Interchromosomal associations between alternatively expressed loci

Abstract

The T-helper-cell 1 and 2 (TH1 and TH2) pathways, defined by cytokines interferon-γ (IFN-γ) and interleukin-4 (IL-4), respectively, comprise two alternative CD4+ T-cell fates, with functional consequences for the host immune system. These cytokine genes are encoded on different chromosomes. The recently described TH2 locus control region (LCR) coordinately regulates the TH2 cytokine genes by participating in a complex between the LCR and promoters of the cytokine genes Il4, Il5 and Il13. Although they are spread over 120 kilobases, these elements are closely juxtaposed in the nucleus in a poised chromatin conformation. In addition to these intrachromosomal interactions, we now describe interchromosomal interactions between the promoter region of the IFN-γ gene on chromosome 10 and the regulatory regions of the TH2 cytokine locus on chromosome 11. DNase I hypersensitive sites that comprise the TH2 LCR developmentally regulate these interchromosomal interactions. Furthermore, there seems to be a cell-type-specific dynamic interaction between interacting chromatin partners whereby interchromosomal interactions are apparently lost in favour of intrachromosomal ones upon gene activation. Thus, we provide an example of eukaryotic genes located on separate chromosomes associating physically in the nucleus via interactions that may have a function in coordinating gene expression.

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Figure 1: Spatial organization of the genetic loci used for the 3C analysis.
Figure 2: Interchromosomal, TH2 LCR-regulated interactions.
Figure 3: Intrachromosomal enhancer–promoter interactions in the Ifng gene.
Figure 4: Co-localization of the Ifng and TH2 loci as revealed by FISH.
Figure 5: Deletion of RHS7 hypersensitive site on chromosome 11 affects the expression of Ifng on chromosome 10.

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Acknowledgements

We thank Wyeth Laboratories for donation of IL-12. We also thank F. Manzo for assistance with manuscript preparation, T. Gerasimova for suggestions with the FISH protocols, and D. Sakkas for use of his fluorescence microscope. We are also grateful to F. G. Grosveld and W. de Laat for originally providing us with detailed protocols and help with establishing the 3C technique. We would like to thank C. Szekely for assistance with graphs. C.S. is supported by a Cancer Research Institute fellowship; M.D.L is partly supported by a Human Frontiers Science Program long-term fellowship; T.T. is supported by a Ruth L. Kirchstein NIH/NRSA/NIA post-doctoral fellowship; R.A.F. is an Investigator of the Howard Hughes Medical Institute.

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Correspondence to Richard A. Flavell.

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Supplementary information

Supplementary Figure S1

The IFN-γ and TH2 loci are colocalized in the nucleus as detected by two dimensional-fluorescence in situ hybridization (PPT 69 kb)

Supplementary Figure S2

Immuno-DNA FISH experiments reveal that the colocalized signals reside in euchromatin (PPT 902 kb)

Supplementary Figure S3 xm-repla ce_text {title}

Digestion of chromatinized genomic DNA within the nuclei of different cells types. (PPT 79 kb)

Supplementary Figure S4

IFNγ and TH2 loci colocalize in a more loose manner in the T cell nucleus. (PPT 45 kb)

Supplementary Figure Legends

Legends to accompany the above Supplementary Information (DOC 26 kb)

Supplementary Methods

Additional descripton of the methods used in this study, including Chromosome conformation capture analysis. (DOC 36 kb)

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Spilianakis, C., Lalioti, M., Town, T. et al. Interchromosomal associations between alternatively expressed loci. Nature 435, 637–645 (2005). https://doi.org/10.1038/nature03574

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