The KCNQ1OT1 Imprinting Control Region and non-coding RNA: new properties derived from the study of Beckwith-Wiedemann syndrome and Silver-Russell syndrome cases.

A cluster of imprinted genes at chromosome 11p15.5 is associated with the growth disorders Silver-Russell Syndrome (SRS) and Beckwith-Wiedemann Syndrome (BWS). The cluster is divided in two domains with independent Imprinting Control Centers (ICRs). We describe two maternal 11p15.5 microduplications with contrasting phenotypes. The first is an inverted and in cis duplication of the entire 11p15.5 cluster associated with maintenance of genomic imprinting and with SRS phenotype. The second is a 160 kbp duplication also inverted and in cis but resulting in imprinting alteration of the centromeric domain. It includes the centromeric ICR (ICR2) and the most 5' 20 kb of the noncoding KCNQ1OT1 gene. Its maternal transmission is associated with ICR2 hypomethylation and the BWS phenotype. By excluding epigenetic mosaicism, cell clones analysis indicated that the two closely located ICR2 sequences resulting from the 160 kbp duplication carried discordant DNA methylation on the maternal chromosome and supported the hypothesis that the ICR2 sequence is not sufficient for establishing imprinted methylation but some other property, possibly orientation-dependent, is needed. Furthermore, the 1.2 Mbp duplication demonstrated that all features for correct imprinting are present at ICR2 when this is duplicated and inverted within the entire cluster. In the individuals maternally inheriting the 160 kbp duplication, ICR2 hypomethylation led to expression of a truncated KCNQ1OT1 transcript and to down-regulation of CDKN1C. We demonstrated by ChRIP that the KCNQ1OT1 RNA interacts with chromatin through its most 5' 20 kb sequence, providing a mechanism likely mediating the silencing activity of this long noncoding RNA.