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An oestrogen-receptor-α-bound human chromatin interactome


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 α (ER-α) in the human genome. We found that most high-confidence remote ER-α-binding sites are anchored at gene promoters through long-range chromatin interactions, suggesting that ER-α 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.

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Figure 1: ChIA-PET method with validations.
Figure 2: ER-αBS reproducibility and association with chromatin interactions.
Figure 3: Association of ER-α-bound chromatin interactions with functional marks.
Figure 4: Proposed ER-α-bound chromatin interaction and transcription regulation mechanism.
Figure 5: ER-α-bound chromatin interactions are required for transcription activation.

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Gene Expression Omnibus

Data deposits

The data in the ChIA-PET libraries have been deposited in NCBI’s Gene Expression Omnibus and are accessible through GEO Series accession number GSE18046.


  1. Fraser, P. Transcriptional control thrown for a loop. Curr. Opin. Genet. Dev. 16, 490–495 (2006)

    Article  CAS  Google Scholar 

  2. Collas, P. & Dahl, J. A. Chop it, ChIP it, check it: the current status of chromatin immunoprecipitation. Front. Biosci. 13, 929–943 (2008)

    Article  CAS  Google Scholar 

  3. Wei, C. L. et al. A global map of p53 transcription-factor binding sites in the human genome. Cell 124, 207–219 (2006)

    Article  CAS  Google Scholar 

  4. Wold, B. & Myers, R. M. Sequence census methods for functional genomics. Nature Methods 5, 19–21 (2008)

    Article  CAS  Google Scholar 

  5. Massie, C. E. & Mills, I. G. ChIPping away at gene regulation. EMBO Rep. 9, 337–343 (2008)

    Article  CAS  Google Scholar 

  6. Carroll, J. S. et al. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell 122, 33–43 (2005)

    Article  CAS  Google Scholar 

  7. Carroll, J. S. et al. Genome-wide analysis of estrogen receptor binding sites. Nature Genet. 38, 1289–1297 (2006)

    Article  CAS  Google Scholar 

  8. Lin, C. Y. et al. Whole-genome cartography of estrogen receptor α binding sites. PLoS Genet. 3, e87 (2007)

    Article  Google Scholar 

  9. Lupien, M. et al. FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell 132, 958–970 (2008)

    Article  CAS  Google Scholar 

  10. Welboren, W. J. et al. ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands. EMBO J. 28, 1418–1428 (2009)

    Article  CAS  Google Scholar 

  11. West, A. G. & Fraser, P. Remote control of gene transcription. Hum. Mol. Genet. 14 (Review Issue 1) R101–R111 (2005)

  12. Woodcock, C. L. Chromatin architecture. Curr. Opin. Struct. Biol. 16, 213–220 (2006)

    Article  CAS  Google Scholar 

  13. Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. Capturing chromosome conformation. Science 295, 1306–1311 (2002)

    Article  CAS  ADS  Google Scholar 

  14. Hagege, H. et al. Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nature Protocols 2, 1722–1733 (2007)

    Article  CAS  Google Scholar 

  15. Horike, S., Cai, S., Miyano, M., Cheng, J. F. & Kohwi-Shigematsu, T. Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome. Nature Genet. 37, 31–40 (2005)

    Article  CAS  Google Scholar 

  16. Cai, S., Lee, C. C. & Kohwi-Shigematsu, T. SATB1 packages densely looped, transcriptionally active chromatin for coordinated expression of cytokine genes. Nature Genet. 38, 1278–1288 (2006)

    Article  CAS  Google Scholar 

  17. Zhao, Z. et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nature Genet. 38, 1341–1347 (2006)

    Article  CAS  Google Scholar 

  18. Ling, J. Q. et al. CTCF mediates interchromosomal colocalization between Igf2/H19 and Wsb1/Nf1. Science 312, 269–272 (2006)

    Article  CAS  ADS  Google Scholar 

  19. Simonis, M. et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nature Genet. 38, 1348–1354 (2006)

    Article  CAS  Google Scholar 

  20. Wurtele, H. & Chartrand, P. Genome-wide scanning of HoxB1-associated loci in mouse ES cells using an open-ended Chromosome Conformation Capture methodology. Chromosome Res. 14, 477–495 (2006)

    Article  Google Scholar 

  21. Dostie, J. et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 16, 1299–1309 (2006)

    Article  CAS  Google Scholar 

  22. Tiwari, V. K., Cope, L., McGarvey, K. M., Ohm, J. E. & Baylin, S. B. A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations. Genome Res. 18, 1171–1179 (2008)

    Article  CAS  Google Scholar 

  23. Carter, D., Chakalova, L., Osborne, C. S., Dai, Y. F. & Fraser, P. Long-range chromatin regulatory interactions in vivo . Nature Genet. 32, 623–626 (2002)

