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Non-random, individual-specific methylation profiles are present at the sixth CTCF binding site in the human H19/IGF2 imprinting control region.

Tost J, Jammes H, Dupont JM, Buffat C, Robert B, Mignot TM, Mondon F, Carbonne B, Siméoni U, Grangé G, Kerjean A, Ferré F, Gut IG, Vaiman D - Nucleic Acids Res. (2006)

Bottom Line: Expression of imprinted genes is classically associated with differential methylation of specific CpG-rich DNA regions (DMRs).This epigenetic polymorphism was confined to the sixth CTCF binding site while a unique median-methylated profile was found at the third CTCF binding site as well as in the H19 promoter.The existence of three individual-specific epigenotypes in the H19 DMR in a non-pathological situation means it is important to reconsider the diagnostic value and functional importance of the sixth CTCF binding site.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire d'Epigénétique, Centre National de Génotypage, 2 rue Gaston Crémieux, 91000 Evry, France. tost@cng.fr

ABSTRACT
Expression of imprinted genes is classically associated with differential methylation of specific CpG-rich DNA regions (DMRs). The H19/IGF2 locus is considered a paradigm for epigenetic regulation. In mice, as in humans, the essential H19 DMR--target of the CTCF insulator--is located between the two genes. Here, we performed a pyrosequencing-based quantitative analysis of its CpG methylation in normal human tissues. The quantitative analysis of the methylation level in the H19 DMR revealed three unexpected discrete, individual-specific methylation states. This epigenetic polymorphism was confined to the sixth CTCF binding site while a unique median-methylated profile was found at the third CTCF binding site as well as in the H19 promoter. Monoallelic expression of H19 and IGF2 was maintained independently of the methylation status at the sixth CTCF binding site and the IGF2 DMR2 displayed a median-methylated profile in all individuals and tissues analyzed. Interestingly, the methylation profile was genetically transmitted. Transgenerational inheritance of the H19 methylation profile was compatible with a simple model involving one gene with three alleles. The existence of three individual-specific epigenotypes in the H19 DMR in a non-pathological situation means it is important to reconsider the diagnostic value and functional importance of the sixth CTCF binding site.

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DNA methylation profiles of the third CTCF binding site obtained by pyrosequencing. The degree of methylation (%) was analyzed for 11 CpGs. Analysis was performed on the same samples as for the IGF2 DMR2 (Figure 6). A unique profile was obtained. Only 14 samples are shown for clarity.
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fig5: DNA methylation profiles of the third CTCF binding site obtained by pyrosequencing. The degree of methylation (%) was analyzed for 11 CpGs. Analysis was performed on the same samples as for the IGF2 DMR2 (Figure 6). A unique profile was obtained. Only 14 samples are shown for clarity.

Mentions: To determine the extent of the variable epigenetic profiles, we analyzed 10 CpGs encompassing the third CTCF site (Figure 5) as well as 9 CpGs in the direct proximal promoter region of H19. All samples displayed ∼40% methylation at these two loci.


Non-random, individual-specific methylation profiles are present at the sixth CTCF binding site in the human H19/IGF2 imprinting control region.

Tost J, Jammes H, Dupont JM, Buffat C, Robert B, Mignot TM, Mondon F, Carbonne B, Siméoni U, Grangé G, Kerjean A, Ferré F, Gut IG, Vaiman D - Nucleic Acids Res. (2006)

DNA methylation profiles of the third CTCF binding site obtained by pyrosequencing. The degree of methylation (%) was analyzed for 11 CpGs. Analysis was performed on the same samples as for the IGF2 DMR2 (Figure 6). A unique profile was obtained. Only 14 samples are shown for clarity.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1636469&req=5

fig5: DNA methylation profiles of the third CTCF binding site obtained by pyrosequencing. The degree of methylation (%) was analyzed for 11 CpGs. Analysis was performed on the same samples as for the IGF2 DMR2 (Figure 6). A unique profile was obtained. Only 14 samples are shown for clarity.
Mentions: To determine the extent of the variable epigenetic profiles, we analyzed 10 CpGs encompassing the third CTCF site (Figure 5) as well as 9 CpGs in the direct proximal promoter region of H19. All samples displayed ∼40% methylation at these two loci.

Bottom Line: Expression of imprinted genes is classically associated with differential methylation of specific CpG-rich DNA regions (DMRs).This epigenetic polymorphism was confined to the sixth CTCF binding site while a unique median-methylated profile was found at the third CTCF binding site as well as in the H19 promoter.The existence of three individual-specific epigenotypes in the H19 DMR in a non-pathological situation means it is important to reconsider the diagnostic value and functional importance of the sixth CTCF binding site.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire d'Epigénétique, Centre National de Génotypage, 2 rue Gaston Crémieux, 91000 Evry, France. tost@cng.fr

ABSTRACT
Expression of imprinted genes is classically associated with differential methylation of specific CpG-rich DNA regions (DMRs). The H19/IGF2 locus is considered a paradigm for epigenetic regulation. In mice, as in humans, the essential H19 DMR--target of the CTCF insulator--is located between the two genes. Here, we performed a pyrosequencing-based quantitative analysis of its CpG methylation in normal human tissues. The quantitative analysis of the methylation level in the H19 DMR revealed three unexpected discrete, individual-specific methylation states. This epigenetic polymorphism was confined to the sixth CTCF binding site while a unique median-methylated profile was found at the third CTCF binding site as well as in the H19 promoter. Monoallelic expression of H19 and IGF2 was maintained independently of the methylation status at the sixth CTCF binding site and the IGF2 DMR2 displayed a median-methylated profile in all individuals and tissues analyzed. Interestingly, the methylation profile was genetically transmitted. Transgenerational inheritance of the H19 methylation profile was compatible with a simple model involving one gene with three alleles. The existence of three individual-specific epigenotypes in the H19 DMR in a non-pathological situation means it is important to reconsider the diagnostic value and functional importance of the sixth CTCF binding site.

Show MeSH
Related in: MedlinePlus