Interchromosomal associations between alternatively expressed loci

Nature. 2005 Jun 2;435(7042):637-45. doi: 10.1038/nature03574. Epub 2005 May 8.


The T-helper-cell 1 and 2 (T(H)1 and T(H)2) pathways, defined by cytokines interferon-gamma (IFN-gamma) 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 T(H)2 locus control region (LCR) coordinately regulates the T(H)2 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-gamma gene on chromosome 10 and the regulatory regions of the T(H)2 cytokine locus on chromosome 11. DNase I hypersensitive sites that comprise the T(H)2 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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Alleles
  • Animals
  • Cell Nucleus / genetics
  • Cell Nucleus / metabolism
  • Cells, Cultured
  • Chromatin / genetics*
  • Chromatin / metabolism*
  • Chromosome Positioning / genetics*
  • Chromosomes, Mammalian / genetics*
  • Chromosomes, Mammalian / metabolism*
  • Cytokines / genetics*
  • Deoxyribonuclease I / metabolism
  • Enhancer Elements, Genetic / genetics
  • Gene Expression Regulation*
  • In Situ Hybridization, Fluorescence
  • Interferon-gamma / genetics
  • Interleukins / genetics
  • Locus Control Region / genetics
  • Mice
  • Mice, Inbred C57BL
  • Polymerase Chain Reaction
  • Promoter Regions, Genetic / genetics
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Th1 Cells / cytology
  • Th1 Cells / metabolism
  • Th2 Cells / cytology
  • Th2 Cells / metabolism
  • Transcriptional Activation


  • Chromatin
  • Cytokines
  • Interleukins
  • RNA, Messenger
  • Interferon-gamma
  • Deoxyribonuclease I