bc89d914072839790b75b4571fa schema:name readcube_id
    134 schema:value 4d7edeb4b57231c9eb70467ecb06fa4bbdffc52acf531f88978a99ccc6bb8561
    135 rdf:type schema:PropertyValue
    136 N9f48fafcaf4c4c02b83aabb4d21918f7 schema:name doi
    137 schema:value 10.1038/s41467-019-08906-7
    138 rdf:type schema:PropertyValue
    139 Na1f3fb18308b440da1d0a6c9e98c0b27 rdf:first Nabe0b40883994952b32f89532c7ce269
    140 rdf:rest N0476a49511824f61bb0efdbe02773aca
    141 Na686e9c08a20472db9954faf5ba320c9 schema:name Springer Nature - SN SciGraph project
    142 rdf:type schema:Organization
    143 Na9c275962b49486b80ee7b98ba61d29a rdf:first N2c77bf38482040279457bb26964caa02
    144 rdf:rest Nf70476003104416e9ae195a98e507e0a
    145 Nabe0b40883994952b32f89532c7ce269 schema:affiliation https://www.grid.ac/institutes/grid.419681.3
    146 schema:familyName Chu
    147 schema:givenName Jonathan
    148 rdf:type schema:Person
    149 Nbadf667869bb40cfa53b843bea26e781 rdf:first N187a351b1c8a4f16902d0027d9655b49
    150 rdf:rest Nfd10e1315118479daecb22144e08b1dd
    151 Nc75ce222e7b04d93a23d6a6e734a600d schema:affiliation https://www.grid.ac/institutes/grid.419681.3
    152 schema:familyName Sun
    153 schema:givenName Peter D.
    154 rdf:type schema:Person
    155 Nd6cf041bc5e74f869d4b6f47dafb1a75 rdf:first N5889cad464464d419c3d7cbb6db5b9a8
    156 rdf:rest N1a3b49a0c7fa4e4bba5b96695542c5db
    157 Nd6fef5a8fb8e453ab1f9c9ca53c3b9e5 schema:affiliation https://www.grid.ac/institutes/grid.419681.3
    158 schema:familyName Lu
    159 schema:givenName Jinghua
    160 rdf:type schema:Person
    161 Ndaa079689ccc4f36b7b7d0f37ef78eeb schema:name pubmed_id
    162 schema:value 30833553
    163 rdf:type schema:PropertyValue
    164 Ne2db4358cc974eaf911f2a4eda24a54e rdf:first Nc75ce222e7b04d93a23d6a6e734a600d
    165 rdf:rest rdf:nil
    166 Ne306d96bc03240198fa92c8d052e46d2 schema:affiliation https://www.grid.ac/institutes/grid.48336.3a
    167 schema:familyName Saba
    168 schema:givenName Ingrid
    169 rdf:type schema:Person
    170 Ne42222d702ed4fbbad81d48f9a30283f schema:affiliation https://www.grid.ac/institutes/grid.48336.3a
    171 schema:familyName Van Laethem
    172 schema:givenName François
    173 rdf:type schema:Person
    174 Ne7015ac2d50d4bdbbb36226a8648390c rdf:first N8c29313ac88948b2a0d7b737e62ca2d8
    175 rdf:rest N3841cf3605f540ec89ebbd1db1ccdd44
    176 Ne9481f6146e64febabb0945475ba613f schema:issueNumber 1
    177 rdf:type schema:PublicationIssue
    178 Nf52d8f3dbf09486abe3a9c41bcd4820a rdf:first Nd6fef5a8fb8e453ab1f9c9ca53c3b9e5
    179 rdf:rest N4d0ec5c09680468bac0b722a19888963
    180 Nf70476003104416e9ae195a98e507e0a rdf:first Ne306d96bc03240198fa92c8d052e46d2
    181 rdf:rest Na1f3fb18308b440da1d0a6c9e98c0b27
    182 Nfa297bfe8bba42d5a75f2e336d8edf84 schema:volumeNumber 10
    183 rdf:type schema:PublicationVolume
    184 Nfd10e1315118479daecb22144e08b1dd rdf:first N6efdad14e5aa4e0e940bdba9eac4a2ed
    185 rdf:rest Ne2db4358cc974eaf911f2a4eda24a54e
    186 anzsrc-for:11 schema:inDefinedTermSet anzsrc-for:
    187 schema:name Medical and Health Sciences
    188 rdf:type schema:DefinedTerm
    189 anzsrc-for:1107 schema:inDefinedTermSet anzsrc-for:
    190 schema:name Immunology
    191 rdf:type schema:DefinedTerm
    192 sg:journal.1043282 schema:issn 2041-1723
    193 schema:name Nature Communications
    194 rdf:type schema:Periodical
    195 sg:pub.10.1038/163001a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049864460
    196 https://doi.org/10.1038/163001a0
    197 rdf:type schema:CreativeWork
    198 sg:pub.10.1038/310387a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013108288
    199 https://doi.org/10.1038/310387a0
    200 rdf:type schema:CreativeWork
    201 sg:pub.10.1038/nature07812 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017171182
    202 https://doi.org/10.1038/nature07812
    203 rdf:type schema:CreativeWork
    204 sg:pub.10.1038/ncomms8484 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003682647
    205 https://doi.org/10.1038/ncomms8484
    206 rdf:type schema:CreativeWork
    207 sg:pub.10.1038/ni.2292 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032395563
    208 https://doi.org/10.1038/ni.2292
    209 rdf:type schema:CreativeWork
    210 sg:pub.10.1038/ni.2494 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052081172
    211 https://doi.org/10.1038/ni.2494
    212 rdf:type schema:CreativeWork
    213 sg:pub.10.1038/ni.3271 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040464787
    214 https://doi.org/10.1038/ni.3271
    215 rdf:type schema:CreativeWork
    216 sg:pub.10.1038/ni.3491 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046358698
    217 https://doi.org/10.1038/ni.3491
    218 rdf:type schema:CreativeWork
    219 sg:pub.10.1038/ni.f.219 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016211641
    220 https://doi.org/10.1038/ni.f.219
    221 rdf:type schema:CreativeWork
    222 sg:pub.10.1038/nmeth.2960 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016186405
    223 https://doi.org/10.1038/nmeth.2960
    224 rdf:type schema:CreativeWork
    225 sg:pub.10.1038/nri2657 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041558860
    226 https://doi.org/10.1038/nri2657
    227 rdf:type schema:CreativeWork
    228 sg:pub.10.1038/srep35006 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031025433
    229 https://doi.org/10.1038/srep35006
    230 rdf:type schema:CreativeWork
    231 sg:pub.10.1186/1742-4682-11-30 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037611761
    232 https://doi.org/10.1186/1742-4682-11-30
    233 rdf:type schema:CreativeWork
    234 https://doi.org/10.1016/j.cell.2005.05.013 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012919320
    235 rdf:type schema:CreativeWork
    236 https://doi.org/10.1016/j.cell.2013.08.009 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033189184
    237 rdf:type schema:CreativeWork
    238 https://doi.org/10.1016/j.celrep.2017.03.072 schema:sameAs https://app.dimensions.ai/details/publication/pub.1084925911
    239 rdf:type schema:CreativeWork
    240 https://doi.org/10.1016/j.immuni.2007.10.007 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000139030
    241 rdf:type schema:CreativeWork
    242 https://doi.org/10.1016/j.immuni.2011.11.013 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051662692
    243 rdf:type schema:CreativeWork
    244 https://doi.org/10.1016/j.immuni.2016.09.007 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025504678
    245 rdf:type schema:CreativeWork
    246 https://doi.org/10.1016/j.it.2012.05.005 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011793128
    247 rdf:type schema:CreativeWork
    248 https://doi.org/10.1016/j.it.2012.05.006 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052394955
    249 rdf:type schema:CreativeWork
    250 https://doi.org/10.1016/s0065-2776(01)78004-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030458628
    251 rdf:type schema:CreativeWork
    252 https://doi.org/10.1016/s0145-305x(02)00039-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023004273
    253 rdf:type schema:CreativeWork
    254 https://doi.org/10.1073/pnas.1525510113 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040682341
    255 rdf:type schema:CreativeWork
    256 https://doi.org/10.1073/pnas.90.9.3913 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044250198
    257 rdf:type schema:CreativeWork
    258 https://doi.org/10.1084/jem.179.1.323 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016985351
    259 rdf:type schema:CreativeWork
    260 https://doi.org/10.1101/gr.092924.109 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025925546
    261 rdf:type schema:CreativeWork
    262 https://doi.org/10.1101/gr.170753.113 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001588090
    263 rdf:type schema:CreativeWork
    264 https://doi.org/10.1111/imcb.12047 schema:sameAs https://app.dimensions.ai/details/publication/pub.1103783173
    265 rdf:type schema:CreativeWork
    266 https://doi.org/10.1126/science.279.5354.1166 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062559670
    267 rdf:type schema:CreativeWork
    268 https://doi.org/10.1128/jvi.00460-11 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035215399
    269 rdf:type schema:CreativeWork
    270 https://doi.org/10.1146/annurev.immunol.21.120601.141107 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007566154
    271 rdf:type schema:CreativeWork
    272 https://doi.org/10.1146/annurev.immunol.26.021607.090421 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004718812
    273 rdf:type schema:CreativeWork
    274 https://doi.org/10.7554/elife.22057 schema:sameAs https://app.dimensions.ai/details/publication/pub.1090828309
    275 rdf:type schema:CreativeWork
    276 https://www.grid.ac/institutes/grid.13992.30 schema:alternateName Weizmann Institute of Science
    277 schema:name Department of Immunology, Weizmann Institute of Science, 76100, Rehovot, Israel
    278 rdf:type schema:Organization
    279 https://www.grid.ac/institutes/grid.252018.c schema:alternateName Alfred University
    280 schema:name Department of Immunology, Weizmann Institute of Science, 76100, Rehovot, Israel
    281 Department of Physics and Astronomy, Alfred University, 1 Saxon Drive, 14802, Alfred, NY, USA
    282 rdf:type schema:Organization
    283 https://www.grid.ac/institutes/grid.419475.a schema:alternateName National Institute on Aging
    284 schema:name Lymphocyte Differentiation Section, Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institute of Health, 21224, Baltimore, MD, USA
    285 rdf:type schema:Organization
    286 https://www.grid.ac/institutes/grid.419681.3 schema:alternateName National Institute of Allergy and Infectious Diseases
    287 schema:name Structural Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, 20852, Rockville, MD, USA
    288 rdf:type schema:Organization
    289 https://www.grid.ac/institutes/grid.48336.3a schema:alternateName National Cancer Institute
    290 schema:name Experimental Immunology Branch, National Cancer Institute, 20892, Bethesda, MD, USA
    291 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...