A DNA-tethered cleavage probe reveals the path for promoter DNA in the yeast preinitiation complex View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2006-07

AUTHORS

Gail Miller, Steven Hahn

ABSTRACT

To directly map the position of promoter DNA within the RNA polymerase II (Pol II) transcription preinitiation complex (PIC), FeBABE was tethered to specific sites within the HIS4 promoter and used to map exposed surfaces of Pol II and the general transcription factors in proximity to DNA. Our results distinguish between previously proposed models for PIC structure and demonstrate that downstream promoter DNA is positioned over the central cleft of Pol II, with DNA upstream of TATA extending toward the Pol II subunit Rpb3. Also mapped were segments of TFIIB, TFIIE, TFIIF and TFIIH in proximity to promoter DNA. DNA downstream of the transcription bubble maps to a path between the two helicase subdomains of the TFIIH subunit Rad25 (also called XPB). Together, our results show how the general factors and Pol II converge on promoter DNA within the PIC. More... »

PAGES

603-610

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nsmb1117

DOI

http://dx.doi.org/10.1038/nsmb1117

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1019909427

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/16819517


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": "Base Sequence", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA Helicases", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA Polymerase II", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA, Fungal", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Hydroxyl Radical", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Models, Molecular", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Nucleic Acid Conformation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Promoter Regions, Genetic", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Saccharomyces cerevisiae", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Saccharomyces cerevisiae Proteins", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Transcription Factor TFIIH", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Transcription, Genetic", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Fred Hutchinson Cancer Research Center", 
          "id": "https://www.grid.ac/institutes/grid.270240.3", 
          "name": [
            "Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Seattle, Washington 98109, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Miller", 
        "givenName": "Gail", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Fred Hutchinson Cancer Research Center", 
          "id": "https://www.grid.ac/institutes/grid.270240.3", 
          "name": [
            "Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Seattle, Washington 98109, USA."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hahn", 
        "givenName": "Steven", 
        "id": "sg:person.01127561726.48", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01127561726.48"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1128/mcb.20.21.8168-8177.2000", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000476715"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nsmb949", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000739982", 
          "https://doi.org/10.1038/nsmb949"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nsmb949", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000739982", 
          "https://doi.org/10.1038/nsmb949"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nsmb949", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000739982", 
          "https://doi.org/10.1038/nsmb949"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0092-8674(02)00646-3", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000825991"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s1097-2765(03)00387-3", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001216189"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/mcb.24.9.3983-3991.2004", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001900322"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0092-8674(03)00598-1", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003046185"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.286.5448.2305", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004253385"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1090838", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004847683"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.92.8.3127", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005255373"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.molcel.2004.11.040", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006261602"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/mcb.24.3.1122-1131.2004", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007678266"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1059493", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015760622"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.288.5470.1418", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016316092"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.molcel.2005.03.029", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016911129"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/mcb.24.24.10975-10985.2004", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017977115"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.1030608100", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019574256"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/368160a0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022812854", 
          "https://doi.org/10.1038/368160a0"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.1130601100", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023101111"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gad.1192204", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023683653"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/emboj/16.24.7468", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026838567"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0968-0004(00)01652-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027510807"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gad.10.21.2657", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027560421"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0959-440x(02)00298-1", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027916800"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1074/jbc.m307874200", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028140656"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1038/sj.embor.7400663", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028687563"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1038/sj.embor.7400663", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028687563"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nsmb763", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032525772", 
