Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2021-06-03

AUTHORS

Tobias Jores, Jackson Tonnies, Travis Wrightsman, Edward S. Buckler, Josh T. Cuperus, Stanley Fields, Christine Queitsch

ABSTRACT

Targeted engineering of plant gene expression holds great promise for ensuring food security and for producing biopharmaceuticals in plants. However, this engineering requires thorough knowledge of cis-regulatory elements to precisely control either endogenous or introduced genes. To generate this knowledge, we used a massively parallel reporter assay to measure the activity of nearly complete sets of promoters from Arabidopsis, maize and sorghum. We demonstrate that core promoter elements—notably the TATA box—as well as promoter GC content and promoter-proximal transcription factor binding sites influence promoter strength. By performing the experiments in two assay systems, leaves of the dicot tobacco and protoplasts of the monocot maize, we detect species-specific differences in the contributions of GC content and transcription factors to promoter strength. Using these observations, we built computational models to predict promoter strength in both assay systems, allowing us to design highly active promoters comparable in activity to the viral 35S minimal promoter. Our results establish a promising experimental approach to optimize native promoter elements and generate synthetic ones with desirable features. More... »

PAGES

842-855

References to SciGraph publications

  • 2009-11-15. High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis in NATURE BIOTECHNOLOGY
  • 2000-04. pGreen: a versatile and flexible binary Ti vector for Agrobacterium-mediated plant transformation in PLANT MOLECULAR BIOLOGY
  • 2021-06-07. The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution in NATURE COMMUNICATIONS
  • 2019-11-18. Widespread long-range cis-regulatory elements in the maize genome in NATURE PLANTS
  • 2021-04-06. Single-cell transcriptome atlas and chromatin accessibility landscape reveal differentiation trajectories in the rice root in NATURE COMMUNICATIONS
  • 2020-03-11. Mass-spectrometry-based draft of the Arabidopsis proteome in NATURE
  • 2019-12-02. Deciphering eukaryotic gene-regulatory logic with 100 million random promoters in NATURE BIOTECHNOLOGY
  • 2017-06-12. Improved maize reference genome with single-molecule technologies in NATURE
  • 2005-09-14. Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts in BMC GENOMICS
  • 2020-04-30. Model-driven generation of artificial yeast promoters in NATURE COMMUNICATIONS
  • 2012-05-20. Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters in NATURE BIOTECHNOLOGY
  • 2009-11-08. Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos in NATURE METHODS
  • 2016-04-12. Comparative Analysis of GC Content Variations in Plant Genomes in TROPICAL PLANT BIOLOGY
  • 2019-10-11. Determinants of enhancer and promoter activities of regulatory elements in NATURE REVIEWS GENETICS
  • 2016-12-26. Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution in NATURE BIOTECHNOLOGY
  • 2005-02-25. Genome wide analysis of Arabidopsis core promoters in BMC GENOMICS
  • 2016-12-26. Genome-wide mapping of autonomous promoter activity in human cells in NATURE BIOTECHNOLOGY
  • 2010-03-12. TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation in BMC GENOMICS
  • 2012-02-14. PANDAseq: paired-end assembler for illumina sequences in BMC BIOINFORMATICS
  • 2020-10-12. A systematic evaluation of the design and context dependencies of massively parallel reporter assays in NATURE METHODS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41477-021-00932-y

