Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C) View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2006-11

AUTHORS

Marieke Simonis, Petra Klous, Erik Splinter, Yuri Moshkin, Rob Willemsen, Elzo de Wit, Bas van Steensel, Wouter de Laat

ABSTRACT

The spatial organization of DNA in the cell nucleus is an emerging key contributor to genomic function. We developed 4C technology (chromosome conformation capture (3C)-on-chip), which allows for an unbiased genome-wide search for DNA loci that contact a given locus in the nuclear space. We demonstrate here that active and inactive genes are engaged in many long-range intrachromosomal interactions and can also form interchromosomal contacts. The active beta-globin locus in fetal liver preferentially contacts transcribed, but not necessarily tissue-specific, loci elsewhere on chromosome 7, whereas the inactive locus in fetal brain contacts different transcriptionally silent loci. A housekeeping gene in a gene-dense region on chromosome 8 forms long-range contacts predominantly with other active gene clusters, both in cis and in trans, and many of these intra- and interchromosomal interactions are conserved between the tissues analyzed. Our data demonstrate that chromosomes fold into areas of active chromatin and areas of inactive chromatin and establish 4C technology as a powerful tool to study nuclear architecture. More... »

PAGES

1348-1354

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/ng1896

DOI

http://dx.doi.org/10.1038/ng1896

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1003840508

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/17033623


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": "Brain", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Cell Nucleus", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Chromatin", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Chromatin Assembly and Disassembly", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Chromosome Mapping", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Chromosomes, Mammalian", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA-Binding Proteins", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Expression Regulation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Globins", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "In Situ Hybridization, Fluorescence", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Liver", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Mice", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Models, Biological", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Nucleic Acid Conformation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Oligonucleotide Array Sequence Analysis", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Erasmus University Medical Center", 
          "id": "https://www.grid.ac/institutes/grid.5645.2", 
          "name": [
            "Department of Cell Biology and Genetics, Erasmus Medical Centre, PO Box 2040, 3000 CA Rotterdam, The Netherlands."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Simonis", 
        "givenName": "Marieke", 
        "id": "sg:person.0605361744.29", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0605361744.29"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Erasmus University Medical Center", 
          "id": "https://www.grid.ac/institutes/grid.5645.2", 
          "name": [
            "Department of Cell Biology and Genetics, Erasmus Medical Centre, PO Box 2040, 3000 CA Rotterdam, The Netherlands."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Klous", 
        "givenName": "Petra", 
        "id": "sg:person.0720232345.05", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0720232345.05"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Erasmus University Medical Center", 
          "id": "https://www.grid.ac/institutes/grid.5645.2", 
          "name": [
            "Department of Cell Biology and Genetics, Erasmus Medical Centre, PO Box 2040, 3000 CA Rotterdam, The Netherlands."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Splinter", 
        "givenName": "Erik", 
        "id": "sg:person.0712325005.14", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0712325005.14"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Erasmus University Medical Center", 
          "id": "https://www.grid.ac/institutes/grid.5645.2", 
          "name": [
            "Department of Biochemistry, Erasmus Medical Centre, PO Box 2040, 3000 CA Rotterdam, The Netherlands."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Moshkin", 
        "givenName": "Yuri", 
        "id": "sg:person.0774232717.13", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0774232717.13"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Erasmus University Medical Center", 
          "id": "https://www.grid.ac/institutes/grid.5645.2", 
          "name": [
            "Department of Clinical Genetics, Erasmus Medical Centre, PO Box 2040, 3000 CA Rotterdam, The Netherlands."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Willemsen", 
        "givenName": "Rob", 
        "id": "sg:person.01031667437.50", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01031667437.50"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Antoni van Leeuwenhoek Hospital", 
          "id": "https://www.grid.ac/institutes/grid.430814.a", 
          "name": [
            "Division of Molecular Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands."
          ], 
          "type": "Organization"
        }, 
        "familyName": "de Wit", 
        "givenName": "Elzo", 
        "id": "sg:person.01173243361.71", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01173243361.71"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Antoni van Leeuwenhoek Hospital", 
          "id": "https://www.grid.ac/institutes/grid.430814.a", 
          "name": [
            "Division of Molecular Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands."
          ], 
          "type": "Organization"
        }, 
        "familyName": "van Steensel", 
        "givenName": "Bas", 
        "id": "sg:person.01176344257.88", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01176344257.88"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Erasmus University Medical Center", 
          "id": "https://www.grid.ac/institutes/grid.5645.2", 
          "name": [
            "Department of Cell Biology and Genetics, Erasmus Medical Centre, PO Box 2040, 3000 CA Rotterdam, The Netherlands."
          ], 
          "type": "Organization"
        }, 
        "familyName": "de Laat", 
        "givenName": "Wouter", 
        "id": "sg:person.01355306151.09", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01355306151.09"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1016/s0076-6879(03)75030-7", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000517339"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2005.08.045", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001592744"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gad.292104", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002405627"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrg1673", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002484013", 
