Engineer chimeric Cas9 to expand PAM recognition based on evolutionary information View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2019-12

AUTHORS

Dacheng Ma, Zhimeng Xu, Zhaoyu Zhang, Xi Chen, Xiangzhi Zeng, Yiyang Zhang, Tingyue Deng, Mengfei Ren, Zheng Sun, Rui Jiang, Zhen Xie

ABSTRACT

Although Cas9 nucleases are remarkably diverse in microorganisms, the range of genomic sequences targetable by a CRISPR/Cas9 system is restricted by the requirement of a short protospacer adjacent motif (PAM) at the target site. Here, we generate a group of chimeric Cas9 (cCas9) variants by replacing the key region in the PAM interaction (PI) domain of Staphylococcus aureus Cas9 (SaCas9) with the corresponding region in a panel of SaCas9 orthologs. By using a functional assay at target sites with different nucleotide recombinations at PAM position 3-6, we identify several cCas9 variants with expanded recognition capability at NNVRRN, NNVACT, NNVATG, NNVATT, NNVGCT, NNVGTG, and NNVGTT PAM sequences. In summary, we provide a panel of cCas9 variants accessible up to 1/4 of all the possible genomic targets in mammalian cells. More... »

PAGES

560

References to SciGraph publications

  • 2016-12. Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells in NATURE METHODS
  • 2016-05. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage in NATURE
  • 2014-09. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease in NATURE
  • 2017-11. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage in NATURE
  • 2014-06. Target specificity of the CRISPR-Cas9 system in QUANTITATIVE BIOLOGY
  • 2017-06-05. Engineered Cpf1 variants with altered PAM specificities in NATURE BIOTECHNOLOGY
  • 2015-12. Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition in NATURE BIOTECHNOLOGY
  • 2016-03. A dual AAV system enables the Cas9-mediated correction of a metabolic liver disease in newborn mice in NATURE BIOTECHNOLOGY
  • 2018-04. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity in NATURE
  • 2015-11. An updated evolutionary classification of CRISPR–Cas systems in NATURE REVIEWS MICROBIOLOGY
  • 2016-05. Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow in NATURE BIOTECHNOLOGY
  • 2015-04. In vivo genome editing using Staphylococcus aureus Cas9 in NATURE
  • 2015-05. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers in NATURE BIOTECHNOLOGY
  • 2016-10-03. Integration and exchange of split dCas9 domains for transcriptional controls in mammalian cells in NATURE COMMUNICATIONS
  • 2015-06-22. Engineered CRISPR-Cas9 nucleases with altered PAM specificities in NATURE
  • 2016-12-22. New CRISPR–Cas systems from uncultivated microbes in NATURE
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41467-019-08395-8

