Topological domains in mammalian genomes identified by analysis of chromatin interactions View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2012-04-11

AUTHORS

Jesse R. Dixon, Siddarth Selvaraj, Feng Yue, Audrey Kim, Yan Li, Yin Shen, Ming Hu, Jun S. Liu, Bing Ren

ABSTRACT

The spatial organization of the genome is intimately linked to its biological function, yet our understanding of higher order genomic structure is coarse, fragmented and incomplete. In the nucleus of eukaryotic cells, interphase chromosomes occupy distinct chromosome territories, and numerous models have been proposed for how chromosomes fold within chromosome territories. These models, however, provide only few mechanistic details about the relationship between higher order chromatin structure and genome function. Recent advances in genomic technologies have led to rapid advances in the study of three-dimensional genome organization. In particular, Hi-C has been introduced as a method for identifying higher order chromatin interactions genome wide. Here we investigate the three-dimensional organization of the human and mouse genomes in embryonic stem cells and terminally differentiated cell types at unprecedented resolution. We identify large, megabase-sized local chromatin interaction domains, which we term 'topological domains', as a pervasive structural feature of the genome organization. These domains correlate with regions of the genome that constrain the spread of heterochromatin. The domains are stable across different cell types and highly conserved across species, indicating that topological domains are an inherent property of mammalian genomes. Finally, we find that the boundaries of topological domains are enriched for the insulator binding protein CTCF, housekeeping genes, transfer RNAs and short interspersed element (SINE) retrotransposons, indicating that these factors may have a role in establishing the topological domain structure of the genome. More... »