          "https://doi.org/10.1038/nrg1673"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrg1673", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002484013", 
          "https://doi.org/10.1038/nrg1673"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrg1673", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002484013", 
          "https://doi.org/10.1038/nrg1673"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1083/jcb.200507073", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005057417"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng1423", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013569568", 
          "https://doi.org/10.1038/ng1423"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng1423", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013569568", 
          "https://doi.org/10.1038/ng1423"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature03574", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020949401", 
          "https://doi.org/10.1038/nature03574"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature03574", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020949401", 
          "https://doi.org/10.1038/nature03574"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature03574", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020949401", 
          "https://doi.org/10.1038/nature03574"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1067799", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021591890"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s1074-7613(01)00103-0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026445873"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pbio.0040138", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026789123"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1123191", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026843212"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s10577-006-1075-0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028074491", 
          "https://doi.org/10.1007/s10577-006-1075-0"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s10577-006-1075-0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028074491", 
          "https://doi.org/10.1007/s10577-006-1075-0"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/bies.20226", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033755396"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0968-0004(00)89117-3", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040960868"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2006.06.035", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043250877"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1159/000084979", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044099907"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1159/000084979", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044099907"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrg1688", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045156533", 
          "https://doi.org/10.1038/nrg1688"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrg1688", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045156533", 
          "https://doi.org/10.1038/nrg1688"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0092-8674(00)80472-9", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051991361"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng1177", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053023169", 
          "https://doi.org/10.1038/ng1177"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng1177", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053023169", 
          "https://doi.org/10.1038/ng1177"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1089/10665270050081478", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1059204834"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1126689", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062453725"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1074618044", 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2006-11", 
    "datePublishedReg": "2006-11-01", 
    "description": "The spatial organization of DNA in the cell nucleus is an emerging key contributor to genomic function. We developed 4C technology (chromosome conformation capture (3C)-on-chip), which allows for an unbiased genome-wide search for DNA loci that contact a given locus in the nuclear space. We demonstrate here that active and inactive genes are engaged in many long-range intrachromosomal interactions and can also form interchromosomal contacts. The active beta-globin locus in fetal liver preferentially contacts transcribed, but not necessarily tissue-specific, loci elsewhere on chromosome 7, whereas the inactive locus in fetal brain contacts different transcriptionally silent loci. A housekeeping gene in a gene-dense region on chromosome 8 forms long-range contacts predominantly with other active gene clusters, both in cis and in trans, and many of these intra- and interchromosomal interactions are conserved between the tissues analyzed. Our data demonstrate that chromosomes fold into areas of active chromatin and areas of inactive chromatin and establish 4C technology as a powerful tool to study nuclear architecture.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1038/ng1896", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": false, 
    "isPartOf": [
      {
        "id": "sg:journal.1103138", 
        "issn": [
          "1061-4036", 
          "1546-1718"
        ], 
        "name": "Nature Genetics", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "11", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "38"
      }
    ], 
    "name": "Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture\u2013on-chip (4C)", 
    "pagination": "1348-1354", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "124c047a734e45ff1375b4a250907c762965efd837c9660bb2cc79d4edf266e6"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "17033623"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "9216904"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/ng1896"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1003840508"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/ng1896", 
      "https://app.dimensions.ai/details/publication/pub.1003840508"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-11T12:25", 
    "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/v90/0000000362_0000000362/records_87109_00000000.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://www.nature.com/articles/ng1896"
  }
]
 

