Determinants of nucleosome organization in primary human cells View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2011-06

AUTHORS

Anton Valouev, Steven M. Johnson, Scott D. Boyd, Cheryl L. Smith, Andrew Z. Fire, Arend Sidow

ABSTRACT

Nucleosomes are the basic packaging units of chromatin, modulating accessibility of regulatory proteins to DNA and thus influencing eukaryotic gene regulation. Elaborate chromatin remodelling mechanisms have evolved that govern nucleosome organization at promoters, regulatory elements, and other functional regions in the genome. Analyses of chromatin landscape have uncovered a variety of mechanisms, including DNA sequence preferences, that can influence nucleosome positions. To identify major determinants of nucleosome organization in the human genome, we used deep sequencing to map nucleosome positions in three primary human cell types and in vitro. A majority of the genome showed substantial flexibility of nucleosome positions, whereas a small fraction showed reproducibly positioned nucleosomes. Certain sites that position in vitro can anchor the formation of nucleosomal arrays that have cell type-specific spacing in vivo. Our results unveil an interplay of sequence-based nucleosome preferences and non-nucleosomal factors in determining nucleosome organization within mammalian cells. More... »

PAGES

516

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nature10002

DOI

http://dx.doi.org/10.1038/nature10002

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1048856019

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/21602827


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": "CD4-Positive T-Lymphocytes", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "CD8-Positive T-Lymphocytes", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Cells, Cultured", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Chromatin Assembly and Disassembly", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Expression Regulation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome, Human", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Granulocytes", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "High-Throughput Nucleotide Sequencing", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Humans", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Micrococcal Nuclease", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Nucleosomes", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Organ Specificity", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Transcription, Genetic", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Stanford University", 
          "id": "https://www.grid.ac/institutes/grid.168010.e", 
          "name": [
            "Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Valouev", 
        "givenName": "Anton", 
        "id": "sg:person.01050144667.57", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01050144667.57"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Brigham Young University", 
          "id": "https://www.grid.ac/institutes/grid.253294.b", 
          "name": [
            "Department of Microbiology and Molecular Biology, Brigham Young University, 757 WIDB, Provo, Utah 84602-5253, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Johnson", 
        "givenName": "Steven M.", 
        "id": "sg:person.0671352501.38", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0671352501.38"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Stanford University", 
          "id": "https://www.grid.ac/institutes/grid.168010.e", 
          "name": [
            "Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Boyd", 
        "givenName": "Scott D.", 
        "id": "sg:person.0713601023.10", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0713601023.10"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Stanford University", 
          "id": "https://www.grid.ac/institutes/grid.168010.e", 
          "name": [
            "Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Smith", 
        "givenName": "Cheryl L.", 
        "id": "sg:person.01012013267.53", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01012013267.53"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Stanford University", 
          "id": "https://www.grid.ac/institutes/grid.168010.e", 
          "name": [
            "Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, USA", 
            "Department of Genetics, Stanford University School of Medicine, Pasteur Drive, Stanford, California 94305, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Fire", 
        "givenName": "Andrew Z.", 
        "id": "sg:person.01316316510.87", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01316316510.87"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Stanford University", 
          "id": "https://www.grid.ac/institutes/grid.168010.e", 
          "name": [
            "Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, USA", 
            "Department of Genetics, Stanford University School of Medicine, Pasteur Drive, Stanford, California 94305, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Sidow", 
        "givenName": "Arend", 
        "id": "sg:person.0771606520.69", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0771606520.69"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1038/nature06929", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000373198", 
          "https://doi.org/10.1038/nature06929"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0022-2836(86)90452-3", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000854612"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2007.05.009", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002139821"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature07667", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003950085", 
          "https://doi.org/10.1038/nature07667"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature04979", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004695015", 
          "https://doi.org/10.1038/nature04979"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature04979", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004695015", 
          "https://doi.org/10.1038/nature04979"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0005-2787(80)90041-6", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011285604"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0005-2787(80)90041-6", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011285604"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/emboj/16.16.5046", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013025631"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng.324", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016326666", 
          "https://doi.org/10.1038/ng.324"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.89.3.1095", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016427678"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nsmb.1636", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018422844", 