    DOI

    http://dx.doi.org/10.1038/s41477-021-00932-y

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1138573133

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/34083762


    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/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "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/2008/0607", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Plant Biology", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "5' Untranslated Regions", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Arabidopsis", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Binding Sites", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Enhancer Elements, Genetic", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Gene Expression Regulation, Plant", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genes, Reporter", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genetic Techniques", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genome, Plant", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Light", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Plant Leaves", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Plants, Genetically Modified", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Promoter Regions, Genetic", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Regulatory Sequences, Nucleic Acid", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Sorghum", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "TATA Box", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Tobacco", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Zea mays", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Department of Genome Sciences, University of Washington, Seattle, WA, USA", 
              "id": "http://www.grid.ac/institutes/grid.34477.33", 
              "name": [
                "Department of Genome Sciences, University of Washington, Seattle, WA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Jores", 
            "givenName": "Tobias", 
            "id": "sg:person.0763300263.92", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0763300263.92"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Graduate Program in Biology, University of Washington, Seattle, WA, USA", 
              "id": "http://www.grid.ac/institutes/grid.34477.33", 
              "name": [
                "Department of Genome Sciences, University of Washington, Seattle, WA, USA", 
                "Graduate Program in Biology, University of Washington, Seattle, WA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Tonnies", 
            "givenName": "Jackson", 
            "id": "sg:person.012404407425.19", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012404407425.19"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA", 
              "id": "http://www.grid.ac/institutes/grid.5386.8", 
              "name": [
                "Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Wrightsman", 
            "givenName": "Travis", 
            "id": "sg:person.011313006233.39", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011313006233.39"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA", 
              "id": "http://www.grid.ac/institutes/grid.5386.8", 
              "name": [
                "Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA", 
                "Agricultural Research Service, United States Department of Agriculture, Ithaca, NY, USA", 
                "Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Buckler", 
            "givenName": "Edward S.", 
            "id": "sg:person.0761005474.77", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0761005474.77"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Genome Sciences, University of Washington, Seattle, WA, USA", 
              "id": "http://www.grid.ac/institutes/grid.34477.33", 
              "name": [
                "Department of Genome Sciences, University of Washington, Seattle, WA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Cuperus", 
            "givenName": "Josh T.", 
            "id": "sg:person.01175571715.87", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01175571715.87"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Medicine, University of Washington, Seattle, WA, USA", 
              "id": "http://www.grid.ac/institutes/grid.34477.33", 
              "name": [
                "Department of Genome Sciences, University of Washington, Seattle, WA, USA", 
                "Department of Medicine, University of Washington, Seattle, WA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Fields", 
            "givenName": "Stanley", 
            "id": "sg:person.014624417057.73", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014624417057.73"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Genome Sciences, University of Washington, Seattle, WA, USA", 
              "id": "http://www.grid.ac/institutes/grid.34477.33", 
              "name": [
                "Department of Genome Sciences, University of Washington, Seattle, WA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Queitsch", 
            "givenName": "Christine", 
            "id": "sg:person.0623027447.86", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0623027447.86"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1038/s41587-019-0315-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1123049966", 
              "https://doi.org/10.1038/s41587-019-0315-8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1023/a:1006496308160", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1041909606", 
              "https://doi.org/10.1023/a:1006496308160"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41576-019-0173-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1121649714", 
              "https://doi.org/10.1038/s41576-019-0173-8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.1589", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010374914", 
              "https://doi.org/10.1038/nbt.1589"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature22971", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1085984616", 
              "https://doi.org/10.1038/nature22971"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2164-11-166", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017236412", 
              "https://doi.org/10.1186/1471-2164-11-166"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2164-6-124", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005715891", 
              "https://doi.org/10.1186/1471-2164-6-124"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.3739", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1048641374", 