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/ng1896'

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/ng1896'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/ng1896'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/ng1896'


 

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

258 TRIPLES      21 PREDICATES      67 URIs      37 LITERALS      25 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/ng1896 schema:about N041f59e1d39348cab161e7d5a1ce3ba1
2 N0671c202c16d463fb6c5873fefd77f26
3 N098cec6de5f84fd789bc45742dbb69b7
4 N0d7097aa1b1744cd8fd25ec1d71da665
5 N275f39f44b1744d8be64d301f8980e32
6 N2ff6a4374be9474692895bcba780f215
7 N3b8a39642fd24cf0a866efb74cc92633
8 N548e5edc2a5a4d3f8bde238329e6231b
9 N5b72467772c24152812712c413802a0a
10 N74a1b8bae8b44943aa6c542e9d2af5c5
11 N907dc359b54a41ee98eff3d80e8019d5
12 N95b3cf231195485c888e280e3230693d
13 N98215da251f14880b8a93b0588b82cdc
14 Na3f77bb52a16493a985a1289b51ed2c9
15 Ne950900942c74ef492dd1c126fe66623
16 Nfcb770c95561401b9416569122abbf4b
17 anzsrc-for:06
18 anzsrc-for:0604
19 schema:author Nb610f10a925644dbb8481a3ccdab07a7
20 schema:citation sg:pub.10.1007/s10577-006-1075-0
21 sg:pub.10.1038/nature03574
22 sg:pub.10.1038/ng1177
23 sg:pub.10.1038/ng1423
24 sg:pub.10.1038/nrg1673
25 sg:pub.10.1038/nrg1688
26 https://app.dimensions.ai/details/publication/pub.1074618044
27 https://doi.org/10.1002/bies.20226
28 https://doi.org/10.1016/j.cell.2005.08.045
29 https://doi.org/10.1016/j.cell.2006.06.035
30 https://doi.org/10.1016/s0076-6879(03)75030-7
31 https://doi.org/10.1016/s0092-8674(00)80472-9
32 https://doi.org/10.1016/s0968-0004(00)89117-3
33 https://doi.org/10.1016/s1074-7613(01)00103-0
34 https://doi.org/10.1083/jcb.200507073
35 https://doi.org/10.1089/10665270050081478
36 https://doi.org/10.1101/gad.292104
37 https://doi.org/10.1126/science.1067799
38 https://doi.org/10.1126/science.1123191
39 https://doi.org/10.1126/science.1126689
40 https://doi.org/10.1159/000084979
41 https://doi.org/10.1371/journal.pbio.0040138
42 schema:datePublished 2006-11
43 schema:datePublishedReg 2006-11-01
44 schema:description The spatial organization of DNA in the cell nucleus is an emerging key contributor to genomic function. We developed 4C technology (chromosome conformation capture (3C)-on-chip), which allows for an unbiased genome-wide search for DNA loci that contact a given locus in the nuclear space. We demonstrate here that active and inactive genes are engaged in many long-range intrachromosomal interactions and can also form interchromosomal contacts. The active beta-globin locus in fetal liver preferentially contacts transcribed, but not necessarily tissue-specific, loci elsewhere on chromosome 7, whereas the inactive locus in fetal brain contacts different transcriptionally silent loci. A housekeeping gene in a gene-dense region on chromosome 8 forms long-range contacts predominantly with other active gene clusters, both in cis and in trans, and many of these intra- and interchromosomal interactions are conserved between the tissues analyzed. Our data demonstrate that chromosomes fold into areas of active chromatin and areas of inactive chromatin and establish 4C technology as a powerful tool to study nuclear architecture.
45 schema:genre research_article
46 schema:inLanguage en
47 schema:isAccessibleForFree false
48 schema:isPartOf N102f33cb9dde444ca85bde7d1ee6984e
49 Ncc93640e95984949b7313e5c1a4c6325
50 sg:journal.1103138
51 schema:name Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C)
52 schema:pagination 1348-1354
53 schema:productId N67a2430a297b460ca81b535b7e948e47
54 N88dd9bd0bad04a5db000b3465470d34e
55 Nb8342634ca6f4111bbc07283833b1f4f
56 Ncddcad08859f42ea97c85b0bd58dc66a