          "https://doi.org/10.1038/nsmb.1636"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nsmb.1636", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018422844", 
          "https://doi.org/10.1038/nsmb.1636"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng.154", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018442414", 
          "https://doi.org/10.1038/ng.154"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.ydbio.2009.06.012", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024982990"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2164-11-465", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027661801", 
          "https://doi.org/10.1186/1471-2164-11-465"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2005.10.028", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029133662"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.076463.108", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030225638"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.082800.108", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032692217"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.1246", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037362623", 
          "https://doi.org/10.1038/nmeth.1246"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pgen.1000138", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037649566"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/jbiol207", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038104328", 
          "https://doi.org/10.1186/jbiol207"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng2117", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038909736", 
          "https://doi.org/10.1038/ng2117"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1146/annurev.bi.46.070177.004435", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040737735"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.5560806", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043445116"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.molcel.2005.06.023", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043698075"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.molcel.2005.06.023", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043698075"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.078261.108", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044165516"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.1226", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045381177", 
          "https://doi.org/10.1038/nmeth.1226"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.77.7.3816", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045408577"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0009129", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046874837"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2008.02.022", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047426433"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature05632", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050363686", 
          "https://doi.org/10.1038/nature05632"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00412-009-0235-3", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051066534", 
          "https://doi.org/10.1007/s00412-009-0235-3"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00412-009-0235-3", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051066534", 
          "https://doi.org/10.1007/s00412-009-0235-3"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00412-009-0235-3", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051066534", 
          "https://doi.org/10.1007/s00412-009-0235-3"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0076-6879(99)04003-3", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051391755"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2004-5-9-r62", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052780836", 
          "https://doi.org/10.1186/gb-2004-5-9-r62"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1112178", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062452190"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1163183", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062458631"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2011-06", 
    "datePublishedReg": "2011-06-01", 
    "description": "Nucleosomes are the basic packaging units of chromatin, modulating accessibility of regulatory proteins to DNA and thus influencing eukaryotic gene regulation. Elaborate chromatin remodelling mechanisms have evolved that govern nucleosome organization at promoters, regulatory elements, and other functional regions in the genome. Analyses of chromatin landscape have uncovered a variety of mechanisms, including DNA sequence preferences, that can influence nucleosome positions. To identify major determinants of nucleosome organization in the human genome, we used deep sequencing to map nucleosome positions in three primary human cell types and in vitro. A majority of the genome showed substantial flexibility of nucleosome positions, whereas a small fraction showed reproducibly positioned nucleosomes. Certain sites that position in vitro can anchor the formation of nucleosomal arrays that have cell type-specific spacing in vivo. Our results unveil an interplay of sequence-based nucleosome preferences and non-nucleosomal factors in determining nucleosome organization within mammalian cells.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1038/nature10002", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.2691261", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.2684533", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.2511935", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1018957", 
        "issn": [
          "0090-0028", 
          "1476-4687"
        ], 
        "name": "Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "7352", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "474"
      }
    ], 
    "name": "Determinants of nucleosome organization in primary human cells", 
    "pagination": "516", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "e8bdb722ff246fc07bf675a873a845533a1b69dfa1bdf2a4e055eb048fb103c1"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "21602827"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "0410462"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/nature10002"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1048856019"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/nature10002", 
      "https://app.dimensions.ai/details/publication/pub.1048856019"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-11T00:05", 
    "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_8695_00000436.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://www.nature.com/articles/nature10002"
  }
]
 

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/nature10002'

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/nature10002'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nature10002'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nature10002'


 

