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 (H19DMR) 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, IGF2DMR0 and H19DMR (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.
INSERM, UMR_S 938, CDR Saint-Antoine, Paris, France Sorbonne Universités, UPMC Univ Paris 06, UMR_S 938, CDR Saint-Antoine, Paris, France Department of Pediatric Endocrinology, APHP, Armand Trousseau Hospital, Paris, France Epigenetics Programme, The Babraham Institute, Cambridge, UK.
Salah
S
Azzi
INSERM, UMR_S 938, CDR Saint-Antoine, Paris, France.
Virginie
V
Steunou
Laboratory for Epigenetics and Environment (LEE), National Genotyping Center, CEA-Institute of Genomics, Evry, France.
Jörg
J
Tost
INSERM, UMR_S 938, CDR Saint-Antoine, Paris, France Sorbonne Universités, UPMC Univ Paris 06, UMR_S 938, CDR Saint-Antoine, Paris, France Department of Pediatric Endocrinology, APHP, Armand Trousseau Hospital, Paris, France.
Sylvie
S
Rossignol
Department of Pediatric Endocrinology, APHP, Armand Trousseau Hospital, Paris, France.
Nathalie
N
Thibaud
Department of Pediatric Endocrinology, APHP, Armand Trousseau Hospital, Paris, France.
Cristina
C
Das Neves
Department of Pediatric Endocrinology, APHP, Armand Trousseau Hospital, Paris, France.
Marilyne
M
Le Jule
INSERM, UMR_S 938, CDR Saint-Antoine, Paris, France Sorbonne Universités, UPMC Univ Paris 06, UMR_S 938, CDR Saint-Antoine, Paris, France Department of Pediatric Endocrinology, APHP, Armand Trousseau Hospital, Paris, France.
Walid Abi
WA
Habib
INSERM, UMR_S 938, CDR Saint-Antoine, Paris, France Sorbonne Universités, UPMC Univ Paris 06, UMR_S 938, CDR Saint-Antoine, Paris, France.
Annick
A
Blaise
INSERM, Centre for research in Epidemiology and Population Health (CESP), U1018, Lifelong epidemiology of obesity, diabetes and renal disease team, Villejuif, France Paris-Sud University, UMRS 1018, Villejuif, France.
Yves
Y
Koudou
Epigenetics Programme, The Babraham Institute, Cambridge, UK.
Florence
F
Busato
INSERM, UMR_S 938, CDR Saint-Antoine, Paris, France Sorbonne Universités, UPMC Univ Paris 06, UMR_S 938, CDR Saint-Antoine, Paris, France Department of Pediatric Endocrinology, APHP, Armand Trousseau Hospital, Paris, France.
Yves
Y
Le Bouc
INSERM, UMR_S 938, CDR Saint-Antoine, Paris, France Sorbonne Universités, UPMC Univ Paris 06, UMR_S 938, CDR Saint-Antoine, Paris, France Department of Pediatric Endocrinology, APHP, Armand Trousseau Hospital, Paris, France.
Irène
I
Netchine
D001483:Base Sequence; D002880:Chromosomes, Human, Pair 11 / Q000235:genetics*; D019175:DNA Methylation / Q000235:genetics*; D005786:Gene Expression Regulation / Q000235:genetics*; D006801:Humans; D007335:Insulin-Like Growth Factor II / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D010297:Paris; D025341:Principal Component Analysis; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D056730:Silver-Russell Syndrome / Q000235:genetics*; D013447:Sulfites
C094335:H19 long non-coding RNA; C035170:IGF2 protein, human; D062085:RNA, Long Noncoding; D013447:Sulfites; D007335:Insulin-Like Growth Factor II; C009279:sodium bisulfite
11p15 region; Growth retardation; IGF2/H19 domain; Imprinting Disorders; Russell Silver Syndrome