57 Nec6bcabd73974b61bc3ac0be2a752c78
58 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003840508
59 https://doi.org/10.1038/ng1896
60 schema:sdDatePublished 2019-04-11T12:25
61 schema:sdLicense https://scigraph.springernature.com/explorer/license/
62 schema:sdPublisher N3cc0f6573d1149468b8a152a83da3cd6
63 schema:url http://www.nature.com/articles/ng1896
64 sgo:license sg:explorer/license/
65 sgo:sdDataset articles
66 rdf:type schema:ScholarlyArticle
67 N041f59e1d39348cab161e7d5a1ce3ba1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
68 schema:name Oligonucleotide Array Sequence Analysis
69 rdf:type schema:DefinedTerm
70 N0671c202c16d463fb6c5873fefd77f26 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
71 schema:name Liver
72 rdf:type schema:DefinedTerm
73 N098cec6de5f84fd789bc45742dbb69b7 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
74 schema:name Cell Nucleus
75 rdf:type schema:DefinedTerm
76 N0d7097aa1b1744cd8fd25ec1d71da665 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
77 schema:name Chromosome Mapping
78 rdf:type schema:DefinedTerm
79 N102f33cb9dde444ca85bde7d1ee6984e schema:issueNumber 11
80 rdf:type schema:PublicationIssue
81 N149fba29d8904a70949abdb268d11393 rdf:first sg:person.0712325005.14
82 rdf:rest Neaf39d356cb948f2bdd4f840c4def633
83 N1a128aa96ac34218833b139675d21c22 rdf:first sg:person.01173243361.71
84 rdf:rest N2e46a79688c840dd8b165b30fb785488
85 N275f39f44b1744d8be64d301f8980e32 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
86 schema:name Gene Expression Regulation
87 rdf:type schema:DefinedTerm
88 N2e46a79688c840dd8b165b30fb785488 rdf:first sg:person.01176344257.88
89 rdf:rest Nac4e6e57c2264c2ea495523045dbd446
90 N2ff6a4374be9474692895bcba780f215 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
91 schema:name Animals
92 rdf:type schema:DefinedTerm
93 N3b8a39642fd24cf0a866efb74cc92633 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
94 schema:name Chromosomes, Mammalian
95 rdf:type schema:DefinedTerm
96 N3cc0f6573d1149468b8a152a83da3cd6 schema:name Springer Nature - SN SciGraph project
97 rdf:type schema:Organization
98 N548e5edc2a5a4d3f8bde238329e6231b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
99 schema:name In Situ Hybridization, Fluorescence
100 rdf:type schema:DefinedTerm
101 N5b72467772c24152812712c413802a0a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
102 schema:name Models, Biological
103 rdf:type schema:DefinedTerm
104 N67a2430a297b460ca81b535b7e948e47 schema:name pubmed_id
105 schema:value 17033623
106 rdf:type schema:PropertyValue
107 N74a1b8bae8b44943aa6c542e9d2af5c5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
108 schema:name Mice
109 rdf:type schema:DefinedTerm
110 N88c208efd06d4553962daf5839d205d6 rdf:first sg:person.0720232345.05
111 rdf:rest N149fba29d8904a70949abdb268d11393
112 N88dd9bd0bad04a5db000b3465470d34e schema:name readcube_id
113 schema:value 124c047a734e45ff1375b4a250907c762965efd837c9660bb2cc79d4edf266e6
114 rdf:type schema:PropertyValue
115 N907dc359b54a41ee98eff3d80e8019d5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
116 schema:name DNA-Binding Proteins
117 rdf:type schema:DefinedTerm
118 N95b3cf231195485c888e280e3230693d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
119 schema:name Globins
120 rdf:type schema:DefinedTerm
121 N98215da251f14880b8a93b0588b82cdc schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
122 schema:name Nucleic Acid Conformation
123 rdf:type schema:DefinedTerm
124 Na3f77bb52a16493a985a1289b51ed2c9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
125 schema:name Chromatin
126 rdf:type schema:DefinedTerm
127 Nac4e6e57c2264c2ea495523045dbd446 rdf:first sg:person.01355306151.09
128 rdf:rest rdf:nil
