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.
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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.).
The authors declare no competing financial interests.
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)
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)
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)
Cytokine production of all the cell types used in 3C assay. (PDF 121 kb)
3C assay-primer sequences. (PDF 352 kb)
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Spilianakis, C., Flavell, R. Long-range intrachromosomal interactions in the T helper type 2 cytokine locus. Nat Immunol 5, 1017–1027 (2004). https://doi.org/10.1038/ni1115
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