Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Long-range intrachromosomal interactions in the T helper type 2 cytokine locus


The T helper type 2 (TH2) locus control region is important in the regulation of the genes encoding the cytokines interleukins 4, 5 and 13. Using the chromosome conformation capture technique, we found that in T cells, natural killer cells, B cells and fibroblasts, the promoters for the genes encoding TH2 cytokines are located in close spatial proximity, forming an initial chromatin core configuration. In CD4+ T cells and natural killer cells, but not B cells and fibroblasts, the TH2 locus control region participates in this configuration. The transcription factors GATA3 and STAT6 are essential for the establishment and/or maintenance of these interactions. Intrachromosomal interactions in the TH2 cytokine locus may form the basis for the coordinated transcriptional regulation of cytokine-encoding genes by the TH2 locus control region.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Chromosome conformation capture assay of the TH2 cytokine locus.
Figure 2: Poised chromatin conformation of the TH2 cytokine gene loci and the TH2 LCR in T cells and NK cells but not in fibroblasts.
Figure 3: The RHS7 site of the TH2 LCR interacts with other hypersensitive sites of the locus and the promoters of the cytokine-encoding genes in T cells but not in fibroblasts.
Figure 4: Absence of STAT6 leads to impairment of interactions between the TH2 LCR and the rest of the TH2 cytokine locus.
Figure 5: The Il13 promoter interacts with the Il4 promoter and several DNase I–hypersensitive sites on the TH2 cytokine locus.
Figure 6: Calcium mobilization in 3T3 fibroblasts expressing GATA3 gain a secondary chromatin conformation in the TH2 locus.

Similar content being viewed by others


  1. Lee, G.R., Fields, P.E., Griffin, T.J. IV, & Flavell, R.A. Regulation of the TH2 cytokine locus by a locus control region. Immunity 19, 145–153 (2003).

    Article  CAS  Google Scholar 

  2. Grosveld, F., van Assendelft, G.B., Greaves, D.R. & Kollias, G. Position-independent, high level expression of the human β-globin gene in transgenic mice. Cell 51, 975–985 (1987).

    Article  CAS  Google Scholar 

  3. Takemoto, N. et al. TH2-specific DNase I-hypersensitive sites in the murine IL-13 and IL-4 intergenic region. Int. Immunol. 10, 1981–1985 (1998).

    Article  CAS  Google Scholar 

  4. Agarwal, S. & Rao, A. Modulation of chromatin structure regulates cytokine gene expression during T cell differentiation. Immunity 9, 765–775 (1998).

    Article  CAS  Google Scholar 

  5. Carey, M. & Smale, S. Transcriptional regulation in eukaryotes: concepts, strategies, and techniques. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 2000).

    Google Scholar 

  6. Loots, G.G. et al. Identification of a coordinate regulator of interleukins-4,13 and 5 by cross-species sequence comparisons. Science 288, 136–140 (2000).

    Article  CAS  Google Scholar 

  7. Agarwal, S., Avni, O. & Rao, A. Cell-type-restricted binding of the transcription factor NFAT to a distal IL-4 enhancer in vivo. Immunity 12, 643–652 (2000).

    Article  CAS  Google Scholar 

  8. Li, Q., Peterson, K.R., Fang, X. & Stamatoyannopoulos, G. Locus control regions. Blood 100, 3077–3086 (2002).

    Article  CAS  Google Scholar 

  9. Carter, D., Chakalova, L., Osborne, C., Dai, Y.-F. & Fraser, P. Long-range chromatin regulatory interactions in vivo. Nat. Genet. 32, 1–4 (2002).

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  11. Dekker, J. A closer look at long-range chromosomal interactions. Trends Biochem. Sci. 28, 277–280 (2003).

    Article  CAS  Google Scholar 

  12. Choi, O. & Engel, J.D. Developmental regulation of β-globin gene switching. Cell 55, 17–26 (1988).

    Article  CAS  Google Scholar 

  13. Dillon, N., Trimborn, T., Strouboulis, J., Fraser, P. & Grosveld, F . The effect of distance on long-range chromatin interactions. Mol. Cell 1, 131–139 (1997).