          "https://doi.org/10.1038/nsmb763"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nsmb763", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032525772", 
          "https://doi.org/10.1038/nsmb763"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.94.23.12268", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033561730"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2004.09.028", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036982343"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s1097-2765(00)80278-6", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038184124"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gki825", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038648763"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gad.13.1.49", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040634590"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.molcel.2006.02.017", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040705027"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s1097-2765(03)00306-x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042583135"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s1097-2765(03)00306-x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042583135"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/377119a0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044250366", 
          "https://doi.org/10.1038/377119a0"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.molcel.2005.05.024", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044289537"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s1097-2765(00)80177-x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045533184"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/mcb.21.14.4427-4440.2001", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047037863"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.bbrc.2005.04.158", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047298505"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1006/jmbi.2000.4110", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051034638"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/mcb.23.8.2914-2926.2003", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051226934"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0092-8674(00)81242-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051683968"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/emboj/19.1.25", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053325470"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi015582r", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055194826"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi015582r", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055194826"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi048993r", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055199483"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bi048993r", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055199483"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1069595", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062445931"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1090839", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062449037"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1310361", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062474504"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.278.5340.1093", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062558575"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.8342041", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062654753"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1082594036", 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/j.1460-2075.1996.tb00512.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1082879612"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/j.1460-2075.1996.tb00425.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1082886332"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1083274813", 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2006-07", 
    "datePublishedReg": "2006-07-01", 
    "description": "To directly map the position of promoter DNA within the RNA polymerase II (Pol II) transcription preinitiation complex (PIC), FeBABE was tethered to specific sites within the HIS4 promoter and used to map exposed surfaces of Pol II and the general transcription factors in proximity to DNA. Our results distinguish between previously proposed models for PIC structure and demonstrate that downstream promoter DNA is positioned over the central cleft of Pol II, with DNA upstream of TATA extending toward the Pol II subunit Rpb3. Also mapped were segments of TFIIB, TFIIE, TFIIF and TFIIH in proximity to promoter DNA. DNA downstream of the transcription bubble maps to a path between the two helicase subdomains of the TFIIH subunit Rad25 (also called XPB). Together, our results show how the general factors and Pol II converge on promoter DNA within the PIC.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1038/nsmb1117", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.2514832", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1295033", 
        "issn": [
          "1545-9993", 
          "2331-365X"
        ], 
        "name": "Nature Structural & Molecular Biology", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "7", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "13"
      }
    ], 
    "name": "A DNA-tethered cleavage probe reveals the path for promoter DNA in the yeast preinitiation complex", 
    "pagination": "603-610", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "5edc1a7d1708de2929876df418788092f095dcb29153b92cc404774b5d848d95"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "16819517"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "101186374"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/nsmb1117"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1019909427"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/nsmb1117", 
      "https://app.dimensions.ai/details/publication/pub.1019909427"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-11T12:11", 
    "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/v90/0000000361_0000000361/records_53978_00000000.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://www.nature.com/articles/nsmb1117"
  }
]
 