129 Nb610f10a925644dbb8481a3ccdab07a7 rdf:first sg:person.0605361744.29
130 rdf:rest N88c208efd06d4553962daf5839d205d6
131 Nb8342634ca6f4111bbc07283833b1f4f schema:name nlm_unique_id
132 schema:value 9216904
133 rdf:type schema:PropertyValue
134 Ncc93640e95984949b7313e5c1a4c6325 schema:volumeNumber 38
135 rdf:type schema:PublicationVolume
136 Ncddcad08859f42ea97c85b0bd58dc66a schema:name doi
137 schema:value 10.1038/ng1896
138 rdf:type schema:PropertyValue
139 Ne950900942c74ef492dd1c126fe66623 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
140 schema:name Brain
141 rdf:type schema:DefinedTerm
142 Neaf39d356cb948f2bdd4f840c4def633 rdf:first sg:person.0774232717.13
143 rdf:rest Nfd97407137964c95844e4e364b3b6c5a
144 Nec6bcabd73974b61bc3ac0be2a752c78 schema:name dimensions_id
145 schema:value pub.1003840508
146 rdf:type schema:PropertyValue
147 Nfcb770c95561401b9416569122abbf4b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
148 schema:name Chromatin Assembly and Disassembly
149 rdf:type schema:DefinedTerm
150 Nfd97407137964c95844e4e364b3b6c5a rdf:first sg:person.01031667437.50
151 rdf:rest N1a128aa96ac34218833b139675d21c22
152 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
153 schema:name Biological Sciences
154 rdf:type schema:DefinedTerm
155 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
156 schema:name Genetics
157 rdf:type schema:DefinedTerm
158 sg:journal.1103138 schema:issn 1061-4036
159 1546-1718
160 schema:name Nature Genetics
161 rdf:type schema:Periodical
162 sg:person.01031667437.50 schema:affiliation https://www.grid.ac/institutes/grid.5645.2
163 schema:familyName Willemsen
164 schema:givenName Rob
165 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01031667437.50
166 rdf:type schema:Person
167 sg:person.01173243361.71 schema:affiliation https://www.grid.ac/institutes/grid.430814.a
168 schema:familyName de Wit
169 schema:givenName Elzo
170 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01173243361.71
171 rdf:type schema:Person
172 sg:person.01176344257.88 schema:affiliation https://www.grid.ac/institutes/grid.430814.a
173 schema:familyName van Steensel
174 schema:givenName Bas
175 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01176344257.88
176 rdf:type schema:Person
177 sg:person.01355306151.09 schema:affiliation https://www.grid.ac/institutes/grid.5645.2
178 schema:familyName de Laat
179 schema:givenName Wouter
180 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01355306151.09
181 rdf:type schema:Person
182 sg:person.0605361744.29 schema:affiliation https://www.grid.ac/institutes/grid.5645.2
183 schema:familyName Simonis
184 schema:givenName Marieke
185 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0605361744.29
186 rdf:type schema:Person
187 sg:person.0712325005.14 schema:affiliation https://www.grid.ac/institutes/grid.5645.2
188 schema:familyName Splinter
189 schema:givenName Erik
190 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0712325005.14
191 rdf:type schema:Person
192 sg:person.0720232345.05 schema:affiliation https://www.grid.ac/institutes/grid.5645.2
193 schema:familyName Klous
194 schema:givenName Petra
195 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0720232345.05
196 rdf:type schema:Person
197 sg:person.0774232717.13 schema:affiliation https://www.grid.ac/institutes/grid.5645.2
198 schema:familyName Moshkin
199 schema:givenName Yuri
200 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0774232717.13
201 rdf:type schema:Person
202 sg:pub.10.1007/s10577-006-1075-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028074491
203 https://doi.org/10.1007/s10577-006-1075-0
204 rdf:type schema:CreativeWork
205 sg:pub.10.1038/nature03574 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020949401