PAGES

376

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nature11082

DOI

http://dx.doi.org/10.1038/nature11082

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1040271530

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/22495300


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": "Animals", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Binding Sites", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "CCCTC-Binding Factor", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Cell Differentiation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Chromatin", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Chromosomes", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Embryonic Stem Cells", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Evolution, Molecular", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Female", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genes, Essential", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Heterochromatin", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Humans", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Male", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Mammals", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Mice", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "RNA, Transfer", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Repressor Proteins", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Short Interspersed Nucleotide Elements", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "University of California, San Diego", 
          "id": "https://www.grid.ac/institutes/grid.266100.3", 
          "name": [
            "Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA", 
            "Medical Scientist Training Program, University of California, San Diego, La Jolla, California 92093, USA", 
            "Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California 92093, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Dixon", 
        "givenName": "Jesse R.", 
        "id": "sg:person.0640665625.97", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0640665625.97"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of California, San Diego", 
          "id": "https://www.grid.ac/institutes/grid.266100.3", 
          "name": [
            "Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA", 
            "Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California 92093, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Selvaraj", 
        "givenName": "Siddarth", 
        "id": "sg:person.01123352652.14", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01123352652.14"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Ludwig Cancer Research", 
          "id": "https://www.grid.ac/institutes/grid.1052.6", 
          "name": [
            "Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Yue", 
        "givenName": "Feng", 
        "id": "sg:person.01323461765.25", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01323461765.25"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Ludwig Cancer Research", 
          "id": "https://www.grid.ac/institutes/grid.1052.6", 
          "name": [
            "Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Kim", 
        "givenName": "Audrey", 
        "id": "sg:person.01002667035.02", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01002667035.02"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Ludwig Cancer Research", 
          "id": "https://www.grid.ac/institutes/grid.1052.6", 
          "name": [
            "Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Li", 
        "givenName": "Yan", 
        "id": "sg:person.01071342625.44", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01071342625.44"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Ludwig Cancer Research", 
          "id": "https://www.grid.ac/institutes/grid.1052.6", 
          "name": [
            "Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Shen", 
        "givenName": "Yin", 
        "id": "sg:person.01023276441.67", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01023276441.67"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Harvard University", 
          "id": "https://www.grid.ac/institutes/grid.38142.3c", 
          "name": [
            "Department of Statistics, Harvard University, 1 Oxford Street, Cambridge, Massachusetts 02138, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hu", 
        "givenName": "Ming", 
        "id": "sg:person.01351361054.30", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01351361054.30"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Harvard University", 
          "id": "https://www.grid.ac/institutes/grid.38142.3c", 
          "name": [
            "Department of Statistics, Harvard University, 1 Oxford Street, Cambridge, Massachusetts 02138, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Liu", 
        "givenName": "Jun S.", 
        "id": "sg:person.01306627540.69", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01306627540.69"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Ludwig Cancer Research", 
          "id": "https://www.grid.ac/institutes/grid.1052.6", 
          "name": [
            "Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA", 
            "University of California, San Diego School of Medicine, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, UCSD Moores Cancer Center, 9500 Gilman Drive, La Jolla, California 92093, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Ren", 
        "givenName": "Bing", 
        "id": "sg:person.01174702157.48", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01174702157.48"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1016/j.molcel.2010.03.016", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004413613"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature06947", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004427899", 
          "https://doi.org/10.1038/nature06947"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature09380", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004695178", 
          "https://doi.org/10.1038/nature09380"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature09380", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004695178", 
          "https://doi.org/10.1038/nature09380"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.stem.2010.03.018", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004760114"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature11049", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004787340", 
          "https://doi.org/10.1038/nature11049"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gad.2005511", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005492124"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2011.11.058", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007206139"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1181369", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007401642"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1181369", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007401642"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.1018279108", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007573614"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1139/o10-110", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009154226"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/cshperspect.a003889", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009170696"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2008.03.024", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011271340"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2009.06.001", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014398227"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng.947", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016541124", 
          "https://doi.org/10.1038/ng.947"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng.857", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017908683", 
          "https://doi.org/10.1038/ng.857"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2011.12.035", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023344056"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2012.01.010", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025469351"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.biolcel.2004.06.004", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028526676"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature09819", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029739875", 
          "https://doi.org/10.1038/nature09819"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature09819", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029739875", 
          "https://doi.org/10.1038/nature09819"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.099655.109", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034553890"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.4161/cc.10.16.17092", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039607803"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/emboj/20.3.520", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040970215"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.molcel.2010.02.032", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042040888"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng.297", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045314212", 
          "https://doi.org/10.1038/ng.297"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gad.1837309", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045357547"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.099796.109", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051206404"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2008.07.020", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051435650"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1207194", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052006741"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature11243", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053162355", 
          "https://doi.org/10.1038/nature11243"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1140871", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062455912"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1074530523", 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2012-04-11", 
    "datePublishedReg": "2012-04-11", 
    "description": "The spatial organization of the genome is intimately linked to its biological function, yet our understanding of higher order genomic structure is coarse, fragmented and incomplete. In the nucleus of eukaryotic cells, interphase chromosomes occupy distinct chromosome territories, and numerous models have been proposed for how chromosomes fold within chromosome territories. These models, however, provide only few mechanistic details about the relationship between higher order chromatin structure and genome function. Recent advances in genomic technologies have led to rapid advances in the study of three-dimensional genome organization. In particular, Hi-C has been introduced as a method for identifying higher order chromatin interactions genome wide. Here we investigate the three-dimensional organization of the human and mouse genomes in embryonic stem cells and terminally differentiated cell types at unprecedented resolution. We identify large, megabase-sized local chromatin interaction domains, which we term 'topological domains', as a pervasive structural feature of the genome organization. These domains correlate with regions of the genome that constrain the spread of heterochromatin. The domains are stable across different cell types and highly conserved across species, indicating that topological domains are an inherent property of mammalian genomes. Finally, we find that the boundaries of topological domains are enriched for the insulator binding protein CTCF, housekeeping genes, transfer RNAs and short interspersed element (SINE) retrotransposons, indicating that these factors may have a role in establishing the topological domain structure of the genome.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1038/nature11082", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.6848888", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.2529272", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1018957", 
        "issn": [
          "0090-0028", 
          "1476-4687"
        ], 
        "name": "Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "7398", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "485"
      }
    ], 
    "name": "Topological domains in mammalian genomes identified by analysis of chromatin interactions", 
    "pagination": "376", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "bfd65fc7daf810bb12f9149d04f384eb67ccd5577a386e1d29e0c058f182dc60"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "22495300"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "0410462"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/nature11082"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1040271530"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/nature11082", 
      "https://app.dimensions.ai/details/publication/pub.1040271530"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T16:49", 
    "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_8669_00000551.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://www.nature.com/articles/nature11082"
  }
]
 