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/nsmb1117'

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/nsmb1117'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nsmb1117'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nsmb1117'


 

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

286 TRIPLES      21 PREDICATES      94 URIs      33 LITERALS      21 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/nsmb1117 schema:about N01ebeac40a3a4cabb02f95fde9a5296c
2 N0371a22bba90413ebf1b1957e3f5c570
3 N3eca157fdc8a49a496c431572cd1c209
4 N6ca92dc1264540e0a836ace7c872cfc8
5 N786b990052004cbb9abca3485a4a5a45
6 N99db0710411c4e04b92fb78408834660
7 N9b50f704207c40cdb2175de2fdc9e5b2
8 Na5b5f8e1c80944b0b16c4120d3ae45eb
9 Na805deb49bae41ffbb0013e9d4f5a531
10 Nc03122dab2f54d968a94c97fa02be7ae
11 Nc3dedb5d71294be7ba82095b1b7e40a2
12 Nf785645690bf4597b0821159f65e6b42
13 anzsrc-for:06
14 anzsrc-for:0604
15 schema:author N63989643d74443b09d949f56e5527e15
16 schema:citation sg:pub.10.1038/368160a0
17 sg:pub.10.1038/377119a0
18 sg:pub.10.1038/nsmb763
19 sg:pub.10.1038/nsmb949
20 https://app.dimensions.ai/details/publication/pub.1082594036
21 https://app.dimensions.ai/details/publication/pub.1083274813
22 https://doi.org/10.1002/j.1460-2075.1996.tb00425.x
23 https://doi.org/10.1002/j.1460-2075.1996.tb00512.x
24 https://doi.org/10.1006/jmbi.2000.4110
25 https://doi.org/10.1016/j.bbrc.2005.04.158
26 https://doi.org/10.1016/j.cell.2004.09.028
27 https://doi.org/10.1016/j.molcel.2004.11.040
28 https://doi.org/10.1016/j.molcel.2005.03.029
29 https://doi.org/10.1016/j.molcel.2005.05.024
30 https://doi.org/10.1016/j.molcel.2006.02.017
31 https://doi.org/10.1016/s0092-8674(00)81242-8
32 https://doi.org/10.1016/s0092-8674(02)00646-3
33 https://doi.org/10.1016/s0092-8674(03)00598-1
34 https://doi.org/10.1016/s0959-440x(02)00298-1
35 https://doi.org/10.1016/s0968-0004(00)01652-2
36 https://doi.org/10.1016/s1097-2765(00)80177-x
37 https://doi.org/10.1016/s1097-2765(00)80278-6
38 https://doi.org/10.1016/s1097-2765(03)00306-x
39 https://doi.org/10.1016/s1097-2765(03)00387-3
40 https://doi.org/10.1021/bi015582r
41 https://doi.org/10.1021/bi048993r
42 https://doi.org/10.1038/sj.embor.7400663
43 https://doi.org/10.1073/pnas.1030608100
44 https://doi.org/10.1073/pnas.1130601100
45 https://doi.org/10.1073/pnas.92.8.3127
46 https://doi.org/10.1073/pnas.94.23.12268
47 https://doi.org/10.1074/jbc.m307874200
48 https://doi.org/10.1093/emboj/16.24.7468
49 https://doi.org/10.1093/emboj/19.1.25
50 https://doi.org/10.1093/nar/gki825
51 https://doi.org/10.1101/gad.10.21.2657
52 https://doi.org/10.1101/gad.1192204
53 https://doi.org/10.1101/gad.13.1.49
54 https://doi.org/10.1126/science.1059493
55 https://doi.org/10.1126/science.1069595
56 https://doi.org/10.1126/science.1090838
57 https://doi.org/10.1126/science.1090839
58 https://doi.org/10.1126/science.1310361
59 https://doi.org/10.1126/science.278.5340.1093
60 https://doi.org/10.1126/science.286.5448.2305
61 https://doi.org/10.1126/science.288.5470.1418
62 https://doi.org/10.1126/science.8342041
63 https://doi.org/10.1128/mcb.20.21.8168-8177.2000
64 https://doi.org/10.1128/mcb.21.14.4427-4440.2001
65 https://doi.org/10.1128/mcb.23.8.2914-2926.2003
66 https://doi.org/10.1128/mcb.24.24.10975-10985.2004
67 https://doi.org/10.1128/mcb.24.3.1122-1131.2004
68 https://doi.org/10.1128/mcb.24.9.3983-3991.2004
69 schema:datePublished 2006-07
70 schema:datePublishedReg 2006-07-01
71 schema:description To directly map the position of promoter DNA within the RNA polymerase II (Pol II) transcription preinitiation complex (PIC), FeBABE was tethered to specific sites within the HIS4 promoter and used to map exposed surfaces of Pol II and the general transcription factors in proximity to DNA. Our results distinguish between previously proposed models for PIC structure and demonstrate that downstream promoter DNA is positioned over the central cleft of Pol II, with DNA upstream of TATA extending toward the Pol II subunit Rpb3. Also mapped were segments of TFIIB, TFIIE, TFIIF and TFIIH in proximity to promoter DNA. DNA downstream of the transcription bubble maps to a path between the two helicase subdomains of the TFIIH subunit Rad25 (also called XPB). Together, our results show how the general factors and Pol II converge on promoter DNA within the PIC.
