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An oestrogen-receptor-alpha-bound human chromatin interactome.

Nature | Nov 5, 2009

Genomes are organized into high-level three-dimensional structures, and DNA elements separated by long genomic distances can in principle interact functionally. Many transcription factors bind to regulatory DNA elements distant from gene promoters. Although distal binding sites have been shown to regulate transcription by long-range chromatin interactions at a few loci, chromatin interactions and their impact on transcription regulation have not been investigated in a genome-wide manner. Here we describe the development of a new strategy, chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) for the de novo detection of global chromatin interactions, with which we have comprehensively mapped the chromatin interaction network bound by oestrogen receptor alpha (ER-alpha) in the human genome. We found that most high-confidence remote ER-alpha-binding sites are anchored at gene promoters through long-range chromatin interactions, suggesting that ER-alpha functions by extensive chromatin looping to bring genes together for coordinated transcriptional regulation. We propose that chromatin interactions constitute a primary mechanism for regulating transcription in mammalian genomes.

Pubmed ID: 19890323 RIS Download

Mesh terms: Binding Sites | Cell Line | Chromatin | Chromatin Immunoprecipitation | Cross-Linking Reagents | Estrogen Receptor alpha | Formaldehyde | Genome, Human | Humans | Promoter Regions, Genetic | Protein Binding | Reproducibility of Results | Sequence Analysis, DNA | Transcription, Genetic | Transcriptional Activation

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Associated grants

  • Agency: NHGRI NIH HHS, Id: U54 HG004557-04
  • Agency: NHGRI NIH HHS, Id: U54 HG004557-03
  • Agency: NHGRI NIH HHS, Id: R01 HG004456-03
  • Agency: NHGRI NIH HHS, Id: U54 HG004557-02
  • Agency: NHGRI NIH HHS, Id: R01 HG003521
  • Agency: NHGRI NIH HHS, Id: R01HG003521-01
  • Agency: NHGRI NIH HHS, Id: U54 HG004557
  • Agency: NHGRI NIH HHS, Id: R01HG004456-01
  • Agency: NHGRI NIH HHS, Id: U54 HG004557-01
  • Agency: NHGRI NIH HHS, Id: 1U54HG004557-01
  • Agency: NHGRI NIH HHS, Id: R01 HG004456-01
  • Agency: NHGRI NIH HHS, Id: R01 HG004456-02
  • Agency: NHGRI NIH HHS, Id: R01 HG004456

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