206 https://doi.org/10.1038/nature03574
207 rdf:type schema:CreativeWork
208 sg:pub.10.1038/ng1177 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053023169
209 https://doi.org/10.1038/ng1177
210 rdf:type schema:CreativeWork
211 sg:pub.10.1038/ng1423 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013569568
212 https://doi.org/10.1038/ng1423
213 rdf:type schema:CreativeWork
214 sg:pub.10.1038/nrg1673 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002484013
215 https://doi.org/10.1038/nrg1673
216 rdf:type schema:CreativeWork
217 sg:pub.10.1038/nrg1688 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045156533
218 https://doi.org/10.1038/nrg1688
219 rdf:type schema:CreativeWork
220 https://app.dimensions.ai/details/publication/pub.1074618044 schema:CreativeWork
221 https://doi.org/10.1002/bies.20226 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033755396
222 rdf:type schema:CreativeWork
223 https://doi.org/10.1016/j.cell.2005.08.045 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001592744
224 rdf:type schema:CreativeWork
225 https://doi.org/10.1016/j.cell.2006.06.035 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043250877
226 rdf:type schema:CreativeWork
227 https://doi.org/10.1016/s0076-6879(03)75030-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000517339
228 rdf:type schema:CreativeWork
229 https://doi.org/10.1016/s0092-8674(00)80472-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051991361
230 rdf:type schema:CreativeWork
231 https://doi.org/10.1016/s0968-0004(00)89117-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040960868
232 rdf:type schema:CreativeWork
233 https://doi.org/10.1016/s1074-7613(01)00103-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026445873
234 rdf:type schema:CreativeWork
235 https://doi.org/10.1083/jcb.200507073 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005057417
236 rdf:type schema:CreativeWork
237 https://doi.org/10.1089/10665270050081478 schema:sameAs https://app.dimensions.ai/details/publication/pub.1059204834
238 rdf:type schema:CreativeWork
239 https://doi.org/10.1101/gad.292104 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002405627
240 rdf:type schema:CreativeWork
241 https://doi.org/10.1126/science.1067799 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021591890
242 rdf:type schema:CreativeWork
243 https://doi.org/10.1126/science.1123191 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026843212
244 rdf:type schema:CreativeWork
245 https://doi.org/10.1126/science.1126689 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062453725
246 rdf:type schema:CreativeWork
247 https://doi.org/10.1159/000084979 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044099907
248 rdf:type schema:CreativeWork
249 https://doi.org/10.1371/journal.pbio.0040138 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026789123
250 rdf:type schema:CreativeWork
251 https://www.grid.ac/institutes/grid.430814.a schema:alternateName Antoni van Leeuwenhoek Hospital
252 schema:name Division of Molecular Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
253 rdf:type schema:Organization
254 https://www.grid.ac/institutes/grid.5645.2 schema:alternateName Erasmus University Medical Center
255 schema:name Department of Biochemistry, Erasmus Medical Centre, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
256 Department of Cell Biology and Genetics, Erasmus Medical Centre, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
257 Department of Clinical Genetics, Erasmus Medical Centre, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
258 rdf:type schema:Organization
 




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


...