Long-range Chromatin Regulatory Interactions in Vivo

Nat Genet. 2002 Dec;32(4):623-6. doi: 10.1038/ng1051. Epub 2002 Nov 11.


Communication between distal chromosomal elements is essential for control of many nuclear processes. For example, genes in higher eukaryotes often require distant enhancer sequences for high-level expression. The mechanisms proposed for long-range enhancer action fall into two basic categories. Non-contact models propose that enhancers act at a distance to create a favorable environment for gene transcription, or act as entry sites or nucleation points for factors that ultimately communicate with the gene. Contact models propose that communication occurs through direct interaction between the distant enhancer and the gene by various mechanisms that 'loop out' the intervening sequences. Although much attention has focused on contact models, the existence and nature of long-range interactions is still controversial and speculative, as there is no direct evidence that distant sequences physically interact in vivo. Here, we report the development of a widely applicable in situ technique to tag and recover chromatin in the immediate vicinity of an actively transcribed gene. We show that the classical enhancer element, HS2 of the prototypical locus control region (LCR) of the beta-globin gene cluster, is in close physical proximity to an actively transcribed HBB (beta-globin) gene located over 50 kb away in vivo, suggesting a direct regulatory interaction. The results give unprecedented insight into the in vivo structure of the LCR-gene interface and provide the first direct evidence of long-range enhancer communication.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites / genetics
  • Chromatin / genetics
  • Chromatin / metabolism*
  • Deoxyribonuclease I / metabolism
  • Embryo, Mammalian / metabolism
  • Enhancer Elements, Genetic*
  • Gene Expression Regulation, Developmental
  • Globins / chemistry
  • Globins / genetics
  • In Situ Hybridization, Fluorescence / methods
  • Introns
  • Liver / cytology
  • Liver / metabolism
  • Locus Control Region / genetics
  • Mice
  • Mice, Inbred BALB C
  • Models, Genetic
  • Oligonucleotide Array Sequence Analysis / methods
  • Polymerase Chain Reaction
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Transcription, Genetic


  • Chromatin
  • RNA, Messenger
  • Globins
  • Deoxyribonuclease I