72 schema:genre research_article
73 schema:inLanguage en
74 schema:isAccessibleForFree true
75 schema:isPartOf N6471e61664924c3b9a13736703ff4ea5
76 Na1fa4076a7614f7aa308f79aa74012d6
77 sg:journal.1295033
78 schema:name A DNA-tethered cleavage probe reveals the path for promoter DNA in the yeast preinitiation complex
79 schema:pagination 603-610
80 schema:productId N287425ed29eb4c68bbf144c20034a1ac
81 N52303a330adc40e2adab49b2d0e8ab47
82 N6072bb65977c47298be412e3f721d113
83 Naa5d0707bd4443179968d08c1977caaf
84 Ncd7b21702a214c079eae2e2cd7f4a765
85 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019909427
86 https://doi.org/10.1038/nsmb1117
87 schema:sdDatePublished 2019-04-11T12:11
88 schema:sdLicense https://scigraph.springernature.com/explorer/license/
89 schema:sdPublisher N0e80ae362a8c4cd4bae86c97d69be56f
90 schema:url http://www.nature.com/articles/nsmb1117
91 sgo:license sg:explorer/license/
92 sgo:sdDataset articles
93 rdf:type schema:ScholarlyArticle
94 N01ebeac40a3a4cabb02f95fde9a5296c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
95 schema:name Models, Molecular
96 rdf:type schema:DefinedTerm
97 N0371a22bba90413ebf1b1957e3f5c570 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
98 schema:name Transcription, Genetic
99 rdf:type schema:DefinedTerm
100 N0e80ae362a8c4cd4bae86c97d69be56f schema:name Springer Nature - SN SciGraph project
101 rdf:type schema:Organization
102 N287425ed29eb4c68bbf144c20034a1ac schema:name dimensions_id
103 schema:value pub.1019909427
104 rdf:type schema:PropertyValue
105 N3eca157fdc8a49a496c431572cd1c209 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
106 schema:name DNA Polymerase II
107 rdf:type schema:DefinedTerm
108 N52303a330adc40e2adab49b2d0e8ab47 schema:name pubmed_id
109 schema:value 16819517
110 rdf:type schema:PropertyValue
111 N6072bb65977c47298be412e3f721d113 schema:name nlm_unique_id
112 schema:value 101186374
113 rdf:type schema:PropertyValue
114 N63989643d74443b09d949f56e5527e15 rdf:first Nb977b8e98ef243fc90d87780ea81ff7b
115 rdf:rest Nf358277f81584421acb5853d4cb14c7d
116 N6471e61664924c3b9a13736703ff4ea5 schema:issueNumber 7
117 rdf:type schema:PublicationIssue
118 N6ca92dc1264540e0a836ace7c872cfc8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
119 schema:name Hydroxyl Radical
120 rdf:type schema:DefinedTerm
121 N786b990052004cbb9abca3485a4a5a45 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
122 schema:name Nucleic Acid Conformation
123 rdf:type schema:DefinedTerm
124 N99db0710411c4e04b92fb78408834660 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
125 schema:name Transcription Factor TFIIH
126 rdf:type schema:DefinedTerm
127 N9b50f704207c40cdb2175de2fdc9e5b2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
128 schema:name DNA, Fungal
129 rdf:type schema:DefinedTerm
130 Na1fa4076a7614f7aa308f79aa74012d6 schema:volumeNumber 13
131 rdf:type schema:PublicationVolume
132 Na5b5f8e1c80944b0b16c4120d3ae45eb schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
133 schema:name DNA Helicases
134 rdf:type schema:DefinedTerm
135 Na805deb49bae41ffbb0013e9d4f5a531 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
136 schema:name Saccharomyces cerevisiae Proteins
137 rdf:type schema:DefinedTerm
138 Naa5d0707bd4443179968d08c1977caaf schema:name readcube_id
139 schema:value 5edc1a7d1708de2929876df418788092f095dcb29153b92cc404774b5d848d95
140 rdf:type schema:PropertyValue
141 Nb977b8e98ef243fc90d87780ea81ff7b schema:affiliation https://www.grid.ac/institutes/grid.270240.3
142 schema:familyName Miller
143 schema:givenName Gail
144 rdf:type schema:Person
145 Nc03122dab2f54d968a94c97fa02be7ae schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
146 schema:name Promoter Regions, Genetic
147 rdf:type schema:DefinedTerm
148 Nc3dedb5d71294be7ba82095b1b7e40a2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
149 schema:name Saccharomyces cerevisiae
150 rdf:type schema:DefinedTerm
151 Ncd7b21702a214c079eae2e2cd7f4a765 schema:name doi
152 schema:value 10.1038/nsmb1117
153 rdf:type schema:PropertyValue
154 Nf358277f81584421acb5853d4cb14c7d rdf:first sg:person.01127561726.48
155 rdf:rest rdf:nil
156 Nf785645690bf4597b0821159f65e6b42 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
157 schema:name Base Sequence
