• An Erratum to this article was published on 27 July 2011

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Abstract

Mammalian genomes are viewed as functional organizations that orchestrate spatial and temporal gene regulation. CTCF, the most characterized insulator-binding protein, has been implicated as a key genome organizer. However, little is known about CTCF-associated higher-order chromatin structures at a global scale. Here we applied chromatin interaction analysis by paired-end tag (ChIA-PET) sequencing to elucidate the CTCF-chromatin interactome in pluripotent cells. From this analysis, we identified 1,480 cis- and 336 trans-interacting loci with high reproducibility and precision. Associating these chromatin interaction loci with their underlying epigenetic states, promoter activities, enhancer binding and nuclear lamina occupancy, we uncovered five distinct chromatin domains that suggest potential new models of CTCF function in chromatin organization and transcriptional control. Specifically, CTCF interactions demarcate chromatin-nuclear membrane attachments and influence proper gene expression through extensive cross-talk between promoters and regulatory elements. This highly complex nuclear organization offers insights toward the unifying principles that govern genome plasticity and function.

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Change history

  • 11 July 2011

    In the version of this article initially published, the accession codes section contained inaccuracies. The raw sequences and processed data generated from this study can be downloaded with accession number GSE28247. The previously published histone modification data used in this study are found under accession numbers GSE12241 and GSE11172. The error has been corrected in the HTML and PDF versions of the article.

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Gene Expression Omnibus

References

  1. 1.

    , , & Nuclear compartmentalization and gene activity. Nat. Rev. Mol. Cell Biol. 1, 137–143 (2000).

  2. 2.

    Beyond the sequence: cellular organization of genome function. Cell 128, 787–800 (2007).

  3. 3.

    et al. Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol. 3, e157 (2005).

  4. 4.

    & The emerging role of nuclear architecture in DNA repair and genome maintenance. Nat. Rev. Mol. Cell Biol. 10, 243–254 (2009).

  5. 5.

    & Chromatin in pluripotent embryonic stem cells and differentiation. Nat. Rev. Mol. Cell Biol. 7, 540–546 (2006).

  6. 6.

    et al. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462, 58–64 (2009).

  7. 7.

    et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009).

  8. 8.

    et al. A three-dimensional model of the yeast genome. Nature 465, 363–367 (2010).

  9. 9.

    et al. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat. Genet. 42, 53–61 (2010).

  10. 10.

    Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 447, 425–432 (2007).

  11. 11.

    , & The protein CTCF is required for the enhancer blocking activity of vertebrate insulators. Cell 98, 387–396 (1999).

  12. 12.

    & CTCF: master weaver of the genome. Cell 137, 1194–1211 (2009).

  13. 13.

    et al. Chromatin boundaries and chromatin domains. Cold Spring Harb. Symp. Quant. Biol. 69, 245–250 (2004).

  14. 14.

    & Chromatin insulators. Annu. Rev. Genet. 40, 107–138 (2006).

  15. 15.

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

  16. 16.

    et al. Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res. 19, 24–32 (2009).

  17. 17.

    et al. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 128, 1231–1245 (2007).

  18. 18.

    & Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 405, 482–485 (2000).

  19. 19.

    , , & The insulator factor CTCF controls MHC class II gene expression and is required for the formation of long-distance chromatin interactions. J. Exp. Med. 205, 785–798 (2008).

  20. 20.

    , & Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops. Nat. Genet. 36, 889–893 (2004).

  21. 21.

    et al. Analysis of the H19ICR insulator. Mol. Cell Biol. 27, 3499–3510 (2007).

  22. 22.

    , , & CTCF tethers an insulator to subnuclear sites, suggesting shared insulator mechanisms across species. Mol. Cell 13, 291–298 (2004).

  23. 23.

    et al. Sensing X chromosome pairs before X inactivation via a novel X-pairing region of the Xic. Science 318, 1632–1636 (2007).

  24. 24.

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

  25. 25.

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

  26. 26.

    Self-renewal vs. differentiation of mouse embryonic stem cells. Biol. Reprod. 71, 1755–1765 (2004).

  27. 27.

    et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol. 11, R22 (2010).

  28. 28.

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

  29. 29.

    et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457, 854–858 (2009).

  30. 30.

    et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453, 948–951 (2008).

  31. 31.

    et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39, 311–318 (2007).

  32. 32.

    et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133, 1106–1117 (2008).

  33. 33.

    et al. CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus. Genes Dev. 20, 2349–2354 (2006).

  34. 34.

    et al. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol. Cell 38, 603–613 (2010).

  35. 35.

    , & To be or not to be active: the stochastic nature of enhancer action. Bioessays 22, 381–387 (2000).

  36. 36.

    et al. Maintenance of long-range DNA interactions after inhibition of ongoing RNA polymerase II transcription. PLoS ONE 3, e1661 (2008).

  37. 37.

    et al. CTCF interacts with and recruits the largest subunit of RNA polymerase II to CTCF target sites genome-wide. Mol. Cell Biol. 27, 1631–1648 (2007).