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/nature11082'

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/nature11082'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nature11082'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nature11082'


 

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

315 TRIPLES      21 PREDICATES      78 URIs      39 LITERALS      28 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/nature11082 schema:about N073477895f46450ab8007d2674af5b99
2 N1dc4da731c0b452a86f4d36c71c626ef
3 N3e2f2ce1731a4658a539fdbbd303f248
4 N42354af10cf54eb6b547840efbd9231f
5 N44cf2ac2a41640a5918baa803806db27
6 N6bc5fe971311419f954002fd590d4fb6
7 N88ccfd9e7f8a4d899d861b5ba24f4b24
8 N8c70f6907028465a9c711d9e7964dea7
9 N8e5bbe711d4e41239f516306c24a9c8e
10 N8f2bee07db5c4daa8d1bdec74c07bc1a
11 N8f4b69c5ff17464e8fde6a08427860ef
12 N911cbcbab199467c87d4eedc9c7363fd
13 N932c823e2749419b9a28c2ece88eaaf9
14 N9df88520e81d47c3a72a4d4e14e270e3
15 N9f389caff230485ea114411a7312107b
16 Nc7176734e14c4f518eb4e84512d92f5d
17 Nd2447b039e534d9b84c854d29a504e28
18 Nd33c470822104d92a89cc86466869b52
19 Nf1347bc26234469dbd76a650d21fe70c
20 anzsrc-for:06
21 anzsrc-for:0604
22 schema:author N0d6827a9b9e742c6a138283740e21546
23 schema:citation sg:pub.10.1038/nature06947
24 sg:pub.10.1038/nature09380
25 sg:pub.10.1038/nature09819
26 sg:pub.10.1038/nature11049
27 sg:pub.10.1038/nature11243
28 sg:pub.10.1038/ng.297
29 sg:pub.10.1038/ng.857
30 sg:pub.10.1038/ng.947
31 https://app.dimensions.ai/details/publication/pub.1074530523
32 https://doi.org/10.1016/j.biolcel.2004.06.004
33 https://doi.org/10.1016/j.cell.2008.03.024
34 https://doi.org/10.1016/j.cell.2008.07.020
35 https://doi.org/10.1016/j.cell.2009.06.001
36 https://doi.org/10.1016/j.cell.2011.11.058
37 https://doi.org/10.1016/j.cell.2011.12.035
38 https://doi.org/10.1016/j.cell.2012.01.010
39 https://doi.org/10.1016/j.molcel.2010.02.032
40 https://doi.org/10.1016/j.molcel.2010.03.016
41 https://doi.org/10.1016/j.stem.2010.03.018
42 https://doi.org/10.1073/pnas.1018279108
43 https://doi.org/10.1093/emboj/20.3.520
44 https://doi.org/10.1101/cshperspect.a003889
45 https://doi.org/10.1101/gad.1837309
46 https://doi.org/10.1101/gad.2005511
47 https://doi.org/10.1101/gr.099655.109
48 https://doi.org/10.1101/gr.099796.109
49 https://doi.org/10.1126/science.1140871
50 https://doi.org/10.1126/science.1181369
51 https://doi.org/10.1126/science.1207194
52 https://doi.org/10.1139/o10-110
53 https://doi.org/10.4161/cc.10.16.17092
54 schema:datePublished 2012-04-11
55 schema:datePublishedReg 2012-04-11
56 schema:description The spatial organization of the genome is intimately linked to its biological function, yet our understanding of higher order genomic structure is coarse, fragmented and incomplete. In the nucleus of eukaryotic cells, interphase chromosomes occupy distinct chromosome territories, and numerous models have been proposed for how chromosomes fold within chromosome territories. These models, however, provide only few mechanistic details about the relationship between higher order chromatin structure and genome function. Recent advances in genomic technologies have led to rapid advances in the study of three-dimensional genome organization. In particular, Hi-C has been introduced as a method for identifying higher order chromatin interactions genome wide. Here we investigate the three-dimensional organization of the human and mouse genomes in embryonic stem cells and terminally differentiated cell types at unprecedented resolution. We identify large, megabase-sized local chromatin interaction domains, which we term 'topological domains', as a pervasive structural feature of the genome organization. These