158 rdf:type schema:DefinedTerm
159 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
160 schema:name Biological Sciences
161 rdf:type schema:DefinedTerm
162 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
163 schema:name Genetics
164 rdf:type schema:DefinedTerm
165 sg:grant.2514832 http://pending.schema.org/fundedItem sg:pub.10.1038/nsmb1117
166 rdf:type schema:MonetaryGrant
167 sg:journal.1295033 schema:issn 1545-9993
168 2331-365X
169 schema:name Nature Structural & Molecular Biology
170 rdf:type schema:Periodical
171 sg:person.01127561726.48 schema:affiliation https://www.grid.ac/institutes/grid.270240.3
172 schema:familyName Hahn
173 schema:givenName Steven
174 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01127561726.48
175 rdf:type schema:Person
176 sg:pub.10.1038/368160a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022812854
177 https://doi.org/10.1038/368160a0
178 rdf:type schema:CreativeWork
179 sg:pub.10.1038/377119a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044250366
180 https://doi.org/10.1038/377119a0
181 rdf:type schema:CreativeWork
182 sg:pub.10.1038/nsmb763 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032525772
183 https://doi.org/10.1038/nsmb763
184 rdf:type schema:CreativeWork
185 sg:pub.10.1038/nsmb949 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000739982
186 https://doi.org/10.1038/nsmb949
187 rdf:type schema:CreativeWork
188 https://app.dimensions.ai/details/publication/pub.1082594036 schema:CreativeWork
189 https://app.dimensions.ai/details/publication/pub.1083274813 schema:CreativeWork
190 https://doi.org/10.1002/j.1460-2075.1996.tb00425.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1082886332
191 rdf:type schema:CreativeWork
192 https://doi.org/10.1002/j.1460-2075.1996.tb00512.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1082879612
193 rdf:type schema:CreativeWork
194 https://doi.org/10.1006/jmbi.2000.4110 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051034638
195 rdf:type schema:CreativeWork
196 https://doi.org/10.1016/j.bbrc.2005.04.158 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047298505
197 rdf:type schema:CreativeWork
198 https://doi.org/10.1016/j.cell.2004.09.028 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036982343
199 rdf:type schema:CreativeWork
200 https://doi.org/10.1016/j.molcel.2004.11.040 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006261602
201 rdf:type schema:CreativeWork
202 https://doi.org/10.1016/j.molcel.2005.03.029 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016911129
203 rdf:type schema:CreativeWork
204 https://doi.org/10.1016/j.molcel.2005.05.024 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044289537
205 rdf:type schema:CreativeWork
206 https://doi.org/10.1016/j.molcel.2006.02.017 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040705027
207 rdf:type schema:CreativeWork
208 https://doi.org/10.1016/s0092-8674(00)81242-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051683968
209 rdf:type schema:CreativeWork
210 https://doi.org/10.1016/s0092-8674(02)00646-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000825991
211 rdf:type schema:CreativeWork
212 https://doi.org/10.1016/s0092-8674(03)00598-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003046185
213 rdf:type schema:CreativeWork
214 https://doi.org/10.1016/s0959-440x(02)00298-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027916800
215 rdf:type schema:CreativeWork
216 https://doi.org/10.1016/s0968-0004(00)01652-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027510807
217 rdf:type schema:CreativeWork
218 https://doi.org/10.1016/s1097-2765(00)80177-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1045533184
219 rdf:type schema:CreativeWork
220 https://doi.org/10.1016/s1097-2765(00)80278-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038184124
221 rdf:type schema:CreativeWork
222 https://doi.org/10.1016/s1097-2765(03)00306-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1042583135
223 rdf:type schema:CreativeWork
224 https://doi.org/10.1016/s1097-2765(03)00387-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001216189
225 rdf:type schema:CreativeWork
226 https://doi.org/10.1021/bi015582r schema:sameAs https://app.dimensions.ai/details/publication/pub.1055194826
227 rdf:type schema:CreativeWork
228 https://doi.org/10.1021/bi048993r schema:sameAs https://app.dimensions.ai/details/publication/pub.1055199483
229 rdf:type schema:CreativeWork
230 https://doi.org/10.1038/sj.embor.7400663 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028687563
231 rdf:type schema:CreativeWork
232 https://doi.org/10.1073/pnas.1030608100 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019574256
233 rdf:type schema:CreativeWork
234 https://doi.org/10.1073/pnas.1130601100 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023101111
235 rdf:type schema:CreativeWork
236 https://doi.org/10.1073/pnas.92.8.3127 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005255373
237 rdf:type schema:CreativeWork
238 https://doi.org/10.1073/pnas.94.23.12268 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033561730
239 rdf:type schema:CreativeWork
240 https://doi.org/10.1074/jbc.m307874200 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028140656
241 rdf:type schema:CreativeWork
242 https://doi.org/10.1093/emboj/16.24.7468 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026838567
243 rdf:type schema:CreativeWork
244 https://doi.org/10.1093/emboj/19.1.25 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053325470
245 rdf:type schema:CreativeWork
246 https://doi.org/10.1093/nar/gki825 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038648763
247 rdf:type schema:CreativeWork
248 https://doi.org/10.1101/gad.10.21.2657 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027560421
249 rdf:type schema:CreativeWork
250 https://doi.org/10.1101/gad.1192204 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023683653
251 rdf:type schema:CreativeWork
252 https://doi.org/10.1101/gad.13.1.49 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040634590
253 rdf:type schema:CreativeWork
254 https://doi.org/10.1126/science.1059493 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015760622
255 rdf:type schema:CreativeWork
256 https://doi.org/10.1126/science.1069595 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062445931
257 rdf:type schema:CreativeWork
258 https://doi.org/10.1126/science.1090838 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004847683
259 rdf:type schema:CreativeWork
260 https://doi.org/10.1126/science.1090839 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062449037
261 rdf:type schema:CreativeWork
262 https://doi.org/10.1126/science.1310361 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062474504
263 rdf:type schema:CreativeWork
264 https://doi.org/10.1126/science.278.5340.1093 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062558575
265 rdf:type schema:CreativeWork
266 https://doi.org/10.1126/science.286.5448.2305 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004253385
267 rdf:type schema:CreativeWork
268 https://doi.org/10.1126/science.288.5470.1418 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016316092
269 rdf:type schema:CreativeWork
270 https://doi.org/10.1126/science.8342041 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062654753
271 rdf:type schema:CreativeWork
272 https://doi.org/10.1128/mcb.20.21.8168-8177.2000 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000476715
273 rdf:type schema:CreativeWork
274 https://doi.org/10.1128/mcb.21.14.4427-4440.2001 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047037863
275 rdf:type schema:CreativeWork
276 https://doi.org/10.1128/mcb.23.8.2914-2926.2003 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051226934
277 rdf:type schema:CreativeWork
278 https://doi.org/10.1128/mcb.24.24.10975-10985.2004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017977115
279 rdf:type schema:CreativeWork
280 https://doi.org/10.1128/mcb.24.3.1122-1131.2004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007678266
281 rdf:type schema:CreativeWork
282 https://doi.org/10.1128/mcb.24.9.3983-3991.2004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001900322
283 rdf:type schema:CreativeWork
284 https://www.grid.ac/institutes/grid.270240.3 schema:alternateName Fred Hutchinson Cancer Research Center
285 schema:name Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Seattle, Washington 98109, USA.
286 rdf:type schema:Organization
 




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


...