title: The molecular function and clinical phenotype of partial deletions of the IGF2/H19 imprinting control region depends on the spatial arrangement of the remaining CTCF-binding sites.
abstract: At chromosome 11p15.5, the imprinting centre 1 (IC1) controls the parent of origin-specific expression of the IGF2 and H19 genes. The 5 kb IC1 region contains multiple target sites (CTS) for the zinc-finger protein CTCF, whose binding on the maternal chromosome prevents the activation of IGF2 and allows that of H19 by common enhancers. CTCF binding helps maintaining the maternal IC1 methylation-free, whereas on the paternal chromosome gamete-inherited DNA methylation inhibits CTCF interaction and enhancer-blocking activity resulting in IGF2 activation and H19 silencing. Maternally inherited 1.4-2.2 kb deletions are associated with methylation of the residual CTSs and Beckwith-Wiedemann syndrome, although with different penetrance and expressivity. We explored the relationship between IC1 microdeletions and phenotype by analysing a number of previously described and novel mutant alleles. We used a highly quantitative assay based on next generation sequencing to measure DNA methylation in affected families and analysed enhancer-blocking activity and CTCF binding in cultured cells. We demonstrate that the microdeletions mostly affect IC1 function and CTCF binding by changing CTS spacing. Thus, the extent of IC1 inactivation and the clinical phenotype are influenced by the arrangement of the residual CTSs. A CTS spacing similar to the wild-type allele results in moderate IC1 inactivation and is associated with stochastic DNA methylation of the maternal IC1 and incomplete penetrance. Microdeletions with different CTS spacing display severe IC1 inactivation and are associated with IC1 hypermethylation and complete penetrance. Careful characterization of the IC1 microdeletions is therefore needed to predict recurrence risks and phenotypical outcomes.
authors.affiliation: Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany.
authors.forename: Jasmin
authors.initials: J
authors.lastname: Beygo
authors.forename: Valentina
authors.initials: V
authors.lastname: Citro
authors.forename: Angela
authors.initials: A
authors.lastname: Sparago
authors.forename: Agostina
authors.initials: A
authors.lastname: De Crescenzo
authors.forename: Flavia
authors.initials: F
authors.lastname: Cerrato
authors.forename: Melanie
authors.initials: M
authors.lastname: Heitmann
authors.forename: Katrin
authors.initials: K
authors.lastname: Rademacher
authors.forename: Andrea
authors.initials: A
authors.lastname: Guala
authors.forename: Thorsten
authors.initials: T
authors.lastname: Enklaar
authors.forename: Cecilia
authors.initials: C
authors.lastname: Anichini
authors.forename: Margherita
authors.initials: M
authors.lastname: Cirillo Silengo
authors.forename: Notker
authors.initials: N
authors.lastname: Graf
authors.forename: Dirk
authors.initials: D
authors.lastname: Prawitt
authors.forename: Maria Vittoria
authors.initials: MV
authors.lastname: Cubellis
authors.forename: Bernhard
authors.initials: B
authors.lastname: Horsthemke
authors.forename: Karin
authors.initials: K
authors.lastname: Buiting
authors.forename: Andrea
authors.initials: A
authors.lastname: Riccio
mesh_terms: D000483:Alleles; D001665:Binding Sites / Q000235:genetics; D000076246:CCCTC-Binding Factor; D002478:Cells, Cultured; D047369:Chromatin Immunoprecipitation; D002880:Chromosomes, Human, Pair 11 / Q000235:genetics; D019175:DNA Methylation; D017353:Gene Deletion; D005786:Gene Expression Regulation; D020868:Gene Silencing; D056426:Genetic Loci; D018392:Genomic Imprinting; D006801:Humans; D007335:Insulin-Like Growth Factor II / Q000235:genetics* / Q000378:metabolism; D010375:Pedigree; D010641:Phenotype; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D012097:Repressor Proteins / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA
chemical_list: D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; C094335:H19 long non-coding RNA; C035170:IGF2 protein, human; D062085:RNA, Long Noncoding; D012097:Repressor Proteins; D007335:Insulin-Like Growth Factor II