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Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene

Abstract

The expression of the insulin-like growth factor 2 (Igf2) and H19 genes is imprinted. Although these neighbouring genes share an enhancer1, H19 is expressed only from the maternal allele, and Igf2 only from the paternally inherited allele2,3. A region of paternal-specific methylation upstream of H19 appears to be the site of an epigenetic mark that is required for the imprinting of these genes4,5. A deletion within this region results in loss of imprinting of both H19 and Igf2 (ref. 5). Here we show that this methylated region contains an element that blocks enhancer activity. The activity of this element is dependent upon the vertebrate enhancer-blocking protein CTCF. Methylation of CpGs within the CTCF-binding sites eliminates binding of CTCF in vitro, and deletion of these sites results in loss of enhancer-blocking activity in vivo, thereby allowing gene expression. This CTCF-dependent enhancer-blocking element acts as an insulator. We suggest that it controls imprinting of Igf2. The activity of this insulator is restricted to the maternal allele by specific DNA methylation of the paternal allele. Our results reveal that DNA methylation can control gene expression by modulating enhancer access to the gene promoter through regulation of an enhancer boundary.

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Figure 1: A differentially methylated region upstream of H19 has the enhancer-blocking properties of an insulator.
Figure 2: Conserved CTCF sites within the H19 ICR.
Figure 3: CTCF is responsible for the methylation-sensitive enhancer-blocking activities of the mouse and human ICRs.
Figure 4: A model for methylation-dependent modulation of insulator action in the epigenetic regulation of Igf2.

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Acknowledgements

We thank S. Tilghman and members of her laboratory for sharing data before publication, and R. Martin, C. Trainor and members of the Felsenfeld laboratory for discussions and comments on the manuscript.

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Correspondence to Gary Felsenfeld.

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Bell, A., Felsenfeld, G. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 405, 482–485 (2000). https://doi.org/10.1038/35013100

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