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The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules


We developed a general approach that combines chromosome conformation capture carbon copy (5C) with the Integrated Modeling Platform (IMP) to generate high-resolution three-dimensional models of chromatin at the megabase scale. We applied this approach to the ENm008 domain on human chromosome 16, containing the α-globin locus, which is expressed in K562 cells and silenced in lymphoblastoid cells (GM12878). The models accurately reproduce the known looping interactions between the α-globin genes and their distal regulatory elements. Further, we find using our approach that the domain folds into a single globular conformation in GM12878 cells, whereas two globules are formed in K562 cells. The central cores of these globules are enriched for transcribed genes, whereas nontranscribed chromatin is more peripheral. We propose that globule formation represents a higher-order folding state related to clustering of transcribed genes around shared transcription machineries, as previously observed by microscopy.

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Figure 1: ENCODE region ENm008 on human chromosome 16.
Figure 2: 5C analysis of the 500-kb ENCODE region ENm008.
Figure 3: Ensemble of solutions.
Figure 4: 3D models of the ENm008 ENCODE region containing the α-globin locus.
Figure 5: Analysis of chromatin globules.
Figure 6


  1. 1

    Birney, E. et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816 (2007).

    CAS  Article  Google Scholar 

  2. 2

    Lamond, A.I. & Spector, D.L. Nuclear speckles: a model for nuclear organelles. Nat. Rev. Mol. Cell Biol. 4, 605–612 (2003).

    CAS  Article  Google Scholar 

  3. 3

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

    CAS  Article  Google Scholar 

  4. 4

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

    CAS  Article  Google Scholar 

  5. 5

    de Laat, W. & Grosveld, F. Spatial organization of gene expression: the active chromatin hub. Chromosome Res. 11, 447–459 (2003).

    CAS  Article  Google Scholar 

  6. 6

    Fraser, P. & Bickmore, W. Nuclear organization of the genome and the potential for gene regulation. Nature 447, 413–417 (2007).

    CAS  Article  Google Scholar 

  7. 7

    Dekker, J. Gene regulation in the third dimension. Science 319, 1793–1794 (2008).

    CAS  Article  Google Scholar 

  8. 8

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

    CAS  Article  Google Scholar 

  9. 9

    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).

    CAS  Article  Google Scholar 

  10. 10

    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).

    CAS  Article  Google Scholar 

  11. 11

    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).

    CAS  Article  Google Scholar 

  12. 12

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

    CAS  Article  Google Scholar 

  13. 13

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

    Article  Google Scholar 

  14. 14

    Tolhuis, B., Palstra, R.J., Splinter, E., Grosveld, F. & de Laat, W. Looping and interaction between hypersensitive sites in the active beta-globin locus. Mol. Cell 10, 1453–1465 (2002).

    CAS  Article  Google Scholar 

  15. 15

    Zhou, G.L. et al. Active chromatin hub of the mouse alpha-globin locus forms in a transcription factory of clustered housekeeping genes. Mol. Cell. Biol. 26, 5096–5105 (2006).

    CAS  Article  Google Scholar 

  16. 16

    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).

    CAS  Article  Google Scholar 

  17. 17

    Ohlsson, R. & Gondor, A. The 4C technique: the ′Rosetta stone′ for genome biology in 3D? Curr. Opin. Cell Biol. 19, 321–325 (2007).

    CAS  Article  Google Scholar 

  18. 18

    Mateos-Langerak, J. et al. Spatially confined folding of chromatin in the interphase nucleus. Proc. Natl. Acad. Sci. USA 106, 3812–3817 (2009).

    CAS  Article  Google Scholar 

  19. 19

    Wedemann, G. & Langowski, J. Computer simulation of the 30-nanometer chromatin fiber. Biophys. J. 82, 2847–2859 (2002).

    CAS  Article  Google Scholar 

  20. 20

    Dekker, J. Mapping in vivo chromatin interactions in yeast suggests an extended chromatin fiber with regional variation in compaction. J. Biol. Chem. 283, 34532–34540 (2008).