              "https://doi.org/10.1038/nbt.3739"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41467-021-23675-y", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1138654011", 
              "https://doi.org/10.1038/s41467-021-23675-y"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41467-021-22352-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1136952141", 
              "https://doi.org/10.1038/s41467-021-22352-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41592-020-0965-y", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1131620145", 
              "https://doi.org/10.1038/s41592-020-0965-y"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s12042-016-9165-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017818544", 
              "https://doi.org/10.1007/s12042-016-9165-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2105-13-31", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1047017534", 
              "https://doi.org/10.1186/1471-2105-13-31"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.2205", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1033405287", 
              "https://doi.org/10.1038/nbt.2205"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41467-020-15977-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1127238712", 
              "https://doi.org/10.1038/s41467-020-15977-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2164-6-25", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017704493", 
              "https://doi.org/10.1186/1471-2164-6-25"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.3754", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002482315", 
              "https://doi.org/10.1038/nbt.3754"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41477-019-0547-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1122670731", 
              "https://doi.org/10.1038/s41477-019-0547-0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.1396", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1047858356", 
              "https://doi.org/10.1038/nmeth.1396"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41586-020-2094-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1125546497", 
              "https://doi.org/10.1038/s41586-020-2094-2"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2021-06-03", 
        "datePublishedReg": "2021-06-03", 
        "description": "Targeted engineering of plant gene expression holds great promise for ensuring food security and for producing biopharmaceuticals in plants. However, this engineering requires thorough knowledge of cis-regulatory elements to precisely control either endogenous or introduced genes. To generate this knowledge, we used a massively parallel reporter assay to measure the activity of nearly complete sets of promoters from Arabidopsis, maize and sorghum. We demonstrate that core promoter elements\u2014notably the TATA box\u2014as well as promoter GC content and promoter-proximal transcription factor binding sites influence promoter strength. By performing the experiments in two assay systems, leaves of the dicot tobacco and protoplasts of the monocot maize, we detect species-specific differences in the contributions of GC content and transcription factors to promoter strength. Using these observations, we built computational models to predict promoter strength in both assay systems, allowing us to design highly active promoters comparable in activity to the viral 35S minimal promoter. Our results establish a promising experimental approach to optimize native promoter elements and generate synthetic ones with desirable features.", 
        "genre": "article", 
        "id": "sg:pub.10.1038/s41477-021-00932-y", 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.2519460", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.2684527", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.7671500", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.9143194", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1051401", 
            "issn": [
              "2055-026X", 
              "2055-0278"
            ], 
            "name": "Nature Plants", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "6", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "7"
          }
        ], 
        "keywords": [
          "GC content", 
          "transcription factors", 
          "promoter elements", 
          "promoter strength", 
          "plant gene expression", 
          "native promoter elements", 
          "cis-regulatory elements", 
          "synthetic promoter design", 
          "core promoter elements", 
          "species-specific differences", 
          "monocot maize", 
          "parallel reporter", 
          "minimal promoter", 
          "TATA box", 
          "active promoters", 
          "Targeted engineering", 
          "assay system", 
          "gene expression", 
          "promoter design", 
          "core promoter", 
          "promoter", 
          "maize", 
          "experimental approach", 
          "Arabidopsis", 
          "promising experimental approach", 
          "protoplasts", 
          "food security", 
          "comprehensive analysis", 
          "genes", 
          "leaves", 
          "plants", 
          "reporter", 
          "sorghum", 
          "expression", 
          "activity", 
          "great promise", 
          "biopharmaceuticals", 
          "tobacco", 
          "complete set", 
          "sites", 
          "elements", 
          "factors", 
          "synthetic ones", 
          "engineering", 
          "content", 
          "box", 
          "knowledge", 
          "computational model", 
          "analysis", 
          "thorough knowledge", 
          "experiments", 
          "promise", 
          "system", 
          "differences", 
          "observations", 
          "contribution", 
          "features", 
          "set", 
          "results", 
          "approach", 
          "one", 
          "model", 
          "desirable features", 
          "strength", 
          "design", 
          "security"
        ], 
        "name": "Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters", 
        "pagination": "842-855", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1138573133"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1038/s41477-021-00932-y"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "34083762"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1038/s41477-021-00932-y", 
          "https://app.dimensions.ai/details/publication/pub.1138573133"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-11-24T21:08", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20221124/entities/gbq_results/article/article_913.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1038/s41477-021-00932-y"
      }
    ]
     

