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Long-range chromatin regulatory interactions in vivo

Nature Genetics volume 32, pages 623–626 (2002)Cite this article

Abstract

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 transcription1,2,3, or act as entry sites4 or nucleation points5 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 sequences6,7,8,9,10,11,12,13. 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 vivo14. 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 β-globin gene cluster, is in close physical proximity to an actively transcribed HBB (β-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.

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Figure 1: RNA TRAP.
Figure 2: Measurement of the spread of biotin deposition.
Figure 3: Quantitative real-time PCR analyses of Hbb-b1-targeted RNA TRAP.
Figure 4: Quantitative real-time PCR analyses of Hbb-b2-targeted RNA TRAP.
Figure 5: Schematic representation of LCR–gene arrangement.

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Acknowledgements

We thank W. Reik for critical review of the manuscript and T. Collins and F. Kemp for their assistance. D.C. is supported by a Biotechnology and Biological Sciences Research Council Studentship. P.F. is a Senior Fellow of the Medical Research Council. This work was supported in part by the Medical Research Council and the Biotechnology and Biological Sciences Research Council, UK.

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  1. Laboratory of Chromatin and Gene Expression, Developmental Genetics Programme, The Babraham Institute, Cambridge, CB2 4AT, UK

    David Carter, Lyubomira Chakalova, Cameron S. Osborne, Yan-feng Dai & Peter Fraser

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  1. David Carter
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Correspondence to Peter Fraser.

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Carter, D., Chakalova, L., Osborne, C. et al. Long-range chromatin regulatory interactions in vivo. Nat Genet 32, 623–626 (2002). https://doi.org/10.1038/ng1051

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