    CAS  Article  Google Scholar 

  21. 21

    Wachsmuth, M., Caudron-Herger, M. & Rippe, K. Genome organization: balancing stability and plasticity. Biochim. Biophys. Acta 1783, 2061–2079 (2008).

    CAS  Article  Google Scholar 

  22. 22

    Jhunjhunwala, S. et al. The 3D structure of the immunoglobulin heavy-chain locus: implications for long-range genomic interactions. Cell 133, 265–279 (2008).

    CAS  Article  Google Scholar 

  23. 23

    Fraser, J. et al. Chromatin conformation signatures of cellular differentiation. Genome Biol. 10, R37 (2009).

    Article  Google Scholar 

  24. 24

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

    CAS  Article  Google Scholar 

  25. 25

    Alber, F. et al. Determining the architectures of macromolecular assemblies. Nature 450, 683–694 (2007).

    CAS  Article  Google Scholar 

  26. 26

    Hughes, J.R. et al. Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences. Proc. Natl. Acad. Sci. USA 102, 9830–9835 (2005).

    CAS  Article  Google Scholar 

  27. 27

    Higgs, D.R., Vernimmen, D., Hughes, J. & Gibbons, R. Using genomics to study how chromatin influences gene expression. Annu. Rev. Genomics Hum. Genet. 8, 299–325 (2007).

    CAS  Article  Google Scholar 

  28. 28

    Higgs, D.R. & Wood, W.G. Long-range regulation of alpha globin gene expression during erythropoiesis. Curr. Opin. Hematol. 15, 176–183 (2008).

    CAS  Article  Google Scholar 

  29. 29

    Lower, K.M. et al. Adventitious changes in long-range gene expression caused by polymorphic structural variation and promoter competition. Proc. Natl. Acad. Sci. USA 106, 21771–21776 (2009).

    CAS  Article  Google Scholar 

  30. 30

    Vernimmen, D., De Gobbi, M., Sloane-Stanley, J.A., Wood, W.G. & Higgs, D.R. Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression. EMBO J. 26, 2041–2051 (2007).

    CAS  Article  Google Scholar 

  31. 31

    Higgs, D.R. et al. A major positive regulatory region located far upstream of the human alpha-globin gene locus. Genes Dev. 4, 1588–1601 (1990).

    CAS  Article  Google Scholar 

  32. 32

    Chen, H., Lowrey, C.H. & Stamatoyannopoulos, G. Analysis of enhancer function of the HS-40 core sequence of the human alpha-globin cluster. Nucleic Acids Res. 25, 2917–2922 (1997).

    CAS  Article  Google Scholar 

  33. 33

    Bernet, A. et al. Targeted inactivation of the major positive regulatory element (HS-40) of the human alpha-globin gene locus. Blood 86, 1202–1211 (1995).

    CAS  PubMed  Google Scholar 

  34. 34

    De Gobbi, M. et al. Tissue-specific histone modification and transcription factor binding in alpha globin gene expression. Blood 110, 4503–4510 (2007).

    CAS  Article  Google Scholar 

  35. 35

    Dostie, J. & Dekker, J. Mapping networks of physical interactions between genomic elements using 5C technology. Nat. Protoc. 2, 988–1002 (2007).

    CAS  Article  Google Scholar 

  36. 36

    Lajoie, B.R., van Berkum, N.L., Sanyal, A. & Dekker, J. My5C: web tools for chromosome conformation capture studies. Nat. Methods 6, 690–691 (2009).

    CAS  Article  Google Scholar 

  37. 37

    Dekker, J. The three 'C' s of chromosome conformation capture: controls, controls, controls. Nat. Methods 3, 17–21 (2006).

    CAS  Article  Google Scholar 

  38. 38

    Gerchman, S.E. & Ramakrishnan, V. Chromatin higher-order structure studied by neutron scattering and scanning transmission electron microscopy. Proc. Natl. Acad. Sci. USA 84, 7802–7806 (1987).