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

282 TRIPLES      21 PREDICATES      76 URIs      34 LITERALS      22 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/nature10002 schema:about N1134b25702e54f3c89acfe62e737f1ab
2 N1714cfb77e0e49629607ed8784419799
3 N247850276de1489eb361141989ba7115
4 N370767b9f5b14a2f9537d15326396531
5 N3de5162129084e98bd8efae075bd5dfc
6 N3f1f634107164d8a9eb88f3fb2b0ae3d
7 N4f3e383cbe6c4e72a8ca42ae2b0ad0ce
8 N9206fe1d1b44456cbc433639870104ae
9 N95beedc235004346a88e84d4f70f49c9
10 Nc8ce79291a0040b7b611512cc5598991
11 Nd90604e479e9416596cab038864ab6ac
12 Ne61267a705ed426784489a3d2b8c38bd
13 Nfbcb66b7c14b47e183635cf491efd421
14 anzsrc-for:06
15 anzsrc-for:0604
16 schema:author N588aa1d52b1f4654b621caad4084d9a7
17 schema:citation sg:pub.10.1007/s00412-009-0235-3
18 sg:pub.10.1038/nature04979
19 sg:pub.10.1038/nature05632
20 sg:pub.10.1038/nature06929
21 sg:pub.10.1038/nature07667
22 sg:pub.10.1038/ng.154
23 sg:pub.10.1038/ng.324
24 sg:pub.10.1038/ng2117
25 sg:pub.10.1038/nmeth.1226
26 sg:pub.10.1038/nmeth.1246
27 sg:pub.10.1038/nsmb.1636
28 sg:pub.10.1186/1471-2164-11-465
29 sg:pub.10.1186/gb-2004-5-9-r62
30 sg:pub.10.1186/jbiol207
31 https://doi.org/10.1016/0005-2787(80)90041-6
32 https://doi.org/10.1016/0022-2836(86)90452-3
33 https://doi.org/10.1016/j.cell.2005.10.028
34 https://doi.org/10.1016/j.cell.2007.05.009
35 https://doi.org/10.1016/j.cell.2008.02.022
36 https://doi.org/10.1016/j.molcel.2005.06.023
37 https://doi.org/10.1016/j.ydbio.2009.06.012
38 https://doi.org/10.1016/s0076-6879(99)04003-3
39 https://doi.org/10.1073/pnas.77.7.3816
40 https://doi.org/10.1073/pnas.89.3.1095
41 https://doi.org/10.1093/emboj/16.16.5046
42 https://doi.org/10.1101/gr.076463.108
43 https://doi.org/10.1101/gr.078261.108
44 https://doi.org/10.1101/gr.082800.108
45 https://doi.org/10.1101/gr.5560806
46 https://doi.org/10.1126/science.1112178
47 https://doi.org/10.1126/science.1163183
48 https://doi.org/10.1146/annurev.bi.46.070177.004435
49 https://doi.org/10.1371/journal.pgen.1000138
50 https://doi.org/10.1371/journal.pone.0009129
51 schema:datePublished 2011-06
52 schema:datePublishedReg 2011-06-01
53 schema:description Nucleosomes are the basic packaging units of chromatin, modulating accessibility of regulatory proteins to DNA and thus influencing eukaryotic gene regulation. Elaborate chromatin remodelling mechanisms have evolved that govern nucleosome organization at promoters, regulatory elements, and other functional regions in the genome. Analyses of chromatin landscape have uncovered a variety of mechanisms, including DNA sequence preferences, that can influence nucleosome positions. To identify major determinants of nucleosome organization in the human genome, we used deep sequencing to map nucleosome positions in three primary human cell types and in vitro. A majority of the genome showed substantial flexibility of nucleosome positions, whereas a small fraction showed reproducibly positioned nucleosomes. Certain sites that position in vitro can anchor the formation of nucleosomal arrays that have cell type-specific spacing in vivo. Our results unveil an interplay of sequence-based nucleosome preferences and non-nucleosomal factors in determining nucleosome organization within mammalian cells.
54 schema:genre research_article
55 schema:inLanguage en
56 schema:isAccessibleForFree true
57 schema:isPartOf N02a6f33fb8f84f21b7c32f6f76107696
58 N7df3d619dbcb4adfaf25a33b472c34d9
59 sg:journal.1018957
60 schema:name Determinants of nucleosome organization in primary human cells
61 schema:pagination 516
62 schema:productId N3a2f5c19c8914c60ba1fc8d2f888a278
63 N8c27664857c0475ca453b28cd5abf947
64 N9248eb1da414400a8f5b55ed0fd83770
65 N9df12551328047c8b0382901b76ef1be
66 Nf3565b3d9e3341c3ba2af8b8e5c12c04
67 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048856019
68 https://doi.org/10.1038/nature10002
69 schema:sdDatePublished 2019-04-11T00:05
70 schema:sdLicense https://scigraph.springernature.com/explorer/license/
