Exhaustive methylation analysis revealed uneven profiles of methylation at IGF2/ICR1/H19 11p15 loci in Russell Silver syndrome

Background The structural organisation of the human IGF2/ ICR1 /H19 11p15 domain is very complex, and the mechanisms underlying its regulation are poorly understood. The Imprinted Center Region 1 (ICR1) contains seven binding sites for the zinc-finger protein CTCF (CBS: CTCF Binding Sites); three additional differentially methylated regions (DMR) are located at the H19 promoter ( H19 DMR) and two in the IGF2 gene (DMR0 and DMR2), respectively. Loss of imprinting at the IGF2/ ICR1 /H19 domain results in two growth disorders with opposite phenotypes: Beckwith–Wiedemann syndrome and Russell Silver syndrome (RSS). Despite the IGF2/ ICR1 /H19 locus being widely studied, the extent of hypomethylation across the domain remains not yet addressed in patients with RSS. Methods We assessed a detailed investigation of the methylation status of the 11p15 ICR1 CBS1-7, IGF2 DMR0 and H19 DMR ( H19 promoter) in a population of controls (n=50) and RSS carrying (n=104) or not (n=65) carrying a hypomethylation at the 11p15 ICR1 region. Results The methylation indexes (MI) were balanced at all regions in the control population and patients with RSS without any as yet identified molecular anomaly. Interestingly, patients with RSS with ICR1 hypomethylation showed uneven profiles of methylation among the CBSs and DMRs. Furthermore, normal MIs at CBS1 and CBS7 were identified in 9% of patients. Conclusions The hypomethylation does not spread equally throughout the IGF2/ ICR1 /H19 locus, and some loci could have normal MI, which may lead to underdiagnosis of patients with RSS with ICR1 hypomethylation. The uneven pattern of methylation suggests that some CBSs may play different roles in the tridimensional chromosomal looping regulation of this locus.