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Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops

Nature Genetics volume 36, pages 889–893 (2004)Cite this article

Abstract

Imprinted genes are expressed from only one of the parental alleles and are marked epigenetically by DNA methylation and histone modifications1,2,3,4,5. The paternally expressed gene insulin-like growth-factor 2 (Igf2) is separated by ∼100 kb from the maternally expressed noncoding gene H19 on mouse distal chromosome 7. Differentially methylated regions in Igf2 and H19 contain chromatin boundaries6,7,8,9, silencers10,11 and activators12 and regulate the reciprocal expression of the two genes in a methylation-sensitive manner by allowing them exclusive access to a shared set of enhancers13,14,15. Various chromatin models have been proposed that separate Igf2 and H19 into active and silent domains16,17,18,19. Here we used a GAL4 knock-in approach as well as the chromosome conformation capture technique to show that the differentially methylated regions in the imprinted genes Igf2 and H19 interact in mice. These interactions are epigenetically regulated and partition maternal and paternal chromatin into distinct loops. This generates a simple epigenetic switch for Igf2 through which it moves between an active and a silent chromatin domain.

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Figure 1: The Igf2-H19 locus and the GAL4-UAS knock-in strategy to detect physical interactions between the DMRs.
Figure 2: ChIP with an antibody to Myc directed against the transgenic GAL4-Myc–tagged protein after maternal (mat) or paternal (pat) transmission of the H19 DMR-UAS.
Figure 3: Interactions between the H19 and Igf2 DMRs were confirmed by 3C assays.
Figure 4: Parent-specific interactions between the DMRs provide an epigenetic switch for Igf2.

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Acknowledgements

We thank D. Carter and P. Fraser for helpful advice on the 3C method, P. Fraser for comments on the manuscript, D. Drage and T. Saunders of the Babraham Institute Gene Targeting facility for microinjections and S. Lopes and A. Lewis for advice on Q-PCR. This work was supported by Cancer Research UK and Biotechnology and Biological Sciences Research Council.

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  1. Adele Murrell

    Present address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK

  2. Sarah Heeson

    Present address: PDO Welwyn, Roche Products Limited, 40 Broadwater Road, Welwyn Garden City, AL7 3AY, UK

Authors and Affiliations

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

    Adele Murrell, Sarah Heeson & Wolf Reik

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  1. Adele Murrell
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Correspondence to Adele Murrell or Wolf Reik.

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Supplementary information

Supplementary Figure 1

Targeting the GAL4 binding site (UAS) into the H19 DMR. (PDF 71 kb)

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Murrell, A., Heeson, S. & Reik, W. Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops. Nat Genet 36, 889–893 (2004). https://doi.org/10.1038/ng1402

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