domains correlate with regions of the genome that constrain the spread of heterochromatin. The domains are stable across different cell types and highly conserved across species, indicating that topological domains are an inherent property of mammalian genomes. Finally, we find that the boundaries of topological domains are enriched for the insulator binding protein CTCF, housekeeping genes, transfer RNAs and short interspersed element (SINE) retrotransposons, indicating that these factors may have a role in establishing the topological domain structure of the genome.
57 schema:genre research_article
58 schema:inLanguage en
59 schema:isAccessibleForFree true
60 schema:isPartOf N8d8ed772dfc440cf90b198006a0353cc
61 Na6dec18d674944618291b4d267908867
62 sg:journal.1018957
63 schema:name Topological domains in mammalian genomes identified by analysis of chromatin interactions
64 schema:pagination 376
65 schema:productId N0536de40b8c04e0e8c332839df2446bf
66 N4593cb35aab246bd8222a9dd27634183
67 N5e647f5ad7234e35887f59b62943b015
68 N79bdd411de3e421c8791b13a3496430d
69 Nc3b8b49bbdd54a2790e50916c994540c
70 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040271530
71 https://doi.org/10.1038/nature11082
72 schema:sdDatePublished 2019-04-10T16:49
73 schema:sdLicense https://scigraph.springernature.com/explorer/license/
74 schema:sdPublisher N4a0711ddc11349e4b215fdcc6adf74e8
75 schema:url https://www.nature.com/articles/nature11082
76 sgo:license sg:explorer/license/
77 sgo:sdDataset articles
78 rdf:type schema:ScholarlyArticle
79 N0536de40b8c04e0e8c332839df2446bf schema:name dimensions_id
80 schema:value pub.1040271530
81 rdf:type schema:PropertyValue
82 N073477895f46450ab8007d2674af5b99 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
83 schema:name Genome
84 rdf:type schema:DefinedTerm
85 N0d6827a9b9e742c6a138283740e21546 rdf:first sg:person.0640665625.97
86 rdf:rest Nc7dbf0f38c6e4b7ba96c0f2135f73e33
87 N0e1b53e289a943ea925a3310c6ab3633 rdf:first sg:person.01323461765.25
88 rdf:rest Nbc8782144ded4aa49276eaad09404030
89 N1dc4da731c0b452a86f4d36c71c626ef schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
90 schema:name Embryonic Stem Cells
91 rdf:type schema:DefinedTerm
92 N27d20f67c3924008aa396302b4c69b4d rdf:first sg:person.01023276441.67
93 rdf:rest Ne9c56452e1344bc7bc5adb7b48cd21cb
94 N2857e31239a548feb82df55552702af2 rdf:first sg:person.01071342625.44
95 rdf:rest N27d20f67c3924008aa396302b4c69b4d
96 N38a0b76f96e140fcb83bad16458adb0d rdf:first sg:person.01174702157.48
97 rdf:rest rdf:nil
98 N3e2f2ce1731a4658a539fdbbd303f248 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
99 schema:name Chromatin
100 rdf:type schema:DefinedTerm
101 N42354af10cf54eb6b547840efbd9231f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
102 schema:name Repressor Proteins
103 rdf:type schema:DefinedTerm
104 N44cf2ac2a41640a5918baa803806db27 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
105 schema:name Humans
106 rdf:type schema:DefinedTerm
107 N4593cb35aab246bd8222a9dd27634183 schema:name doi
108 schema:value 10.1038/nature11082
109 rdf:type schema:PropertyValue
110 N4a0711ddc11349e4b215fdcc6adf74e8 schema:name Springer Nature - SN SciGraph project
111 rdf:type schema:Organization
112 N5e647f5ad7234e35887f59b62943b015 schema:name nlm_unique_id
113 schema:value 0410462
114 rdf:type schema:PropertyValue
115 N6bc5fe971311419f954002fd590d4fb6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
116 schema:name Genes, Essential
117 rdf:type schema:DefinedTerm
118 N79bdd411de3e421c8791b13a3496430d schema:name readcube_id
119 schema:value bfd65fc7daf810bb12f9149d04f384eb67ccd5577a386e1d29e0c058f182dc60
120 rdf:type schema:PropertyValue