    CAS  Article  Google Scholar 

  39. 39

    Rosa, A., Becker, N.B. & Everaers, R. Looping probabilities in model interphase chromosomes. Biophys. J. 98, 2410–2419 (2010).

    CAS  Article  Google Scholar 

  40. 40

    Voss, T.C. & Hager, G.L. Visualizing chromatin dynamics in intact cells. Biochim. Biophys. Acta 1783, 2044–2051 (2008).

    CAS  Article  Google Scholar 

  41. 41

    Lawrence, J.B., Singer, R.H. & McNeil, J.A. Interphase and metaphase resolution of different distances within the human dystrophin gene. Science 249, 928–932 (1990).

    CAS  Article  Google Scholar 

  42. 42

    Kuhn, R.M. et al. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res. 37, D755–D761 (2009).

    CAS  Article  Google Scholar 

  43. 43

    Osborne, C.S. et al. Myc dynamically and preferentially relocates to a transcription factory occupied by Igh. PLoS Biol. 5, e192 (2007).

    Article  Google Scholar 

  44. 44

    Münkel, C. et al. Compartmentalization of interphase chromosomes observed in simulation and experiment. J. Mol. Biol. 285, 1053–1065 (1999).

    Article  Google Scholar 

  45. 45

    Müller, W.G. et al. Generic features of tertiary chromatin structure as detected in natural chromosomes. Mol. Cell. Biol. 24, 9359–9370 (2004).

    Article  Google Scholar 

  46. 46

    Martin, S. & Pombo, A. Transcription factories: quantitative studies of nanostructures in the mammalian nucleus. Chromosome Res. 11, 461–470 (2003).

    CAS  Article  Google Scholar 

  47. 47

    Sutherland, H. & Bickmore, W.A. Transcription factories: gene expression in unions? Nat. Rev. Genet. 10, 457–466 (2009).

    CAS  Article  Google Scholar 

  48. 48

    Iborra, F.J., Pombo, A., Jackson, D.A. & Cook, P.R. Active RNA polymerases are localized within discrete transcription 'factories' in human nuclei. J. Cell Sci. 109, 1427–1436 (1996).

    CAS  PubMed  Google Scholar 

  49. 49

    Pombo, A. et al. Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III. EMBO J. 18, 2241–2253 (1999).

    CAS  Article  Google Scholar 

  50. 50

    Eskiw, C.H., Rapp, A., Carter, D.R. & Cook, P.R. RNA polymerase II activity is located on the surface of protein-rich transcription factories. J. Cell Sci. 121, 1999–2007 (2008).

    CAS  Article  Google Scholar 

  51. 51

    Carter, D.R., Eskiw, C. & Cook, P.R. Transcription factories. Biochem. Soc. Trans. 36, 585–589 (2008).

    CAS  Article  Google Scholar 

  52. 52

    Goetze, S. et al. The 3D structure of human interphase chromosomes is related to the transcriptome map. Mol. Cell. Biol. 27, 4475–4487 (2007).

    CAS  Article  Google Scholar 

  53. 53

    Hu, Y., Kireev, I., Plutz, M., Ashourian, N. & Belmont, A.S. Large-scale chromatin structure of inducible genes: transcription on a condensed, linear template. J. Cell Biol. 185, 87–100 (2009).

    CAS  Article  Google Scholar 

  54. 54

    Boeger, H., Griesenbeck, J. & Kornberg, R.D. Nucleosome retention and the stochastic nature of promoter chromatin remodeling for transcription. Cell 133, 716–726 (2008).

    CAS  Article  Google Scholar 

  55. 55

    Gheldof, N., Tabuchi, T.M. & Dekker, J. The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications. Proc. Natl. Acad. Sci. USA 103, 12463–12468 (2006).

    CAS  Article  Google Scholar 

  56. 56

    Xi, H. et al. Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet. 3, e136 (2007).

    Article  Google Scholar 

  57. 57

    Crawford, G.E. et al. DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat. Methods 3, 503–509 (2006).

    CAS  Article  Google Scholar 

  58. 58

    Harrow, J. et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol 7 (Suppl. 1), S4 (2006).