    DOI

    http://dx.doi.org/10.1038/s41467-019-08395-8

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1111911034

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/30718489


    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/2008/0604", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Genetics", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Biological Evolution", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "CRISPR-Associated Protein 9", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "CRISPR-Cas Systems", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Flow Cytometry", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "HEK293 Cells", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Humans", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Staphylococcus aureus", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Substrate Specificity", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Tsinghua University", 
              "id": "https://www.grid.ac/institutes/grid.12527.33", 
              "name": [
                "MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, 100084, Beijing, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Ma", 
            "givenName": "Dacheng", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Tsinghua University", 
              "id": "https://www.grid.ac/institutes/grid.12527.33", 
              "name": [
                "MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, 100084, Beijing, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Xu", 
            "givenName": "Zhimeng", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Tsinghua University", 
              "id": "https://www.grid.ac/institutes/grid.12527.33", 
              "name": [
                "MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, 100084, Beijing, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Zhang", 
            "givenName": "Zhaoyu", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Tsinghua University", 
              "id": "https://www.grid.ac/institutes/grid.12527.33", 
              "name": [
                "MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, 100084, Beijing, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Chen", 
            "givenName": "Xi", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Tsinghua University", 
              "id": "https://www.grid.ac/institutes/grid.12527.33", 
              "name": [
                "MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, 100084, Beijing, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Zeng", 
            "givenName": "Xiangzhi", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Tsinghua University", 
              "id": "https://www.grid.ac/institutes/grid.12527.33", 
              "name": [
                "MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, 100084, Beijing, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Zhang", 
            "givenName": "Yiyang", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Tsinghua University", 
              "id": "https://www.grid.ac/institutes/grid.12527.33", 
              "name": [
                "MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, 100084, Beijing, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Deng", 
            "givenName": "Tingyue", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Tsinghua University", 
              "id": "https://www.grid.ac/institutes/grid.12527.33", 
              "name": [
                "MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, 100084, Beijing, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Ren", 
            "givenName": "Mengfei", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Tsinghua University", 
              "id": "https://www.grid.ac/institutes/grid.12527.33", 
              "name": [
                "MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, 100084, Beijing, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Sun", 
            "givenName": "Zheng", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Tsinghua University", 
              "id": "https://www.grid.ac/institutes/grid.12527.33", 
              "name": [
                "MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, 100084, Beijing, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Jiang", 
            "givenName": "Rui", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Tsinghua University", 
              "id": "https://www.grid.ac/institutes/grid.12527.33", 
              "name": [
                "MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, 100084, Beijing, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Xie", 
            "givenName": "Zhen", 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "https://doi.org/10.1093/nar/gkv1533", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000263118"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.cell.2014.02.001", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1004290844"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.cell.2014.02.001", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1004290844"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.cell.2015.08.007", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1004984500"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.cell.2015.08.007", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1004984500"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.3526", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007681398", 
              "https://doi.org/10.1038/nbt.3526"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.molcel.2016.02.031", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008240498"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.molcel.2016.02.031", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008240498"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.molcel.2016.02.031", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008240498"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.cell.2013.02.022", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008291683"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.cell.2013.02.022", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008291683"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature17946", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1009172001", 
              "https://doi.org/10.1038/nature17946"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrmicro3569", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010036058", 