121 N88ccfd9e7f8a4d899d861b5ba24f4b24 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
122 schema:name Evolution, Molecular
123 rdf:type schema:DefinedTerm
124 N8c70f6907028465a9c711d9e7964dea7 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
125 schema:name Short Interspersed Nucleotide Elements
126 rdf:type schema:DefinedTerm
127 N8d8ed772dfc440cf90b198006a0353cc schema:issueNumber 7398
128 rdf:type schema:PublicationIssue
129 N8e5bbe711d4e41239f516306c24a9c8e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
130 schema:name Chromosomes
131 rdf:type schema:DefinedTerm
132 N8f2bee07db5c4daa8d1bdec74c07bc1a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
133 schema:name Mice
134 rdf:type schema:DefinedTerm
135 N8f4b69c5ff17464e8fde6a08427860ef schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
136 schema:name Heterochromatin
137 rdf:type schema:DefinedTerm
138 N911cbcbab199467c87d4eedc9c7363fd schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
139 schema:name Cell Differentiation
140 rdf:type schema:DefinedTerm
141 N932c823e2749419b9a28c2ece88eaaf9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
142 schema:name CCCTC-Binding Factor
143 rdf:type schema:DefinedTerm
144 N9df88520e81d47c3a72a4d4e14e270e3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
145 schema:name Binding Sites
146 rdf:type schema:DefinedTerm
147 N9f389caff230485ea114411a7312107b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
148 schema:name Male
149 rdf:type schema:DefinedTerm
150 Na6dec18d674944618291b4d267908867 schema:volumeNumber 485
151 rdf:type schema:PublicationVolume
152 Nbc8782144ded4aa49276eaad09404030 rdf:first sg:person.01002667035.02
153 rdf:rest N2857e31239a548feb82df55552702af2
154 Nc3b8b49bbdd54a2790e50916c994540c schema:name pubmed_id
155 schema:value 22495300
156 rdf:type schema:PropertyValue
157 Nc7176734e14c4f518eb4e84512d92f5d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
158 schema:name RNA, Transfer
159 rdf:type schema:DefinedTerm
160 Nc7dbf0f38c6e4b7ba96c0f2135f73e33 rdf:first sg:person.01123352652.14
161 rdf:rest N0e1b53e289a943ea925a3310c6ab3633
162 Nd2447b039e534d9b84c854d29a504e28 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
163 schema:name Mammals
164 rdf:type schema:DefinedTerm
165 Nd33c470822104d92a89cc86466869b52 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
166 schema:name Animals
167 rdf:type schema:DefinedTerm
168 Ne3a1d871d83549c39f953f18a8c05a7c rdf:first sg:person.01306627540.69
169 rdf:rest N38a0b76f96e140fcb83bad16458adb0d
170 Ne9c56452e1344bc7bc5adb7b48cd21cb rdf:first sg:person.01351361054.30
171 rdf:rest Ne3a1d871d83549c39f953f18a8c05a7c
172 Nf1347bc26234469dbd76a650d21fe70c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
173 schema:name Female
174 rdf:type schema:DefinedTerm
175 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
176 schema:name Biological Sciences
177 rdf:type schema:DefinedTerm
178 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
179 schema:name Genetics
180 rdf:type schema:DefinedTerm
181 sg:grant.2529272 http://pending.schema.org/fundedItem sg:pub.10.1038/nature11082
182 rdf:type schema:MonetaryGrant
183 sg:grant.6848888 http://pending.schema.org/fundedItem sg:pub.10.1038/nature11082
184 rdf:type schema:MonetaryGrant
185 sg:journal.1018957 schema:issn 0090-0028
186 1476-4687
187 schema:name Nature
188 rdf:type schema:Periodical
189 sg:person.01002667035.02 schema:affiliation https://www.grid.ac/institutes/grid.1052.6
190 schema:familyName Kim
191 schema:givenName Audrey
192 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01002667035.02
193 rdf:type schema:Person
194 sg:person.01023276441.67 schema:affiliation https://www.grid.ac/institutes/grid.1052.6
195 schema:familyName Shen
196 schema:givenName Yin