71 schema:sdPublisher N15e373c83dec431d85865b210cd109aa
72 schema:url https://www.nature.com/articles/nature10002
73 sgo:license sg:explorer/license/
74 sgo:sdDataset articles
75 rdf:type schema:ScholarlyArticle
76 N02a6f33fb8f84f21b7c32f6f76107696 schema:volumeNumber 474
77 rdf:type schema:PublicationVolume
78 N08583949763845db8c2d89df20106693 rdf:first sg:person.0713601023.10
79 rdf:rest N1a3e5b6a04f3429a90108b0d9f99257e
80 N10092024e29a40a1be98482cb5eb91d1 rdf:first sg:person.0771606520.69
81 rdf:rest rdf:nil
82 N1134b25702e54f3c89acfe62e737f1ab schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
83 schema:name Transcription, Genetic
84 rdf:type schema:DefinedTerm
85 N15e373c83dec431d85865b210cd109aa schema:name Springer Nature - SN SciGraph project
86 rdf:type schema:Organization
87 N1714cfb77e0e49629607ed8784419799 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
88 schema:name Nucleosomes
89 rdf:type schema:DefinedTerm
90 N1a3e5b6a04f3429a90108b0d9f99257e rdf:first sg:person.01012013267.53
91 rdf:rest Nf8da460ddaa341a591da1bdfbc8b0959
92 N247850276de1489eb361141989ba7115 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
93 schema:name CD8-Positive T-Lymphocytes
94 rdf:type schema:DefinedTerm
95 N2c378aca97834749b994ca79f6c3eaf6 rdf:first sg:person.0671352501.38
96 rdf:rest N08583949763845db8c2d89df20106693
97 N370767b9f5b14a2f9537d15326396531 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
98 schema:name Organ Specificity
99 rdf:type schema:DefinedTerm
100 N3a2f5c19c8914c60ba1fc8d2f888a278 schema:name pubmed_id
101 schema:value 21602827
102 rdf:type schema:PropertyValue
103 N3de5162129084e98bd8efae075bd5dfc schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
104 schema:name Humans
105 rdf:type schema:DefinedTerm
106 N3f1f634107164d8a9eb88f3fb2b0ae3d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
107 schema:name Gene Expression Regulation
108 rdf:type schema:DefinedTerm
109 N4f3e383cbe6c4e72a8ca42ae2b0ad0ce schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
110 schema:name Genome, Human
111 rdf:type schema:DefinedTerm
112 N588aa1d52b1f4654b621caad4084d9a7 rdf:first sg:person.01050144667.57
113 rdf:rest N2c378aca97834749b994ca79f6c3eaf6
114 N7df3d619dbcb4adfaf25a33b472c34d9 schema:issueNumber 7352
115 rdf:type schema:PublicationIssue
116 N8c27664857c0475ca453b28cd5abf947 schema:name readcube_id
117 schema:value e8bdb722ff246fc07bf675a873a845533a1b69dfa1bdf2a4e055eb048fb103c1
118 rdf:type schema:PropertyValue
119 N9206fe1d1b44456cbc433639870104ae schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
120 schema:name High-Throughput Nucleotide Sequencing
121 rdf:type schema:DefinedTerm
122 N9248eb1da414400a8f5b55ed0fd83770 schema:name nlm_unique_id
123 schema:value 0410462
124 rdf:type schema:PropertyValue
125 N95beedc235004346a88e84d4f70f49c9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
126 schema:name CD4-Positive T-Lymphocytes
127 rdf:type schema:DefinedTerm
128 N9df12551328047c8b0382901b76ef1be schema:name dimensions_id
129 schema:value pub.1048856019
130 rdf:type schema:PropertyValue
131 Nc8ce79291a0040b7b611512cc5598991 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
132 schema:name Micrococcal Nuclease
133 rdf:type schema:DefinedTerm
134 Nd90604e479e9416596cab038864ab6ac schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
135 schema:name Cells, Cultured
136 rdf:type schema:DefinedTerm
137 Ne61267a705ed426784489a3d2b8c38bd schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
138 schema:name Granulocytes
139 rdf:type schema:DefinedTerm
140 Nf3565b3d9e3341c3ba2af8b8e5c12c04 schema:name doi
141 schema:value 10.1038/nature10002
142 rdf:type schema:PropertyValue
143 Nf8da460ddaa341a591da1bdfbc8b0959 rdf:first sg:person.01316316510.87
144 rdf:rest N10092024e29a40a1be98482cb5eb91d1
145 Nfbcb66b7c14b47e183635cf491efd421 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
146 schema:name Chromatin Assembly and Disassembly
147 rdf:type schema:DefinedTerm
