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CTCF-binding sites flank CTG/CAG repeats and form a methylation-sensitive insulator at the DM1 locus

Abstract

An expansion of a CTG repeat at the DM1 locus causes myotonic dystrophy (DM) by altering the expression of the two adjacent genes, DMPK and SIX5, and through a toxic effect of the repeat-containing RNA. Here we identify two CTCF-binding sites that flank the CTG repeat and form an insulator element between DMPK and SIX5. Methylation of these sites prevents binding of CTCF, indicating that the DM1 locus methylation in congenital DM would disrupt insulator function. Furthermore, CTCF-binding sites are associated with CTG/CAG repeats at several other loci. We suggest a general role for CTG/CAG repeats as components of insulator elements at multiple sites in the human genome.

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Figure 1: In vitro matrix-attachment site assays identified MAR sites flanking the DM1 locus.
Figure 2: Identification of CTCF-binding sites in the vicinity of the DM1 CTG repeats.
Figure 3: Characterization of CTCF sites 1 and 2 at the DM1 locus.
Figure 4: Binding of CTCF occurs at the DM1 locus in vivo.
Figure 5: Nucleosome positioning at the DM1 locus CTG repeat.
Figure 6: The CTG repeats and surrounding CTCF-binding sites form a functional insulator.
Figure 7: CpG methylation prevents binding of CTCF to DM1 site 1 and DM1 site 2.
Figure 8: CTCF-binding sites are associated with the CTG/CAG repeat at other loci.

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Acknowledgements

This work was supported by National Institutes of Health, National Institute of Arthritis and Musculoskeletal and Skin Disease R01-AR45203 (S.J.T.) and National Institutes of Health R01-CA68360 (G.N.F.). We thank P. Rollini and K. Fournier for help with MAR assays, L. Ashworth at the Lawrence Livermore National Laboratory Genome Center for her help in compiling a contiguous sequence for the DM1 locus, J.D. Brook and M.G. Hamshere for cosmids, A.C. Bell, G. Felsenfeld, and C.A. Thornton for plasmids and P. Neiman, S. Collins, M. Groudine and B. Trask for critical comments on the manuscript.

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Correspondence to Victor V. Lobanenkov or Stephen J. Tapscott.

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Filippova, G., Thienes, C., Penn, B. et al. CTCF-binding sites flank CTG/CAG repeats and form a methylation-sensitive insulator at the DM1 locus. Nat Genet 28, 335–343 (2001). https://doi.org/10.1038/ng570

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