              "https://doi.org/10.1038/nrmicro3569"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.3469", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010987794", 
              "https://doi.org/10.1038/nbt.3469"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s40484-014-0030-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1014529473", 
              "https://doi.org/10.1007/s40484-014-0030-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature14299", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019168198", 
              "https://doi.org/10.1038/nature14299"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.1231143", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019873131"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.aad5227", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1020934192"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ncomms13056", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1022181254", 
              "https://doi.org/10.1038/ncomms13056"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature21059", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023889809", 
              "https://doi.org/10.1038/nature21059"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.3199", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1031267114", 
              "https://doi.org/10.1038/nbt.3199"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.1138140", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1036312168"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature13579", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1036390967", 
              "https://doi.org/10.1038/nature13579"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.4027", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1038829252", 
              "https://doi.org/10.1038/nmeth.4027"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.1225829", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1041850060"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.molcel.2016.02.020", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1042856379"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature14592", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1047292250", 
              "https://doi.org/10.1038/nature14592"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.3404", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1052861805", 
              "https://doi.org/10.1038/nbt.3404"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.3900", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1085865597", 
              "https://doi.org/10.1038/nbt.3900"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.molcel.2017.09.007", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1092116987"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature24644", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1092351376", 
              "https://doi.org/10.1038/nature24644"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature24644", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1092351376", 
              "https://doi.org/10.1038/nature24644"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature26155", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1101264077", 
              "https://doi.org/10.1038/nature26155"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature26155", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1101264077", 
              "https://doi.org/10.1038/nature26155"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1021/acssynbio.7b00404", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1101676200"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1021/acssynbio.7b00404", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1101676200"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.aas9129", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1106419440"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.aas9129", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1106419440"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.aas9129", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1106419440"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.aas9129", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1106419440"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/sciadv.aau0766", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1107823623"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2019-12", 
        "datePublishedReg": "2019-12-01", 
        "description": "Although Cas9 nucleases are remarkably diverse in microorganisms, the range of genomic sequences targetable by a CRISPR/Cas9 system is restricted by the requirement of a short protospacer adjacent motif (PAM) at the target site. Here, we generate a group of chimeric Cas9 (cCas9) variants by replacing the key region in the PAM interaction (PI) domain of Staphylococcus aureus Cas9 (SaCas9) with the corresponding region in a panel of SaCas9 orthologs. By using a functional assay at target sites with different nucleotide recombinations at PAM position 3-6, we identify several cCas9 variants with expanded recognition capability at NNVRRN, NNVACT, NNVATG, NNVATT, NNVGCT, NNVGTG, and NNVGTT PAM sequences. In summary, we provide a panel of cCas9 variants accessible up to 1/4 of all the possible genomic targets in mammalian cells.", 
        "genre": "research_article", 
        "id": "sg:pub.10.1038/s41467-019-08395-8", 
        "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": "Engineer chimeric Cas9 to expand PAM recognition based on evolutionary information", 
        "pagination": "560", 
        "productId": [
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1038/s41467-019-08395-8"
            ]
          }, 
          {
            "name": "readcube_id", 
            "type": "PropertyValue", 
            "value": [
              "5c4d18689246b0aa8ba2e06f468f83ffc5cac629d2f7c1c444eb4c223762d1cd"
            ]
          }, 
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1111911034"
            ]
          }, 
          {
            "name": "nlm_unique_id", 
            "type": "PropertyValue", 
            "value": [
              "101528555"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "30718489"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1038/s41467-019-08395-8", 
          "https://app.dimensions.ai/details/publication/pub.1111911034"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2019-04-15T09:13", 
        "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/v90/0000000376_0000000376/records_56159_00000006.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://www.nature.com/articles/s41467-019-08395-8"
      }
    ]
     

