Silencing of CDKN1C (p57KIP2) is associated with hypomethylation at KvDMR1 in Beckwith-Wiedemann syndrome

Abstract

Context: Beckwith-Wiedemann syndrome (BWS) arises by several genetic and epigenetic mechanisms affecting the balance of imprinted gene expression in chromosome 11p15.5. The most frequent alteration associated with BWS is the absence of methylation at the maternal allele of KvDMR1, an intronic CpG island within the KCNQ1 gene. Targeted deletion of KvDMR1 suggests that this locus is an imprinting control region (ICR) that regulates multiple genes in 11p15.5. Cell culture based enhancer blocking assays indicate that KvDMR1 may function as a methylation modulated chromatin insulator and/or silencer. Objective: To determine the potential consequence of loss of methylation (LOM) at KvDMR1 in the development of BWS. Methods: The steady state levels of CDKN1C gene expression in fibroblast cells from normal individuals, and from persons with BWS who have LOM at KvDMR1, was determined by both real time quantitative polymerase chain reaction (qPCR) and ribonuclease protection assay (RPA). Methylation of the CDKN1C promoter region was assessed by Southern hybridisation using a methylation sensitive restriction endonuclease. Results: Both qPCR and RPA clearly demonstrated a marked decrease (86-93%) in the expression level of the CDKN1C gene in cells derived from patients with BWS, who had LOM at KvDMR1. Southern analysis indicated that downregulation of CDKN1C in these patients was not associated with hypermethylation at the presumptive CDKN1C promoter. Conclusions: An epimutation at KvDMR1, the absence of maternal methylation, causes the aberrant silencing of CDKN1C, some 180 kb away on the maternal chromosome. Similar to mutations at this locus, this silencing may give rise to BWS.

Epigenetic deregulation of imprinting in congenital diseases of aberrant growth

“…This loss of methylation correlates with biallelic expression of the KCNQ1OT1 non-coding transcript, (25,26) and strongly reduced CDKN1C expression. (27,28) The reduced expression of CDKN1C, a growth-reducing factor, is thought to be causally involved in the syndrome. This is supported by the finding that some BWS cases are caused by genetic mutations in CDKN1C, (29) and it was shown recently that this negative growth regulator can become epigenetically silenced by altered histone methylation as well.…”

Asymétrie des génomes parentaux

“…Chez de nombreux patients atteints du syndrome de BWS, la perte de fonction de l'allèle maternel est due à un défaut de méthylation au niveau de l'ICR qui régule le domaine KCNQ1. Cette perte de méthylation entraîne une répression biallélique du domaine et est corrélée à une diminution de l'expression du gène CDKN1C qui est un gène suppresseur de tumeur [28]. Par ailleurs, environ 10 % des patients présentent un gain de méthylation au niveau de l'ICR du domaine IGF2-H19 (Figure 2).…”

Imprinting centers, chromatin structure, and disease

“…Imprinting defects leading to absence of CpG methylation and loss of H3 K9 methylation on the maternal DMR-LIT1 allele cause diminished KIP2 expression [Diaz-Meyer et al, 2003]. It is plausible that the imprinting defect with loss of CpG methylation and loss of H3 Lys9 dimethylation causes a change of epigenotype of the KIP2/LIT1 region from maternal to paternal, reducing KIP2 expression.…”