    Article  CAS  Google Scholar 

  14. Wijgerde, M., Grosveld, F. & Fraser, P. Transcription complex stability and chromatin dynamics in vivo. Nature 377, 209–213 (1995).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  16. Zhu, J., Guo, L., Watson, C.J., Hu-Li, J. & Paul, W.E. STAT6 is necessary and sufficient for IL-4's role in TH2 differentiation and cell expansion. J. Immunol. 166, 7276–7281 (2001).

    Article  CAS  Google Scholar 

  17. Zheng, W.P. & Flavell, R.A. The transcription factor GATA-3 is necessary and sufficient for TH2 cytokine gene expression in CD4 T cells. Cell 89, 587–596 (1997).

    Article  CAS  Google Scholar 

  18. Zhang, D.-H., Cohn, L., Ray, P., Bottomly, K. & Ray, A. Transcription factor GATA-3 is differentially expressed in murine TH1 and TH2 cells and controls TH2-specific expression of the interleukin-5 gene. J. Biol. Chem. 272, 21597–21603 (1997).

    Article  CAS  Google Scholar 

  19. Gorelik, L., Fields, P.E. & Flavell, R.A. Cutting edge: TGF-β inhibits TH type 2 development through inhibition of GATA-3 expression. J. Immunol. 165, 4773–4777 (2000).

    Article  CAS  Google Scholar 

  20. Fields, P.E., Kim, S.T. & Flavell, R.A. Cutting edge: changes in histone acetylation at the IL-4 and IFN-γ loci accompany TH1/TH2 differentiation. J. Immunol. 169, 647–650 (2002).

    Article  CAS  Google Scholar 

  21. Avni, O. et al. TH cell differentiation is accompanied by dynamic changes in histone acetylation of cytokine genes. Nat. Immunol. 3, 643–651 (2002).

    Article  CAS  Google Scholar 

  22. Messi, M. et al. Memory and flexibility of cytokine gene expression as separable properties of human TH1 and TH2 lymphocytes. Nat. Immunol. 4, 78–86 (2002).

    Article  Google Scholar 

  23. Guo, L. et al. In TH2 cells the IL-4 gene has a series of accessibility states associated with distinctive probabilities of IL-4 production. Proc. Natl. Acad. Sci. USA 99, 10623–10628 (2002).

    Article  CAS  Google Scholar 

  24. Palstra, R.-J. et al. The β-globin nuclear compartment in development and erythroid differentiation. Nat. Genet. 35, 190–194 (2003).

    Article  CAS  Google Scholar 

  25. Ansel, K.M., Lee, D.U. & Rao, A. An epigenetic view of helper T cell differentiation. Nat. Immunol. 4, 616–623 (2003).

    Article  CAS  Google Scholar 

  26. Spilianakis, C. et al. CIITA regulates transcription onset via Ser5-phosphorylation of RNA Pol II. EMBO J. 22, 5125–5136 (2003).

    Article  CAS  Google Scholar 

  27. Boehm, A.K., Saunders, A., Werner, J. & Lis, J.T. Transcription factor and polymerase recruitment, modification, and movement on dHSP70 in vivo in the minutes following heat shock. Mol. Cell. Biol. 23, 7628–7637 (2003).

    Article  CAS  Google Scholar 

  28. Gilmour, D.S. & Lis, J.T. RNA polymerase II interacts with the promoter region of the noninduced HSP70 gene in Drosophila melanogaster cells. Mol. Cell. Biol. 6, 3984–3989 (1986).

    Article  CAS  Google Scholar 

  29. Graunke, D.M., Fornace A.J. Jr, & Pieper, R.O. Presetting of chromatin structure and transcription factor binding poise the human GADD45 gene for rapid transcriptional up-regulation. Nucleic Acids Res. 27, 3881–3890 (1999).

    Article  CAS  Google Scholar 

  30. Wang, X.Y., Kolb, A., Cannon, W. & Buck, M. Nucleoprotein complex formation by the enhancer binding protein NifA. Nucleic Acids Res. 25, 3478–3485 (1997).

    Article  CAS  Google Scholar 

  31. Ljungman, M. & Hanawalt, P.C. Presence of negative torsional tension in the promoter region of the transcriptionally poised dihydrofolate reductase gene in vivo. Nucleic Acids Res. 23, 1782–1789 (1995).