    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/s41467-019-08395-8'

    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/s41467-019-08395-8'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s41467-019-08395-8'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/s41467-019-08395-8'


     

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

    265 TRIPLES      21 PREDICATES      67 URIs      29 LITERALS      17 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1038/s41467-019-08395-8 schema:about N0fa3f4b1d6254ec68bd87bcf43fd9fa1
    2 N12d94931a6c94ceb8d5cb95dfa620f91
    3 N26e87e1cdc004f648b4dd9c1e928418d
    4 N4952de383b6841059f6e8f5120a68987
    5 N74637597004d478abe2ff5addd713142
    6 N7eb541812ee4489984c7174b508f8130
    7 Na930986939954897b0c716bc780023ae
    8 Ne18c7c23eb1a4a89bf2fde84dbb37579
    9 anzsrc-for:06
    10 anzsrc-for:0604
    11 schema:author N80d4bdd60b9944749361e5a192805dfe
    12 schema:citation sg:pub.10.1007/s40484-014-0030-x
    13 sg:pub.10.1038/nature13579
    14 sg:pub.10.1038/nature14299
    15 sg:pub.10.1038/nature14592
    16 sg:pub.10.1038/nature17946
    17 sg:pub.10.1038/nature21059
    18 sg:pub.10.1038/nature24644
    19 sg:pub.10.1038/nature26155
    20 sg:pub.10.1038/nbt.3199
    21 sg:pub.10.1038/nbt.3404
    22 sg:pub.10.1038/nbt.3469
    23 sg:pub.10.1038/nbt.3526
    24 sg:pub.10.1038/nbt.3900
    25 sg:pub.10.1038/ncomms13056
    26 sg:pub.10.1038/nmeth.4027
    27 sg:pub.10.1038/nrmicro3569
    28 https://doi.org/10.1016/j.cell.2013.02.022
    29 https://doi.org/10.1016/j.cell.2014.02.001
    30 https://doi.org/10.1016/j.cell.2015.08.007
    31 https://doi.org/10.1016/j.molcel.2016.02.020
    32 https://doi.org/10.1016/j.molcel.2016.02.031
    33 https://doi.org/10.1016/j.molcel.2017.09.007
    34 https://doi.org/10.1021/acssynbio.7b00404
    35 https://doi.org/10.1093/nar/gkv1533
    36 https://doi.org/10.1126/sciadv.aau0766
    37 https://doi.org/10.1126/science.1138140
    38 https://doi.org/10.1126/science.1225829
    39 https://doi.org/10.1126/science.1231143
    40 https://doi.org/10.1126/science.aad5227
    41 https://doi.org/10.1126/science.aas9129
    42 schema:datePublished 2019-12
    43 schema:datePublishedReg 2019-12-01
    44 schema:description Although Cas9 nucleases are remarkably diverse in microorganisms, the range of genomic sequences targetable by a CRISPR/Cas9 system is restricted by the requirement of a short protospacer adjacent motif (PAM) at the target site. Here, we generate a group of chimeric Cas9 (cCas9) variants by replacing the key region in the PAM interaction (PI) domain of Staphylococcus aureus Cas9 (SaCas9) with the corresponding region in a panel of SaCas9 orthologs. By using a functional assay at target sites with different nucleotide recombinations at PAM position 3-6, we identify several cCas9 variants with expanded recognition capability at NNVRRN, NNVACT, NNVATG, NNVATT, NNVGCT, NNVGTG, and NNVGTT PAM sequences. In summary, we provide a panel of cCas9 variants accessible up to 1/4 of all the possible genomic targets in mammalian cells.
    45 schema:genre research_article
    46 schema:inLanguage en
    47 schema:isAccessibleForFree true
    48 schema:isPartOf N3780fd982e9640ef96597f94e2dc4d13
    49 Nf2ae9d41a27244a3b250b0dd34a5854c
    50 sg:journal.1043282
    51 schema:name Engineer chimeric Cas9 to expand PAM recognition based on evolutionary information
    52 schema:pagination 560
    53 schema:productId Naa1643812407475e9a32d0f6b2ec625b
    54 Nad4851c7e5fd4a5b846b20691d1553f7
    55 Nb6d7336b5ddb457089bdd24ad14473e2
    56 Nd61761fd95824aceb2962e150e263bc8
    57 Nf2cb1f9f88614cf1af14ed68f9f1dd6e
    58 schema:sameAs https://app.dimensions.ai/details/publication/pub.1111911034
    59 https://doi.org/10.1038/s41467-019-08395-8
    60 schema:sdDatePublished 2019-04-15T09:13
    61 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    62 schema:sdPublisher Nf4470c543f8c449994424187b7af51a0