    Article  Google Scholar 

  59. 59

    Tam, R., Shopland, L.S., Johnson, C.V., McNeil, J. & Lawrence, J.B. Applications of RNA FISH for visualizing gene expression and nuclear architecture in FISH: A Practical Approach (eds. Beatty, B.G., Mai, S. & Squire, J.) 93–118 (Oxford University Press, New York, 2002).

  60. 60

    Pettersen, E.F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

    CAS  Article  Google Scholar 

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We thank the IMP community (, especially D. Russell, B. Webb and A. Sali, as well as the Chimera developers (, especially T. Goddard and T. Ferrin. We also thank M. Umbarger, M. Wright, G. Church, M.S. Madhusudhan, M. Walhout and Dekker laboratory members for fruitful discussions. We acknowledge support from the Spanish Ministerio de Ciencia e Innovación (BIO2007/66670 and BFU2010/19310 to M.A.M.-R.), the US National Institutes of Health (NIH; HG003143 to J.D. and GM053234 to J.B.L.) and the Keck Foundation (J.D.). Finally, we are grateful to the ENCODE project (funded by the NIH and the US National Human Genome Research Institute) for providing annotations of the ENm008 region. In particular, we thank the ENCODE groups led by T. Gingeras (expression data, Cold Spring Harbor Laboratory), G. Crawford (DNase I data, Duke University) and B. Bernstein (CTCF data, H3K4me3 data, Broad Institute of Harvard and MIT). ENCODE data are publicly available through the ENCODE Data Coordination Center at the University of California, Santa Cruz (

Author information




B.R.L. performed the bioinformatics design and analysis of the 5C experiments. A.S. performed the 5C experiments. D.B., E.C. and M.A.M.-R. carried out the IMP computational modeling. M.B., A.S. and J.B.L. performed the FISH experiments. D.B., B.R.L., A.S., J.D. and M.A.M.-R. wrote the manuscript. J.D. and M.A.M.-R. conceived the work.

Corresponding authors

Correspondence to Job Dekker or Marc A Marti-Renom.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Methods, Supplementary Table 1 and Supplementary Figures 1–6 (PDF 3508 kb)

Supplementary Video 1

Video of the spinning 3D structure for the ENm008 region in GM12878 cell lines. The region includes the α-globin locus, which contains, from telomere to centromere, the ζ, μ (also known as αD), α2, α1, and θ globin genes. Colored fragments contain annotated genes. Red (HS40), orange (other HSs) and green (CTCF-bound elements) spheres localize regulatory elements. (MOV 3657 kb)

Supplementary Video 2

Video of the spinning 3D structure for the ENm008 region in K562 cell lines. The region includes the α-globin locus, which contains, from telomere to centromere, the ζ, μ (also known as αD), α2, α1, and θ globin genes. Colored fragments contain annotated genes. Red (HS40), orange (other HSs) and green (CTCF-bound elements) spheres localize regulatory elements. (MOV 3627 kb)

Supplementary Data 1

Zip file with 5C results and model analysis. (TXT 15 kb)

Supplementary Data 2

5C frequency counts matrix for ENm008 in GM12878 cells in a tabulated text file. (TXT 4 kb)

Supplementary Data 3

5C frequency counts matrix for ENm008 in K562 cells in a tabulated text file. (TXT 4 kb)

Supplementary Data 4

Contact map for ENm008 in GM12878 cells in a tabulated text file. (TXT 21 kb)

Supplementary Data 5

Contact map for ENm008 in K562 cells in a tabulated text file. (TXT 17 kb)

Supplementary Data 6

Contact map for ENm008 in GM12878 cells as BED formatted file for direct upload into the UCSC Genome Browser. (TXT 403 kb)

Supplementary Data 7

Contact map for ENm008 in K562 cells as BED formatted file for direct upload into the UCSC Genome Browser. (TXT 246 kb)

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Baù, D., Sanyal, A., Lajoie, B. et al. The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules. Nat Struct Mol Biol 18, 107–114 (2011).

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