    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/s41477-021-00932-y'

    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/s41477-021-00932-y'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s41477-021-00932-y'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/s41477-021-00932-y'


     

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

    339 TRIPLES      21 PREDICATES      129 URIs      100 LITERALS      24 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1038/s41477-021-00932-y schema:about N01d4cb94d28343828b719b280f7a209d
    2 N1786cdc58bb542ec94bc7bc2b5f7cba0
    3 N28bcb4d1539645968f806de495d142d3
    4 N4e3eb20fc8254b8b963c37745f984ca9
    5 N65117d7f3a424affa426349a6c6a0173
    6 N79079cb2ebac4b1db9fa95420daa82dd
    7 N7ac218cd1e694080ac40741d6be743b6
    8 N94826c8e33bb43b9a2118a1f4012aeb2
    9 N9c68243a966c4756897256bcac245edf
    10 Na4b74acbb5f94d42a8362eb8882e0f83
    11 Na82de13d6e6f42ac998e906e6bd2410e
    12 Nb11a9312ac534c6a816a6864196f700a
    13 Nbe71ee0cd9ba429dbfbcf847659bfac4
    14 Nd4a44e19b6d54e88b0d4875565ed0c3f
    15 Nd8d366e4d74240918256e2a1a2b68b40
    16 Nd96eab85e16442b5bc45e87ab638613a
    17 Ne2d7d7c390b645f28e13a52315d3f7af
    18 anzsrc-for:06
    19 anzsrc-for:0604
    20 anzsrc-for:0607
    21 schema:author N040d6e2f4e83443689dd07e5db3c06fd
    22 schema:citation sg:pub.10.1007/s12042-016-9165-4
    23 sg:pub.10.1023/a:1006496308160
    24 sg:pub.10.1038/nature22971
    25 sg:pub.10.1038/nbt.1589
    26 sg:pub.10.1038/nbt.2205
    27 sg:pub.10.1038/nbt.3739
    28 sg:pub.10.1038/nbt.3754
    29 sg:pub.10.1038/nmeth.1396
    30 sg:pub.10.1038/s41467-020-15977-4
    31 sg:pub.10.1038/s41467-021-22352-4
    32 sg:pub.10.1038/s41467-021-23675-y
    33 sg:pub.10.1038/s41477-019-0547-0
    34 sg:pub.10.1038/s41576-019-0173-8
    35 sg:pub.10.1038/s41586-020-2094-2
    36 sg:pub.10.1038/s41587-019-0315-8
    37 sg:pub.10.1038/s41592-020-0965-y
    38 sg:pub.10.1186/1471-2105-13-31
    39 sg:pub.10.1186/1471-2164-11-166
    40 sg:pub.10.1186/1471-2164-6-124
    41 sg:pub.10.1186/1471-2164-6-25
    42 schema:datePublished 2021-06-03
    43 schema:datePublishedReg 2021-06-03
    44 schema:description Targeted engineering of plant gene expression holds great promise for ensuring food security and for producing biopharmaceuticals in plants. However, this engineering requires thorough knowledge of cis-regulatory elements to precisely control either endogenous or introduced genes. To generate this knowledge, we used a massively parallel reporter assay to measure the activity of nearly complete sets of promoters from Arabidopsis, maize and sorghum. We demonstrate that core promoter elements—notably the TATA box—as well as promoter GC content and promoter-proximal transcription factor binding sites influence promoter strength. By performing the experiments in two assay systems, leaves of the dicot tobacco and protoplasts of the monocot maize, we detect species-specific differences in the contributions of GC content and transcription factors to promoter strength. Using these observations, we built computational models to predict promoter strength in both assay systems, allowing us to design highly active promoters comparable in activity to the viral 35S minimal promoter. Our results establish a promising experimental approach to optimize native promoter elements and generate synthetic ones with desirable features.
    45 schema:genre article
    46 schema:isAccessibleForFree true
    47 schema:isPartOf N0bbff5bdd13f4c2ab4cc673fc1b9dd6c
    48 N326ade7a26ce4fd98db8eb0a479b33b6
    49 sg:journal.1051401
    50 schema:keywords Arabidopsis
    51 GC content
    52 TATA box
    53 Targeted engineering
    54 active promoters
    55 activity
    56 analysis
    57 approach
    58 assay system
    59 biopharmaceuticals
    60 box
    61 cis-regulatory elements
    62 complete set
    63 comprehensive analysis
    64 computational model
    65 content
    66 contribution
    67 core promoter
    68 core promoter elements
    69 design
    70 desirable features
    71 differences
    72 elements
    73 engineering
    74 experimental approach
    75 experiments
    76 expression
    77 factors
    78 features
    79 food security
    80 gene expression
    81 genes
    82 great promise
    83 knowledge
    84 leaves
    85 maize
    86 minimal promoter
    87 model
    88 monocot maize
    89 native promoter elements
    90 observations
    91 one
    92 parallel reporter
    93 plant gene expression
    94 plants
    95 promise
    96 promising experimental approach
    97 promoter
    98 promoter design
    99 promoter elements
    100 promoter strength
    101 protoplasts
    102 reporter
    103 results
    104 security
    105 set
    106 sites
    107 sorghum
    108 species-specific differences
    109 strength
    110 synthetic ones
    111 synthetic promoter design
    112 system
    113 thorough knowledge
    114 tobacco
    115 transcription factors
    116 schema:name Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters
    117 schema:pagination 842-855
    118 schema:productId N5a74dd1a05f14fe0a4e3cabc6a003f6f
    119 N7fa53b9d770c4d58b96c602fb69d02cd
    120 Nff30cf3794de4c05b2a7b6a4af285351
    121 schema:sameAs https://app.dimensions.ai/details/publication/pub.1138573133
    122 https://doi.org/10.1038/s41477-021-00932-y
    123 schema:sdDatePublished 2022-11-24T21:08
    124 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    125 schema:sdPublisher N55a7ce767a2d40978a61735f333cdd03
    126 schema:url https://doi.org/10.1038/s41477-021-00932-y
    127 sgo:license sg:explorer/license/
    128 sgo:sdDataset articles
    129 rdf:type schema:ScholarlyArticle
    130 N01d4cb94d28343828b719b280f7a209d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    131 schema:name Plants, Genetically Modified
    132 rdf:type schema:DefinedTerm
    133 N040d6e2f4e83443689dd07e5db3c06fd rdf:first sg:person.0763300263.92
    134 rdf:rest N0fd41769ce664c20b635f67722c3ee31
    135 N0bbff5bdd13f4c2ab4cc673fc1b9dd6c schema:issueNumber 6
    136 rdf:type schema:PublicationIssue
    137 N0fd41769ce664c20b635f67722c3ee31 rdf:first sg:person.012404407425.19
    138 rdf:rest N4b80ff8517084e2fb1684353017e7514
    139 N1786cdc58bb542ec94bc7bc2b5f7cba0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    140 schema:name Genes, Reporter
    141 rdf:type schema:DefinedTerm
    142 N220cbc6eb65c4690ab1bef998b92e145 rdf:first sg:person.014624417057.73
    143 rdf:rest Ne93b681090104d13b51d039df17ef96e
    144 N28bcb4d1539645968f806de495d142d3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    145 schema:name Genetic Techniques
    146 rdf:type schema:DefinedTerm
    147 N326ade7a26ce4fd98db8eb0a479b33b6 schema:volumeNumber 7
    148 rdf:type schema:PublicationVolume
    149 N4b80ff8517084e2fb1684353017e7514 rdf:first sg:person.011313006233.39
    150 rdf:rest Ne451964b5e3540519f9d613fd196ad54
    151 N4e3eb20fc8254b8b963c37745f984ca9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    152 schema:name Zea mays
    153 rdf:type schema:DefinedTerm
    154 N55a7ce767a2d40978a61735f333cdd03 schema:name Springer Nature - SN SciGraph project
    155 rdf:type schema:Organization
    156 N5a74dd1a05f14fe0a4e3cabc6a003f6f schema:name doi
    157 schema:value 10.1038/s41477-021-00932-y
    158 rdf:type schema:PropertyValue
    159 N65117d7f3a424affa426349a6c6a0173 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    160 schema:name Genome, Plant
    161 rdf:type schema:DefinedTerm
    162 N79079cb2ebac4b1db9fa95420daa82dd schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    163 schema:name Enhancer Elements, Genetic
    164 rdf:type schema:DefinedTerm
    165 N7ac218cd1e694080ac40741d6be743b6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    166 schema:name Light
    167 rdf:type schema:DefinedTerm
    168 N7fa53b9d770c4d58b96c602fb69d02cd schema:name dimensions_id
    169 schema:value pub.1138573133
    170 rdf:type schema:PropertyValue
    171 N8cdb91651ac9434f99f75dbae958688d rdf:first sg:person.01175571715.87
    172 rdf:rest N220cbc6eb65c4690ab1bef998b92e145
    173 N94826c8e33bb43b9a2118a1f4012aeb2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    174 schema:name Binding Sites
    175 rdf:type schema:DefinedTerm
    176 N9c68243a966c4756897256bcac245edf schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    177 schema:name 5' Untranslated Regions
    178 rdf:type schema:DefinedTerm
    179 Na4b74acbb5f94d42a8362eb8882e0f83 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    180 schema:name Gene Expression Regulation, Plant
    181 rdf:type schema:DefinedTerm
    182 Na82de13d6e6f42ac998e906e6bd2410e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    183 schema:name Arabidopsis
    184 rdf:type schema:DefinedTerm
    185 Nb11a9312ac534c6a816a6864196f700a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    186 schema:name Plant Leaves