    Article  CAS  Google Scholar 

  32. Smale, S.T. & Fisher, A.G. Chromatin structure and gene regulation in the immune system. Annu. Rev. Immunol. 20, 427–462 (2002).

    Article  CAS  Google Scholar 

  33. Grogan, J.L. et al. Early transcription and silencing of cytokine genes underlie polarization of T helper cell subsets. Immunity 14, 205–215 (2001).

    Article  CAS  Google Scholar 

  34. Lee, B.H. et al. GATA-3 induces T helper cell type 2 (TH2) cytokine expression and chromatin remodeling in committed TH1 cells. J. Exp. Med. 192, 105–115 (2000).

    Article  CAS  Google Scholar 

  35. Ouyang, W. et al. Inhibition of TH1 development mediated by GATA-3 through an IL-4-independent mechanism. Immunity 9, 745–755 (1998).

    Article  CAS  Google Scholar 

  36. Rosmaraki, E.E. et al. Identification of committed NK cell progenitors in adult murine bone marrow. Eur. J. Immunol. 31, 1900–1909 (2001).

    Article  CAS  Google Scholar 

  37. Samson, S.I. et al. GATA-3 promotes maturation, IFN-γ production, and liver-specific homing of NK cells. Immunity 19, 701–711 (2003).

    Article  CAS  Google Scholar 

  38. Takemoto, N., Arai, K. & Miyatake, S. Cutting edge: the differential involvement of the N-finger of GATA-3 in chromatin remodeling and transactivation during TH2 development. J. Immunol. 169, 4103–4107 (2002).

    Article  CAS  Google Scholar 

  39. Rao, A., Luo, C. & Hogan, P.G. Transcription factors of the NFAT family: regulation and function. Annu. Rev. Immunol. 15, 707–747 (1997).

    Article  CAS  Google Scholar 

  40. Feske, S., Giltrane, J., Dolmetsch, R., Staudt, L. & Rao, A. Gene regulation mediated by calcium signals in T lymphocytes. Nat. Immunol. 2, 316–324 (2001).

    Article  CAS  Google Scholar 

  41. Okamura, H. & Rao, A. Transcriptional regulation in lymphocytes. Curr. Opin. Cell Biol. 13, 239–243 (2001).

    Article  CAS  Google Scholar 

  42. Kovac, Z. & Schwartz, R. The molecular basis of the requirement for antigen processing of pigeon cytochrome c prior to T cell activation. J. Immunol. 134, 3233–3240 (1985).

    CAS  PubMed  Google Scholar 

Download references


We thank F. Manzo for assistance with manuscript preparation; C. Hughes for technical assistance; P.E. Fields, G.R. Lee, S.T. Kim and L. Jones for discussions; F. Grosveld and W. de Laat for protocols on chromosome conformation capture technique and for suggestions on improving the manuscript; and Wyeth Laboratories for the donation of IL-12. Experiments in this study were approved by the Yale University Institutional Animal Care and Use Committee. Supported with a Cancer Research Institute fellowship (C.S.) and Howard Hughes Medical Institute (R.A.F.).

Author information

Authors and Affiliations


Corresponding author

Correspondence to Richard A Flavell.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

The Il5 cytokine gene promoter interacts with the Il4 promoter and DNase I hypersensitive sites located at the 3′ end of the Il4 gene, in T cells. (PDF 182 kb)

Supplementary Fig. 2

The Rad50 gene promoter does not participate in the higher order chromatin conformation of the TH2 cytokine genes and the TH2 LCR. (PDF 139 kb)

Supplementary Fig. 3

DNase hypersensitive sites at the 5′ and 3′ of the Il4 gene participate in the higher order chromatin organization of the TH2 cytokine locus. (PDF 207 kb)

Supplementary Fig. 4

Cytokine production of all the cell types used in 3C assay. (PDF 121 kb)

Supplementary Fig. 5

3C assay-primer sequences. (PDF 352 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Spilianakis, C., Flavell, R. Long-range intrachromosomal interactions in the T helper type 2 cytokine locus. Nat Immunol 5, 1017–1027 (2004).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing