Ontology type: schema:ScholarlyArticle Open Access: True
2015-11
AUTHORSSamuel H. Sternberg, Benjamin LaFrance, Matias Kaplan, Jennifer A. Doudna
ABSTRACTCas9 is an RNA-guided DNA endonuclease that targets foreign DNA for destruction as part of a bacterial adaptive immune system mediated by clustered regularly interspaced short palindromic repeats (CRISPR). Together with single-guide RNAs, Cas9 also functions as a powerful genome engineering tool in plants and animals, and efforts are underway to increase the efficiency and specificity of DNA targeting for potential therapeutic applications. Studies of off-target effects have shown that DNA binding is far more promiscuous than DNA cleavage, yet the molecular cues that govern strand scission have not been elucidated. Here we show that the conformational state of the HNH nuclease domain directly controls DNA cleavage activity. Using intramolecular Förster resonance energy transfer experiments to detect relative orientations of the Cas9 catalytic domains when associated with on- and off-target DNA, we find that DNA cleavage efficiencies scale with the extent to which the HNH domain samples an activated conformation. We furthermore uncover a surprising mode of allosteric communication that ensures concerted firing of both Cas9 nuclease domains. Our results highlight a proofreading mechanism beyond initial protospacer adjacent motif (PAM) recognition and RNA-DNA base-pairing that serves as a final specificity checkpoint before DNA double-strand break formation. More... »
PAGES110
http://scigraph.springernature.com/pub.10.1038/nature15544
DOIhttp://dx.doi.org/10.1038/nature15544
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1047311922
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/26524520
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/2008/0601",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Biochemistry and Cell Biology",
"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": "Allosteric Regulation",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Bacterial Proteins",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Base Pairing",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Binding Sites",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "CRISPR-Associated Proteins",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "CRISPR-Cas Systems",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Catalytic Domain",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "DNA",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "DNA Breaks, Double-Stranded",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "DNA Cleavage",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Endonucleases",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Fluorescence Resonance Energy Transfer",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Genetic Engineering",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Models, Molecular",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "RNA, Guide",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Streptococcus pyogenes",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "University of California, Berkeley",
"id": "https://www.grid.ac/institutes/grid.47840.3f",
"name": [
"Department of Chemistry, University of California, Berkeley, California 94720, USA"
],
"type": "Organization"
},
"familyName": "Sternberg",
"givenName": "Samuel H.",
"id": "sg:person.01101567113.85",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01101567113.85"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of California, Berkeley",
"id": "https://www.grid.ac/institutes/grid.47840.3f",
"name": [
"Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA"
],
"type": "Organization"
},
"familyName": "LaFrance",
"givenName": "Benjamin",
"id": "sg:person.01063206573.29",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01063206573.29"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of California, Berkeley",
"id": "https://www.grid.ac/institutes/grid.47840.3f",
"name": [
"Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA"
],
"type": "Organization"
},
"familyName": "Kaplan",
"givenName": "Matias",
"id": "sg:person.01053417366.42",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01053417366.42"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Lawrence Berkeley National Laboratory",
"id": "https://www.grid.ac/institutes/grid.184769.5",
"name": [
"Department of Chemistry, University of California, Berkeley, California 94720, USA",
"Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA",
"Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA",
"Innovative Genomics Initiative, University of California, Berkeley, California 94720, USA",
"Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA"
],
"type": "Organization"
},
"familyName": "Doudna",
"givenName": "Jennifer A.",
"id": "sg:person.01147702313.96",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01147702313.96"
],
"type": "Person"
}
],
"citation": [
{
"id": "https://doi.org/10.1073/pnas.1501698112",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1001192089"
],
"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": "sg:pub.10.1038/nature06152",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1004547802",
"https://doi.org/10.1038/nature06152"
],
"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/10.1126/science.1247997",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1010970903"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1073/pnas.1208507109",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1011954581"
],
"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/nrmicro3279",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1014837318",
"https://doi.org/10.1038/nrmicro3279"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1261/rna.030882.111",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1015360819"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.molcel.2014.09.019",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1015567429"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pone.0109213",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1016908281"
],
"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": "sg:pub.10.1038/nbt.3117",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1021849416",
"https://doi.org/10.1038/nbt.3117"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/gkq399",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1026387524"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/gkq399",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1026387524"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1073/pnas.1402597111",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1027756035"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.jmb.2005.06.027",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1029053547"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.jmb.2005.06.027",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1029053547"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1126/science.1258096",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1033404992"
],
"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/nature13011",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1037342101",
"https://doi.org/10.1038/nature13011"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.cell.2014.05.010",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1039182708"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/0076-6879(92)11020-j",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1039886159"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.celrep.2015.01.067",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1040347869"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.celrep.2015.01.067",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1040347869"
],
"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/10.1126/science.aab1452",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1042265317"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1089/hum.2015.074",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1042975645"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1073/pnas.1313587110",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1042978468"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nbt.2889",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1043519930",
"https://doi.org/10.1038/nbt.2889"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.molcel.2014.03.011",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1044439504"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.molcel.2015.02.032",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1048019629"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nbt.2808",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1048637524",
"https://doi.org/10.1038/nbt.2808"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/gku316",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1049119825"
],
"type": "CreativeWork"
}
],
"datePublished": "2015-11",
"datePublishedReg": "2015-11-01",
"description": "Cas9 is an RNA-guided DNA endonuclease that targets foreign DNA for destruction as part of a bacterial adaptive immune system mediated by clustered regularly interspaced short palindromic repeats (CRISPR). Together with single-guide RNAs, Cas9 also functions as a powerful genome engineering tool in plants and animals, and efforts are underway to increase the efficiency and specificity of DNA targeting for potential therapeutic applications. Studies of off-target effects have shown that DNA binding is far more promiscuous than DNA cleavage, yet the molecular cues that govern strand scission have not been elucidated. Here we show that the conformational state of the HNH nuclease domain directly controls DNA cleavage activity. Using intramolecular F\u00f6rster resonance energy transfer experiments to detect relative orientations of the Cas9 catalytic domains when associated with on- and off-target DNA, we find that DNA cleavage efficiencies scale with the extent to which the HNH domain samples an activated conformation. We furthermore uncover a surprising mode of allosteric communication that ensures concerted firing of both Cas9 nuclease domains. Our results highlight a proofreading mechanism beyond initial protospacer adjacent motif (PAM) recognition and RNA-DNA base-pairing that serves as a final specificity checkpoint before DNA double-strand break formation. ",
"genre": "research_article",
"id": "sg:pub.10.1038/nature15544",
"inLanguage": [
"en"
],
"isAccessibleForFree": true,
"isFundedItemOf": [
{
"id": "sg:grant.2683710",
"type": "MonetaryGrant"
}
],
"isPartOf": [
{
"id": "sg:journal.1018957",
"issn": [
"0090-0028",
"1476-4687"
],
"name": "Nature",
"type": "Periodical"
},
{
"issueNumber": "7576",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "527"
}
],
"name": "Conformational control of DNA target cleavage by CRISPR\u2013Cas9",
"pagination": "110",
"productId": [
{
"name": "readcube_id",
"type": "PropertyValue",
"value": [
"e16130563f175474c3b2f4d7e96e0b99eb4daa11893174188d84eb270dadd3b7"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"26524520"
]
},
{
"name": "nlm_unique_id",
"type": "PropertyValue",
"value": [
"0410462"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1038/nature15544"
]
},
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1047311922"
]
}
],
"sameAs": [
"https://doi.org/10.1038/nature15544",
"https://app.dimensions.ai/details/publication/pub.1047311922"
],
"sdDataset": "articles",
"sdDatePublished": "2019-04-10T21:44",
"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/v90/0000000001_0000000264/records_8687_00000551.jsonl",
"type": "ScholarlyArticle",
"url": "https://www.nature.com/articles/nature15544"
}
]Download the RDF metadata as: json-ld nt turtle xml License info
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/nature15544'
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/nature15544'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nature15544'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nature15544'
This table displays all metadata directly associated to this object as RDF triples.
267 TRIPLES
21 PREDICATES
76 URIs
37 LITERALS
25 BLANK NODES