    187 rdf:type schema:DefinedTerm
    188 Nbe71ee0cd9ba429dbfbcf847659bfac4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    189 schema:name Tobacco
    190 rdf:type schema:DefinedTerm
    191 Nd4a44e19b6d54e88b0d4875565ed0c3f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    192 schema:name Regulatory Sequences, Nucleic Acid
    193 rdf:type schema:DefinedTerm
    194 Nd8d366e4d74240918256e2a1a2b68b40 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    195 schema:name Sorghum
    196 rdf:type schema:DefinedTerm
    197 Nd96eab85e16442b5bc45e87ab638613a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    198 schema:name TATA Box
    199 rdf:type schema:DefinedTerm
    200 Ne2d7d7c390b645f28e13a52315d3f7af schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    201 schema:name Promoter Regions, Genetic
    202 rdf:type schema:DefinedTerm
    203 Ne451964b5e3540519f9d613fd196ad54 rdf:first sg:person.0761005474.77
    204 rdf:rest N8cdb91651ac9434f99f75dbae958688d
    205 Ne93b681090104d13b51d039df17ef96e rdf:first sg:person.0623027447.86
    206 rdf:rest rdf:nil
    207 Nff30cf3794de4c05b2a7b6a4af285351 schema:name pubmed_id
    208 schema:value 34083762
    209 rdf:type schema:PropertyValue
    210 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    211 schema:name Biological Sciences
    212 rdf:type schema:DefinedTerm
    213 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    214 schema:name Genetics
    215 rdf:type schema:DefinedTerm
    216 anzsrc-for:0607 schema:inDefinedTermSet anzsrc-for:
    217 schema:name Plant Biology
    218 rdf:type schema:DefinedTerm
    219 sg:grant.2519460 http://pending.schema.org/fundedItem sg:pub.10.1038/s41477-021-00932-y
    220 rdf:type schema:MonetaryGrant
    221 sg:grant.2684527 http://pending.schema.org/fundedItem sg:pub.10.1038/s41477-021-00932-y
    222 rdf:type schema:MonetaryGrant
    223 sg:grant.7671500 http://pending.schema.org/fundedItem sg:pub.10.1038/s41477-021-00932-y
    224 rdf:type schema:MonetaryGrant
    225 sg:grant.9143194 http://pending.schema.org/fundedItem sg:pub.10.1038/s41477-021-00932-y
    226 rdf:type schema:MonetaryGrant
    227 sg:journal.1051401 schema:issn 2055-026X
    228 2055-0278
    229 schema:name Nature Plants
    230 schema:publisher Springer Nature
    231 rdf:type schema:Periodical
    232 sg:person.011313006233.39 schema:affiliation grid-institutes:grid.5386.8
    233 schema:familyName Wrightsman
    234 schema:givenName Travis
    235 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011313006233.39
    236 rdf:type schema:Person
    237 sg:person.01175571715.87 schema:affiliation grid-institutes:grid.34477.33
    238 schema:familyName Cuperus
    239 schema:givenName Josh T.
    240 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01175571715.87
    241 rdf:type schema:Person
    242 sg:person.012404407425.19 schema:affiliation grid-institutes:grid.34477.33
    243 schema:familyName Tonnies
    244 schema:givenName Jackson
    245 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012404407425.19
    246 rdf:type schema:Person
    247 sg:person.014624417057.73 schema:affiliation grid-institutes:grid.34477.33
    248 schema:familyName Fields
    249 schema:givenName Stanley
    250 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014624417057.73
    251 rdf:type schema:Person
    252 sg:person.0623027447.86 schema:affiliation grid-institutes:grid.34477.33
    253 schema:familyName Queitsch
    254 schema:givenName Christine
    255 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0623027447.86
    256 rdf:type schema:Person
    257 sg:person.0761005474.77 schema:affiliation grid-institutes:grid.5386.8
    258 schema:familyName Buckler
    259 schema:givenName Edward S.
    260 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0761005474.77
    261 rdf:type schema:Person
    262 sg:person.0763300263.92 schema:affiliation grid-institutes:grid.34477.33
    263 schema:familyName Jores
    264 schema:givenName Tobias
    265 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0763300263.92
    266 rdf:type schema:Person
    267 sg:pub.10.1007/s12042-016-9165-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017818544
    268 https://doi.org/10.1007/s12042-016-9165-4
    269 rdf:type schema:CreativeWork
    270 sg:pub.10.1023/a:1006496308160 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041909606
    271 https://doi.org/10.1023/a:1006496308160
