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CTCF-mediated functional chromatin interactome in pluripotent cells

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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Figure 1: Genome-wide CTCF-mediated chromatin interactome.
Figure 2: Validation of CTCF-mediated chromatin interactions.
Figure 3: Cumulative histone modification patterns of CTCF loops.
Figure 4: Distinct types of chromatin domains defined by CTCF-tethered interactions.
Figure 5: Promoter-p300 communications facilitated by CTCF-associated chromatin interactions.
Figure 6: Lamin-associated domains (LADs) in embryonic stem cells.

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Accession codes

Accessions

Gene Expression Omnibus

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.

References

  1. Francastel, C., Schubeler, D., Martin, D.I. & Groudine, M. Nuclear compartmentalization and gene activity. Nat. Rev. Mol. Cell Biol. 1, 137–143 (2000).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  11. Bell, A.C., West, A.G. & Felsenfeld, G. The protein CTCF is required for the enhancer blocking activity of vertebrate insulators. Cell 98, 387–396 (1999).

    Article  CAS  Google Scholar 

  12. Phillips, J.E. & Corces, V.G. CTCF: master weaver of the genome. Cell 137, 1194–1211 (2009).

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  14. Valenzuela, L. & Kamakaka, R.T. Chromatin insulators. Annu. Rev. Genet. 40, 107–138 (2006).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  16. Cuddapah, S. 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).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  19. Majumder, P., Gomez, J.A., Chadwick, B.P. & Boss, J.M. 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).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  22. Yusufzai, T.M., Tagami, H., Nakatani, Y. & Felsenfeld, G. CTCF tethers an insulator to subnuclear sites, suggesting shared insulator mechanisms across species. Mol. Cell 13, 291–298 (2004).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  26. O'Shea, K.S. Self-renewal vs. differentiation of mouse embryonic stem cells. Biol. Reprod. 71, 1755–1765 (2004).

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  35. Fiering, S., Whitelaw, E. & Martin, D.I. To be or not to be active: the stochastic nature of enhancer action. Bioessays 22, 381–387 (2000).

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  37. Chernukhin, I. 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).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  40. Fu, Y., Sinha, M., Peterson, C.L. & Weng, Z. The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet. 4, e1000138 (2008).

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  45. Sandhu, K.S. 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).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  53. Vega, V.B., Cheung, E., Palanisamy, N. & Sung, W.K. Inherent signals in sequencing-based chromatin-immunoprecipitation control libraries. PLoS ONE 4, e5241 (2009).

    Article  Google Scholar 

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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

Authors and Affiliations

Authors

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.

Corresponding authors

Correspondence to Yijun Ruan or Chia-Lin Wei.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Note, Supplementary Figures 1–11 and Supplementary Tables 1, 4, 7 and 10. (PDF 4404 kb)

Supplementary Table 2

CTCF binding sites (XLS 3510 kb)

Supplementary Table 3

Intra-and inter-chromosomal interactions detected by CTCF ChIA-PET (XLS 2214 kb)

Supplementary Table 5

List of 5 categories assigned to intra-chromosomal interactions (XLS 729 kb)

Supplementary Table 6

RNA Pol II, p300 and LADs sites defined by ChIP-Seq (XLS 4340 kb)

Supplementary Table 8

RNAP II interactions defined by ChIA-PET (XLS 177 kb)

Supplementary Table 9

SALL4 interactions defined by ChIA-PET (XLS 179 kb)

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Handoko, L., Xu, H., Li, G. et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet 43, 630–638 (2011). https://doi.org/10.1038/ng.857

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