    Article  CAS  Google Scholar 

  24. Osborne, C. S. et al. Active genes dynamically colocalize to shared sites of ongoing transcription. Nature Genet. 36, 1065–1071 (2004)

    Article  CAS  Google Scholar 

  25. Simonis, M., Kooren, J. & de Laat, W. An evaluation of 3C-based methods to capture DNA interactions. Nature Methods 4, 895–901 (2007)

    Article  CAS  Google Scholar 

  26. Hsu, F. et al. The UCSC Known Genes. Bioinformatics 22, 1036–1046 (2006)

    Article  CAS  Google Scholar 

  27. Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007)

    Article  CAS  Google Scholar 

  28. Phatnani, H. P. & Greenleaf, A. L. Phosphorylation and functions of the RNA polymerase II CTD. Genes Dev. 20, 2922–2936 (2006)

    Article  CAS  Google Scholar 

  29. Laganiere, J. et al. Location analysis of estrogen receptor α target promoters reveals that FOXA1 defines a domain of the estrogen response. Proc. Natl Acad. Sci. USA 102, 11651–11656 (2005)

    Article  CAS  ADS  Google Scholar 

  30. Kushner, P. J. et al. Estrogen receptor pathways to AP-1. J. Steroid Biochem. Mol. Biol. 74, 311–317 (2000)

    Article  CAS  Google Scholar 

  31. Pan, Y. F. et al. Regulation of estrogen receptor-mediated long-range transcription via evolutionarily conserved distal response elements. J. Biol. Chem. 283, 32977–32988 (2008)

    Article  CAS  Google Scholar 

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The authors acknowledge the Genome Technology and Biology Group at the Genome Institute of Singapore for technical support; A. Shahab, C. C. Seng and F. H. Mulawadi for computing support; S. Luo and G. Schroth for Illumina sequencing support; and W. de Laat, B. Ren and X. S. Liu for advice. M.J.F., P.Y.H.H., Y.H., P.Y.T. and Y.K.L. are supported by A*STAR Scholarships. M.J.F. is supported by a L’Oreal-UNESCO For Women In Science National Fellowship. Y.R. and C.L.W. are supported by A*STAR of Singapore and NIH ENCODE grants (R01 HG004456-01, R01HG003521-01 and part of 1U54HG004557-01).

Author Contributions M.J.F. and Y.R. conceptualized the ChIA-PET strategy. M.J.F., E.C. and Y.R. designed the experiments. M.J.F., M.H.L., Y.F.P., J.L., A.H., P.H.M., E.G.Y.C., P.Y.Y.H., W.-J.W., Y.H., Y.L., P.Y.T., P.Y.C., K.D.S.A.W., B.Z., K.S.L., S.C.L., J.S.Y., R.J., K.V.D., J.S.T., Y.K.L., T.H., H.G.S., X.R. and V.C.-R. performed experiments. M.J.F., X.H., Y.B.M., Y.L.O., S.V., H.-S.O., P.N.A., V.B.V., Y.K.L., R.K.M.K., G.B., H.G.S., X.R., V.C.-R., W-K.S., C.-L.W., E.C. and Y.R. analysed experimental data. E.T.L., E.C. and C.-L.W. commented on the manuscript drafts; M.J.F. and Y.R. wrote the paper.

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Correspondence to Edwin Cheung or Yijun Ruan.

Supplementary information

Supplementary Information

This file contains Supplementary Results, Supplementary Methods, Supplementary Notes, Supplementary Tables 4-7 and 9 (see separate files s2-s6 for Supplementary Tables 1-3, 8 and 10), Supplementary Figures 1-21 with Legends, Supplementary References and a Supplementary Glossary. (PDF 16985 kb)

Supplementary Table 1

This file shows all ERα binding sites found by ChIA-PET and supporting datasets, and associated genes. (XLS 3861 kb)

Supplementary Table 2

This file shows all raw interchromosomal and intrachromosomal inter-ligation PET clusters (duplex interactions) found by ChIA-PET experiments. (XLS 1763 kb)

Supplementary Table 3

This file shows processed interaction regions found by ChIA-PET experiments, and associated genes. (XLS 915 kb)

Supplementary Table 8

This file shows loop, anchor and enclosed anchor genes from ChIA-PET experiments, and their transcriptional characteristics. (XLS 2688 kb)

Supplementary Table 10

This file shows sequence and technical information used in the ChIA-PET and validation experiments. (XLS 43 kb)

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Fullwood, M., Liu, M., Pan, Y. et al. An oestrogen-receptor-α-bound human chromatin interactome. Nature 462, 58–64 (2009).

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