  38. 38.

    & CTCF and its protein partners: divide and rule? J. Cell Sci. 122, 1275–1284 (2009).

  39. 39.

    et al. Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell 132, 422–433 (2008).

  40. 40.

    , , & The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet. 4, e1000138 (2008).

  41. 41.

    et al. Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus. Nature 460, 410–413 (2009).

  42. 42.

    et al. A CTCF-independent role for cohesin in tissue-specific transcription. Genome Res. 20, 578–588 (2010).

  43. 43.

    et al. Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature 451, 796–801 (2008).

  44. 44.

    et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 467, 430–435 (2010).

  45. 45.

    et al. Nonallelic transvection of multiple imprinted loci is organized by the H19 imprinting control region during germline development. Genes Dev. 23, 2598–2603 (2009).

  46. 46.

    et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553–560 (2007).

  47. 47.

    et al. A stem cell molecular signature. Science 298, 601–604 (2002).

  48. 48.

    et al. Zic3 is required for maintenance of pluripotency in embryonic stem cells. Mol. Biol. Cell 18, 1348–1358 (2007).

  49. 49.

    et al. A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics 26, 1199–1204 (2010).

  50. 50.

    BLAT–the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002).

  51. 51.

    et al. Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat. Protoc. 2, 1722–1733 (2007).

  52. 52.

    et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766–770 (2008).

  53. 53.

    , , & Inherent signals in sequencing-based chromatin-immunoprecipitation control libraries. PLoS ONE 4, e5241 (2009).

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Acknowledgements

We acknowledge the Genome Technology and Biology Group, particularly the sequencing team, for technical support. We also thank C. Xi and H.H. Ng who provided technical guidance for p300 ChIP optimization, M. Fullwood and B. Han for their 4C assay protocol, L.M. Hui and E. Cheung for 3C optimization and discussion, Z. Jingyao for BAC clone preparation and K. Zawack for reading the manuscript. This work was supported by the Agency for Science, Technology and Research (A*STAR), Singapore, and US National Institutes of Health (NIH) ENCODE grants (R01 HG004456-01, R01HG003521-01 and 1U54HG004557-01) to Y.R. and C.-L.W.

Author information

Author notes

    • Lusy Handoko
    • , Han Xu
    •  & Guoliang Li

    These authors contributed equally to this work.

    • Chia-Lin Wei

    Present address: Joint Genome Institute, Walnut Creek, California, USA.

Affiliations

  1. Genome Institute of Singapore, Singapore.

    • Lusy Handoko
    • , Han Xu
    • , Guoliang Li
    • , Chew Yee Ngan
    • , Elaine Chew
    • , Marie Schnapp
    • , Charlie Wah Heng Lee
    • , Chaopeng Ye
    • , Joanne Lim Hui Ping
    • , Fabianus Mulawadi
    • , Eleanor Wong
    • , Yubo Zhang
    • , Thompson Poh
    • , Chee Seng Chan
    • , Atif Shahab
    • , Guillaume Bourque
    • , Valere Cacheux-Rataboul
    • , Wing-Kin Sung
    • , Yijun Ruan
    •  & Chia-Lin Wei
  2. National University of Singapore, Singapore.

    • Eleanor Wong
    • , Wing-Kin Sung
    •  & Chia-Lin Wei
  3. Nanyang Technological University, Singapore.

    • Jianpeng Sheng
  4. Duke-NUS Graduate Medical School Singapore, Singapore.

    • Galih Kunarso

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Contributions

Y.R. and C.-L.W. designed the study. L.H., H.X. and G.L. conducted experiments and data analyses. C.Y.N., C.Y. and E.W. performed the ChIA-PET and ChIP-Seq experiments. L.H., E.C., M.S., C.Y., J.L.H.P., J.S. and V.C.-R. coordinated all the validation experiments. C.S.C. and A.S. provided sequencing data processing and management. F.M. and W.-K.S. provided ChIA-PET data processing and bioinformatics support. C.W.H.L., Y.Z., G.K. and G.B. carried out additional global bioinformatic analyses. T.P. offered high-throughput sequencing support. L.H., H.X., G.L. and C.L.W. analyzed the data and wrote the manuscript. Y.R. provided critical review of the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Yijun Ruan or Chia-Lin Wei.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Note, Supplementary Figures 1–11 and Supplementary Tables 1, 4, 7 and 10.

Excel files

  1. 1.

    Supplementary Table 2

    CTCF binding sites

  2. 2.

    Supplementary Table 3

    Intra-and inter-chromosomal interactions detected by CTCF ChIA-PET

  3. 3.

    Supplementary Table 5

    List of 5 categories assigned to intra-chromosomal interactions

  4. 4.

    Supplementary Table 6

    RNA Pol II, p300 and LADs sites defined by ChIP-Seq

  5. 5.

    Supplementary Table 8

    RNAP II interactions defined by ChIA-PET

  6. 6.

    Supplementary Table 9

    SALL4 interactions defined by ChIA-PET

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DOI

https://doi.org/10.1038/ng.857

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