    63 schema:url https://www.nature.com/articles/s41467-019-08395-8
    64 sgo:license sg:explorer/license/
    65 sgo:sdDataset articles
    66 rdf:type schema:ScholarlyArticle
    67 N026b99e06f8049ea91c3b90c4cf44012 schema:affiliation https://www.grid.ac/institutes/grid.12527.33
    68 schema:familyName Xu
    69 schema:givenName Zhimeng
    70 rdf:type schema:Person
    71 N03c93dd3dba74eff9791cf6f65359288 schema:affiliation https://www.grid.ac/institutes/grid.12527.33
    72 schema:familyName Ren
    73 schema:givenName Mengfei
    74 rdf:type schema:Person
    75 N0fa3f4b1d6254ec68bd87bcf43fd9fa1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    76 schema:name Humans
    77 rdf:type schema:DefinedTerm
    78 N12d94931a6c94ceb8d5cb95dfa620f91 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    79 schema:name Substrate Specificity
    80 rdf:type schema:DefinedTerm
    81 N179fd839467b4d90acb95193821e64e0 rdf:first Nde47805103994627a9d4fcf7ecc15c47
    82 rdf:rest Nc42889903af34bd79ef9a41948a8e565
    83 N1d2b514ff3bc4e57baa805b35f4d368b rdf:first N03c93dd3dba74eff9791cf6f65359288
    84 rdf:rest N61e144d00ebf40c8bd2436e721b13be6
    85 N26e87e1cdc004f648b4dd9c1e928418d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    86 schema:name Staphylococcus aureus
    87 rdf:type schema:DefinedTerm
    88 N2ced9ca4274e441e933d5e970a362505 schema:affiliation https://www.grid.ac/institutes/grid.12527.33
    89 schema:familyName Jiang
    90 schema:givenName Rui
    91 rdf:type schema:Person
    92 N2ee75c68fdb841d9b375a14b7fc267ce rdf:first Nd84799147a2c4a538e4bd7e61d3ae134
    93 rdf:rest Nb46329da2d2e48d89a2cc3f3721a18c5
    94 N3780fd982e9640ef96597f94e2dc4d13 schema:issueNumber 1
    95 rdf:type schema:PublicationIssue
    96 N38a031d793284de986841439d8368595 schema:affiliation https://www.grid.ac/institutes/grid.12527.33
    97 schema:familyName Xie
    98 schema:givenName Zhen
    99 rdf:type schema:Person
    100 N4952de383b6841059f6e8f5120a68987 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    101 schema:name CRISPR-Associated Protein 9
    102 rdf:type schema:DefinedTerm
    103 N4dc0e3e1cece4fe9ab313d6164385793 schema:affiliation https://www.grid.ac/institutes/grid.12527.33
    104 schema:familyName Chen
    105 schema:givenName Xi
    106 rdf:type schema:Person
    107 N61e144d00ebf40c8bd2436e721b13be6 rdf:first Nfc705316b5234b3aa2a54845ea997268
    108 rdf:rest N83087b8fc24f414d9e5f268534cc880d
    109 N66e336578f18445b86ab53893f698640 schema:affiliation https://www.grid.ac/institutes/grid.12527.33
    110 schema:familyName Zeng
    111 schema:givenName Xiangzhi
    112 rdf:type schema:Person
    113 N6a92d37a74a54704a6753ccc694ea149 rdf:first N026b99e06f8049ea91c3b90c4cf44012
    114 rdf:rest N2ee75c68fdb841d9b375a14b7fc267ce
    115 N74637597004d478abe2ff5addd713142 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    116 schema:name Biological Evolution
    117 rdf:type schema:DefinedTerm
    118 N7e49004ed74e474795f96899b64bb2eb schema:affiliation https://www.grid.ac/institutes/grid.12527.33
    119 schema:familyName Ma
    120 schema:givenName Dacheng
    121 rdf:type schema:Person
    122 N7eb541812ee4489984c7174b508f8130 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    123 schema:name Flow Cytometry
    124 rdf:type schema:DefinedTerm
    125 N80d4bdd60b9944749361e5a192805dfe rdf:first N7e49004ed74e474795f96899b64bb2eb
    126 rdf:rest N6a92d37a74a54704a6753ccc694ea149
    127 N83087b8fc24f414d9e5f268534cc880d rdf:first N2ced9ca4274e441e933d5e970a362505
    128 rdf:rest N9bf66999db4040ada95d5a3e79a8cb5c
    129 N9111aaf8b4c549198b03ec788e0b46e4 rdf:first N66e336578f18445b86ab53893f698640
    130 rdf:rest N179fd839467b4d90acb95193821e64e0
    131 N9bf66999db4040ada95d5a3e79a8cb5c rdf:first N38a031d793284de986841439d8368595
    132 rdf:rest rdf:nil
    133 Na930986939954897b0c716bc780023ae schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    134 schema:name HEK293 Cells
    135 rdf:type schema:DefinedTerm
    136 Naa1643812407475e9a32d0f6b2ec625b schema:name nlm_unique_id
    137 schema:value 101528555
    138 rdf:type schema:PropertyValue
    139 Nad4851c7e5fd4a5b846b20691d1553f7 schema:name readcube_id
    140 schema:value 5c4d18689246b0aa8ba2e06f468f83ffc5cac629d2f7c1c444eb4c223762d1cd
    141 rdf:type schema:PropertyValue
    142 Nb46329da2d2e48d89a2cc3f3721a18c5 rdf:first N4dc0e3e1cece4fe9ab313d6164385793
    143 rdf:rest N9111aaf8b4c549198b03ec788e0b46e4
    144 Nb6d7336b5ddb457089bdd24ad14473e2 schema:name doi
    145 schema:value 10.1038/s41467-019-08395-8
    146 rdf:type schema:PropertyValue
    147 Nc42889903af34bd79ef9a41948a8e565 rdf:first Nc769b886ab774e868b75661bba77e8bb
    148 rdf:rest N1d2b514ff3bc4e57baa805b35f4d368b
    149 Nc769b886ab774e868b75661bba77e8bb schema:affiliation https://www.grid.ac/institutes/grid.12527.33
    150 schema:familyName Deng
    151 schema:givenName Tingyue
    152 rdf:type schema:Person
    153 Nd61761fd95824aceb2962e150e263bc8 schema:name dimensions_id
    154 schema:value pub.1111911034
    155 rdf:type schema:PropertyValue
    156 Nd84799147a2c4a538e4bd7e61d3ae134 schema:affiliation https://www.grid.ac/institutes/grid.12527.33
    157 schema:familyName Zhang
    158 schema:givenName Zhaoyu
    159 rdf:type schema:Person
    160 Nde47805103994627a9d4fcf7ecc15c47 schema:affiliation https://www.grid.ac/institutes/grid.12527.33
    161 schema:familyName Zhang
    162 schema:givenName Yiyang
    163 rdf:type schema:Person
    164 Ne18c7c23eb1a4a89bf2fde84dbb37579 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    165 schema:name CRISPR-Cas Systems
    166 rdf:type schema:DefinedTerm
    167 Nf2ae9d41a27244a3b250b0dd34a5854c schema:volumeNumber 10
    168 rdf:type schema:PublicationVolume
    169 Nf2cb1f9f88614cf1af14ed68f9f1dd6e schema:name pubmed_id
    170 schema:value 30718489
    171 rdf:type schema:PropertyValue
    172 Nf4470c543f8c449994424187b7af51a0 schema:name Springer Nature - SN SciGraph project
    173 rdf:type schema:Organization
    174 Nfc705316b5234b3aa2a54845ea997268 schema:affiliation https://www.grid.ac/institutes/grid.12527.33
    175 schema:familyName Sun
    176 schema:givenName Zheng
    177 rdf:type schema:Person
    178 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    179 schema:name Biological Sciences
    180 rdf:type schema:DefinedTerm
    181 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    182 schema:name Genetics
    183 rdf:type schema:DefinedTerm
    184 sg:journal.1043282 schema:issn 2041-1723
    185 schema:name Nature Communications
    186 rdf:type schema:Periodical
    187 sg:pub.10.1007/s40484-014-0030-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1014529473
    188 https://doi.org/10.1007/s40484-014-0030-x
    189 rdf:type schema:CreativeWork
    190 sg:pub.10.1038/nature13579 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036390967
    191 https://doi.org/10.1038/nature13579
    192 rdf:type schema:CreativeWork
    193 sg:pub.10.1038/nature14299 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019168198
    194 https://doi.org/10.1038/nature14299
    195 rdf:type schema:CreativeWork
    196 sg:pub.10.1038/nature14592 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047292250
    197 https://doi.org/10.1038/nature14592
    198 rdf:type schema:CreativeWork
    199 sg:pub.10.1038/nature17946 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009172001
    200 https://doi.org/10.1038/nature17946
    201 rdf:type schema:CreativeWork
    202 sg:pub.10.1038/nature21059 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023889809
    203 https://doi.org/10.1038/nature21059
    204 rdf:type schema:CreativeWork
    205 sg:pub.10.1038/nature24644 schema:sameAs https://app.dimensions.ai/details/publication/pub.1092351376
    206 https://doi.org/10.1038/nature24644
    207 rdf:type schema:CreativeWork
    208 sg:pub.10.1038/nature26155 schema:sameAs https://app.dimensions.ai/details/publication/pub.1101264077