    272 rdf:type schema:CreativeWork
    273 sg:pub.10.1038/nature22971 schema:sameAs https://app.dimensions.ai/details/publication/pub.1085984616
    274 https://doi.org/10.1038/nature22971
    275 rdf:type schema:CreativeWork
    276 sg:pub.10.1038/nbt.1589 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010374914
    277 https://doi.org/10.1038/nbt.1589
    278 rdf:type schema:CreativeWork
    279 sg:pub.10.1038/nbt.2205 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033405287
    280 https://doi.org/10.1038/nbt.2205
    281 rdf:type schema:CreativeWork
    282 sg:pub.10.1038/nbt.3739 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048641374
    283 https://doi.org/10.1038/nbt.3739
    284 rdf:type schema:CreativeWork
    285 sg:pub.10.1038/nbt.3754 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002482315
    286 https://doi.org/10.1038/nbt.3754
    287 rdf:type schema:CreativeWork
    288 sg:pub.10.1038/nmeth.1396 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047858356
    289 https://doi.org/10.1038/nmeth.1396
    290 rdf:type schema:CreativeWork
    291 sg:pub.10.1038/s41467-020-15977-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1127238712
    292 https://doi.org/10.1038/s41467-020-15977-4
    293 rdf:type schema:CreativeWork
    294 sg:pub.10.1038/s41467-021-22352-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1136952141
    295 https://doi.org/10.1038/s41467-021-22352-4
    296 rdf:type schema:CreativeWork
    297 sg:pub.10.1038/s41467-021-23675-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1138654011
    298 https://doi.org/10.1038/s41467-021-23675-y
    299 rdf:type schema:CreativeWork
    300 sg:pub.10.1038/s41477-019-0547-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1122670731
    301 https://doi.org/10.1038/s41477-019-0547-0
    302 rdf:type schema:CreativeWork
    303 sg:pub.10.1038/s41576-019-0173-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1121649714
    304 https://doi.org/10.1038/s41576-019-0173-8
    305 rdf:type schema:CreativeWork
    306 sg:pub.10.1038/s41586-020-2094-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1125546497
    307 https://doi.org/10.1038/s41586-020-2094-2
    308 rdf:type schema:CreativeWork
    309 sg:pub.10.1038/s41587-019-0315-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1123049966
    310 https://doi.org/10.1038/s41587-019-0315-8
    311 rdf:type schema:CreativeWork
    312 sg:pub.10.1038/s41592-020-0965-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1131620145
    313 https://doi.org/10.1038/s41592-020-0965-y
    314 rdf:type schema:CreativeWork
    315 sg:pub.10.1186/1471-2105-13-31 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047017534
    316 https://doi.org/10.1186/1471-2105-13-31
    317 rdf:type schema:CreativeWork
    318 sg:pub.10.1186/1471-2164-11-166 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017236412
    319 https://doi.org/10.1186/1471-2164-11-166
    320 rdf:type schema:CreativeWork
    321 sg:pub.10.1186/1471-2164-6-124 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005715891
    322 https://doi.org/10.1186/1471-2164-6-124
    323 rdf:type schema:CreativeWork
    324 sg:pub.10.1186/1471-2164-6-25 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017704493
    325 https://doi.org/10.1186/1471-2164-6-25
    326 rdf:type schema:CreativeWork
    327 grid-institutes:grid.34477.33 schema:alternateName Department of Genome Sciences, University of Washington, Seattle, WA, USA
    328 Department of Medicine, University of Washington, Seattle, WA, USA
    329 Graduate Program in Biology, University of Washington, Seattle, WA, USA
    330 schema:name Department of Genome Sciences, University of Washington, Seattle, WA, USA
    331 Department of Medicine, University of Washington, Seattle, WA, USA
    332 Graduate Program in Biology, University of Washington, Seattle, WA, USA
    333 rdf:type schema:Organization
    334 grid-institutes:grid.5386.8 schema:alternateName Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
    335 Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
    336 schema:name Agricultural Research Service, United States Department of Agriculture, Ithaca, NY, USA
    337 Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
    338 Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
    339 rdf:type schema:Organization
     




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


    ...