197 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01023276441.67
198 rdf:type schema:Person
199 sg:person.01071342625.44 schema:affiliation https://www.grid.ac/institutes/grid.1052.6
200 schema:familyName Li
201 schema:givenName Yan
202 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01071342625.44
203 rdf:type schema:Person
204 sg:person.01123352652.14 schema:affiliation https://www.grid.ac/institutes/grid.266100.3
205 schema:familyName Selvaraj
206 schema:givenName Siddarth
207 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01123352652.14
208 rdf:type schema:Person
209 sg:person.01174702157.48 schema:affiliation https://www.grid.ac/institutes/grid.1052.6
210 schema:familyName Ren
211 schema:givenName Bing
212 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01174702157.48
213 rdf:type schema:Person
214 sg:person.01306627540.69 schema:affiliation https://www.grid.ac/institutes/grid.38142.3c
215 schema:familyName Liu
216 schema:givenName Jun S.
217 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01306627540.69
218 rdf:type schema:Person
219 sg:person.01323461765.25 schema:affiliation https://www.grid.ac/institutes/grid.1052.6
220 schema:familyName Yue
221 schema:givenName Feng
222 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01323461765.25
223 rdf:type schema:Person
224 sg:person.01351361054.30 schema:affiliation https://www.grid.ac/institutes/grid.38142.3c
225 schema:familyName Hu
226 schema:givenName Ming
227 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01351361054.30
228 rdf:type schema:Person
229 sg:person.0640665625.97 schema:affiliation https://www.grid.ac/institutes/grid.266100.3
230 schema:familyName Dixon
231 schema:givenName Jesse R.
232 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0640665625.97
233 rdf:type schema:Person
234 sg:pub.10.1038/nature06947 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004427899
235 https://doi.org/10.1038/nature06947
236 rdf:type schema:CreativeWork
237 sg:pub.10.1038/nature09380 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004695178
238 https://doi.org/10.1038/nature09380
239 rdf:type schema:CreativeWork
240 sg:pub.10.1038/nature09819 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029739875
241 https://doi.org/10.1038/nature09819
242 rdf:type schema:CreativeWork
243 sg:pub.10.1038/nature11049 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004787340
244 https://doi.org/10.1038/nature11049
245 rdf:type schema:CreativeWork
246 sg:pub.10.1038/nature11243 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053162355
247 https://doi.org/10.1038/nature11243
248 rdf:type schema:CreativeWork
249 sg:pub.10.1038/ng.297 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045314212
250 https://doi.org/10.1038/ng.297
251 rdf:type schema:CreativeWork
252 sg:pub.10.1038/ng.857 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017908683
253 https://doi.org/10.1038/ng.857
254 rdf:type schema:CreativeWork
255 sg:pub.10.1038/ng.947 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016541124
256 https://doi.org/10.1038/ng.947
257 rdf:type schema:CreativeWork
258 https://app.dimensions.ai/details/publication/pub.1074530523 schema:CreativeWork
259 https://doi.org/10.1016/j.biolcel.2004.06.004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028526676
260 rdf:type schema:CreativeWork
261 https://doi.org/10.1016/j.cell.2008.03.024 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011271340
262 rdf:type schema:CreativeWork
263 https://doi.org/10.1016/j.cell.2008.07.020 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051435650
264 rdf:type schema:CreativeWork
265 https://doi.org/10.1016/j.cell.2009.06.001 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014398227
