Non-random, individual-specific methylation profiles are present at the sixth CTCF binding site in the human H19/IGF2 imprinting control region.
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.
Tost
Jörg
J
Laboratoire d'Epigénétique, Centre National de Génotypage, 2 rue Gaston Crémieux, 91000 Evry, France. tost@cng.fr
Jammes
Hélène
H
Dupont
Jean-Michel
JM
Buffat
Christophe
C
Robert
Brigitte
B
Mignot
Thérèse-Marie
TM
Mondon
Françoise
F
Carbonne
Bruno
B
Siméoni
Umberto
U
Grangé
Gilles
G
Kerjean
Antoine
A
Ferré
Françoise
F
Gut
Ivo Glynne
IG
Vaiman
Daniel
D
D001665:Binding Sites; D000076246:CCCTC-Binding Factor; D018899:CpG Islands; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000378:metabolism*; D005260:Female; D015870:Gene Expression; D018392:Genomic Imprinting; D005838:Genotype; D006801:Humans; D007231:Infant, Newborn; D040582:Inheritance Patterns; D007335:Insulin-Like Growth Factor II; D008297:Male; D008957:Models, Genetic; D010375:Pedigree; D010920:Placenta / Q000378:metabolism; D016133:Polymerase Chain Reaction; D011506:Proteins / Q000235:genetics* / Q000378:metabolism; D062085:RNA, Long Noncoding; D022661:RNA, Untranslated / Q000235:genetics* / Q000378:metabolism; D012045:Regulatory Sequences, Nucleic Acid; D012097:Repressor Proteins / Q000378:metabolism*
D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; C000619698:Ctcf protein, mouse; D004268:DNA-Binding Proteins; C094335:H19 long non-coding RNA; C035170:IGF2 protein, human; D011506:Proteins; D062085:RNA, Long Noncoding; D022661:RNA, Untranslated; D012097:Repressor Proteins; D007335:Insulin-Like Growth Factor II