148 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
149 schema:name Biological Sciences
150 rdf:type schema:DefinedTerm
151 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
152 schema:name Genetics
153 rdf:type schema:DefinedTerm
154 sg:grant.2511935 http://pending.schema.org/fundedItem sg:pub.10.1038/nature10002
155 rdf:type schema:MonetaryGrant
156 sg:grant.2684533 http://pending.schema.org/fundedItem sg:pub.10.1038/nature10002
157 rdf:type schema:MonetaryGrant
158 sg:grant.2691261 http://pending.schema.org/fundedItem sg:pub.10.1038/nature10002
159 rdf:type schema:MonetaryGrant
160 sg:journal.1018957 schema:issn 0090-0028
161 1476-4687
162 schema:name Nature
163 rdf:type schema:Periodical
164 sg:person.01012013267.53 schema:affiliation https://www.grid.ac/institutes/grid.168010.e
165 schema:familyName Smith
166 schema:givenName Cheryl L.
167 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01012013267.53
168 rdf:type schema:Person
169 sg:person.01050144667.57 schema:affiliation https://www.grid.ac/institutes/grid.168010.e
170 schema:familyName Valouev
171 schema:givenName Anton
172 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01050144667.57
173 rdf:type schema:Person
174 sg:person.01316316510.87 schema:affiliation https://www.grid.ac/institutes/grid.168010.e
175 schema:familyName Fire
176 schema:givenName Andrew Z.
177 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01316316510.87
178 rdf:type schema:Person
179 sg:person.0671352501.38 schema:affiliation https://www.grid.ac/institutes/grid.253294.b
180 schema:familyName Johnson
181 schema:givenName Steven M.
182 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0671352501.38
183 rdf:type schema:Person
184 sg:person.0713601023.10 schema:affiliation https://www.grid.ac/institutes/grid.168010.e
185 schema:familyName Boyd
186 schema:givenName Scott D.
187 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0713601023.10
188 rdf:type schema:Person
189 sg:person.0771606520.69 schema:affiliation https://www.grid.ac/institutes/grid.168010.e
190 schema:familyName Sidow
191 schema:givenName Arend
192 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0771606520.69
193 rdf:type schema:Person
194 sg:pub.10.1007/s00412-009-0235-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051066534
195 https://doi.org/10.1007/s00412-009-0235-3
196 rdf:type schema:CreativeWork
197 sg:pub.10.1038/nature04979 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004695015
198 https://doi.org/10.1038/nature04979
199 rdf:type schema:CreativeWork
200 sg:pub.10.1038/nature05632 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050363686
201 https://doi.org/10.1038/nature05632
202 rdf:type schema:CreativeWork
203 sg:pub.10.1038/nature06929 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000373198
204 https://doi.org/10.1038/nature06929
205 rdf:type schema:CreativeWork
206 sg:pub.10.1038/nature07667 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003950085
207 https://doi.org/10.1038/nature07667
208 rdf:type schema:CreativeWork
209 sg:pub.10.1038/ng.154 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018442414
210 https://doi.org/10.1038/ng.154
211 rdf:type schema:CreativeWork
212 sg:pub.10.1038/ng.324 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016326666
213 https://doi.org/10.1038/ng.324
214 rdf:type schema:CreativeWork
215 sg:pub.10.1038/ng2117 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038909736
216 https://doi.org/10.1038/ng2117
217 rdf:type schema:CreativeWork
218 sg:pub.10.1038/nmeth.1226 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045381177
219 https://doi.org/10.1038/nmeth.1226
220 rdf:type schema:CreativeWork
221 sg:pub.10.1038/nmeth.1246 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037362623
222 https://doi.org/10.1038/nmeth.1246
223 rdf:type schema:CreativeWork
224 sg:pub.10.1038/nsmb.1636 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018422844
225 https://doi.org/10.1038/nsmb.1636
226 rdf:type schema:CreativeWork