266 rdf:type schema:CreativeWork
267 https://doi.org/10.1016/j.cell.2011.11.058 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007206139
268 rdf:type schema:CreativeWork
269 https://doi.org/10.1016/j.cell.2011.12.035 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023344056
270 rdf:type schema:CreativeWork
271 https://doi.org/10.1016/j.cell.2012.01.010 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025469351
272 rdf:type schema:CreativeWork
273 https://doi.org/10.1016/j.molcel.2010.02.032 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042040888
274 rdf:type schema:CreativeWork
275 https://doi.org/10.1016/j.molcel.2010.03.016 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004413613
276 rdf:type schema:CreativeWork
277 https://doi.org/10.1016/j.stem.2010.03.018 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004760114
278 rdf:type schema:CreativeWork
279 https://doi.org/10.1073/pnas.1018279108 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007573614
280 rdf:type schema:CreativeWork
281 https://doi.org/10.1093/emboj/20.3.520 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040970215
282 rdf:type schema:CreativeWork
283 https://doi.org/10.1101/cshperspect.a003889 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009170696
284 rdf:type schema:CreativeWork
285 https://doi.org/10.1101/gad.1837309 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045357547
286 rdf:type schema:CreativeWork
287 https://doi.org/10.1101/gad.2005511 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005492124
288 rdf:type schema:CreativeWork
289 https://doi.org/10.1101/gr.099655.109 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034553890
290 rdf:type schema:CreativeWork
291 https://doi.org/10.1101/gr.099796.109 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051206404
292 rdf:type schema:CreativeWork
293 https://doi.org/10.1126/science.1140871 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062455912
294 rdf:type schema:CreativeWork
295 https://doi.org/10.1126/science.1181369 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007401642
296 rdf:type schema:CreativeWork
297 https://doi.org/10.1126/science.1207194 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052006741
298 rdf:type schema:CreativeWork
299 https://doi.org/10.1139/o10-110 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009154226
300 rdf:type schema:CreativeWork
301 https://doi.org/10.4161/cc.10.16.17092 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039607803
302 rdf:type schema:CreativeWork
303 https://www.grid.ac/institutes/grid.1052.6 schema:alternateName Ludwig Cancer Research
304 schema:name Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA
305 University of California, San Diego School of Medicine, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, UCSD Moores Cancer Center, 9500 Gilman Drive, La Jolla, California 92093, USA
306 rdf:type schema:Organization
307 https://www.grid.ac/institutes/grid.266100.3 schema:alternateName University of California, San Diego
308 schema:name Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California 92093, USA
309 Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California 92093, USA
310 Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA
311 Medical Scientist Training Program, University of California, San Diego, La Jolla, California 92093, USA
312 rdf:type schema:Organization
313 https://www.grid.ac/institutes/grid.38142.3c schema:alternateName Harvard University
314 schema:name Department of Statistics, Harvard University, 1 Oxford Street, Cambridge, Massachusetts 02138, USA
315 rdf:type schema:Organization
 




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


...