    209 https://doi.org/10.1038/nature26155
    210 rdf:type schema:CreativeWork
    211 sg:pub.10.1038/nbt.3199 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031267114
    212 https://doi.org/10.1038/nbt.3199
    213 rdf:type schema:CreativeWork
    214 sg:pub.10.1038/nbt.3404 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052861805
    215 https://doi.org/10.1038/nbt.3404
    216 rdf:type schema:CreativeWork
    217 sg:pub.10.1038/nbt.3469 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010987794
    218 https://doi.org/10.1038/nbt.3469
    219 rdf:type schema:CreativeWork
    220 sg:pub.10.1038/nbt.3526 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007681398
    221 https://doi.org/10.1038/nbt.3526
    222 rdf:type schema:CreativeWork
    223 sg:pub.10.1038/nbt.3900 schema:sameAs https://app.dimensions.ai/details/publication/pub.1085865597
    224 https://doi.org/10.1038/nbt.3900
    225 rdf:type schema:CreativeWork
    226 sg:pub.10.1038/ncomms13056 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022181254
    227 https://doi.org/10.1038/ncomms13056
    228 rdf:type schema:CreativeWork
    229 sg:pub.10.1038/nmeth.4027 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038829252
    230 https://doi.org/10.1038/nmeth.4027
    231 rdf:type schema:CreativeWork
    232 sg:pub.10.1038/nrmicro3569 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010036058
    233 https://doi.org/10.1038/nrmicro3569
    234 rdf:type schema:CreativeWork
    235 https://doi.org/10.1016/j.cell.2013.02.022 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008291683
    236 rdf:type schema:CreativeWork
    237 https://doi.org/10.1016/j.cell.2014.02.001 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004290844
    238 rdf:type schema:CreativeWork
    239 https://doi.org/10.1016/j.cell.2015.08.007 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004984500
    240 rdf:type schema:CreativeWork
    241 https://doi.org/10.1016/j.molcel.2016.02.020 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042856379
    242 rdf:type schema:CreativeWork
    243 https://doi.org/10.1016/j.molcel.2016.02.031 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008240498
    244 rdf:type schema:CreativeWork
    245 https://doi.org/10.1016/j.molcel.2017.09.007 schema:sameAs https://app.dimensions.ai/details/publication/pub.1092116987
    246 rdf:type schema:CreativeWork
    247 https://doi.org/10.1021/acssynbio.7b00404 schema:sameAs https://app.dimensions.ai/details/publication/pub.1101676200
    248 rdf:type schema:CreativeWork
    249 https://doi.org/10.1093/nar/gkv1533 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000263118
    250 rdf:type schema:CreativeWork
    251 https://doi.org/10.1126/sciadv.aau0766 schema:sameAs https://app.dimensions.ai/details/publication/pub.1107823623
    252 rdf:type schema:CreativeWork
    253 https://doi.org/10.1126/science.1138140 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036312168
    254 rdf:type schema:CreativeWork
    255 https://doi.org/10.1126/science.1225829 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041850060
    256 rdf:type schema:CreativeWork
    257 https://doi.org/10.1126/science.1231143 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019873131
    258 rdf:type schema:CreativeWork
    259 https://doi.org/10.1126/science.aad5227 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020934192
    260 rdf:type schema:CreativeWork
    261 https://doi.org/10.1126/science.aas9129 schema:sameAs https://app.dimensions.ai/details/publication/pub.1106419440
    262 rdf:type schema:CreativeWork
    263 https://www.grid.ac/institutes/grid.12527.33 schema:alternateName Tsinghua University
    264 schema:name MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, 100084, Beijing, China
    265 rdf:type schema:Organization
     




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


    ...