227 sg:pub.10.1186/1471-2164-11-465 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027661801
228 https://doi.org/10.1186/1471-2164-11-465
229 rdf:type schema:CreativeWork
230 sg:pub.10.1186/gb-2004-5-9-r62 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052780836
231 https://doi.org/10.1186/gb-2004-5-9-r62
232 rdf:type schema:CreativeWork
233 sg:pub.10.1186/jbiol207 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038104328
234 https://doi.org/10.1186/jbiol207
235 rdf:type schema:CreativeWork
236 https://doi.org/10.1016/0005-2787(80)90041-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011285604
237 rdf:type schema:CreativeWork
238 https://doi.org/10.1016/0022-2836(86)90452-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000854612
239 rdf:type schema:CreativeWork
240 https://doi.org/10.1016/j.cell.2005.10.028 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029133662
241 rdf:type schema:CreativeWork
242 https://doi.org/10.1016/j.cell.2007.05.009 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002139821
243 rdf:type schema:CreativeWork
244 https://doi.org/10.1016/j.cell.2008.02.022 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047426433
245 rdf:type schema:CreativeWork
246 https://doi.org/10.1016/j.molcel.2005.06.023 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043698075
247 rdf:type schema:CreativeWork
248 https://doi.org/10.1016/j.ydbio.2009.06.012 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024982990
249 rdf:type schema:CreativeWork
250 https://doi.org/10.1016/s0076-6879(99)04003-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051391755
251 rdf:type schema:CreativeWork
252 https://doi.org/10.1073/pnas.77.7.3816 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045408577
253 rdf:type schema:CreativeWork
254 https://doi.org/10.1073/pnas.89.3.1095 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016427678
255 rdf:type schema:CreativeWork
256 https://doi.org/10.1093/emboj/16.16.5046 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013025631
257 rdf:type schema:CreativeWork
258 https://doi.org/10.1101/gr.076463.108 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030225638
259 rdf:type schema:CreativeWork
260 https://doi.org/10.1101/gr.078261.108 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044165516
261 rdf:type schema:CreativeWork
262 https://doi.org/10.1101/gr.082800.108 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032692217
263 rdf:type schema:CreativeWork
264 https://doi.org/10.1101/gr.5560806 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043445116
265 rdf:type schema:CreativeWork
266 https://doi.org/10.1126/science.1112178 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062452190
267 rdf:type schema:CreativeWork
268 https://doi.org/10.1126/science.1163183 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062458631
269 rdf:type schema:CreativeWork
270 https://doi.org/10.1146/annurev.bi.46.070177.004435 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040737735
271 rdf:type schema:CreativeWork
272 https://doi.org/10.1371/journal.pgen.1000138 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037649566
273 rdf:type schema:CreativeWork
274 https://doi.org/10.1371/journal.pone.0009129 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046874837
275 rdf:type schema:CreativeWork
276 https://www.grid.ac/institutes/grid.168010.e schema:alternateName Stanford University
277 schema:name Department of Genetics, Stanford University School of Medicine, Pasteur Drive, Stanford, California 94305, USA
278 Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, USA
279 rdf:type schema:Organization
280 https://www.grid.ac/institutes/grid.253294.b schema:alternateName Brigham Young University
281 schema:name Department of Microbiology and Molecular Biology, Brigham Young University, 757 WIDB, Provo, Utah 84602-5253, USA
282 rdf:type schema:Organization
 




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


...