The KCNQ1OT1 imprinting control region and non-coding RNA: new properties derived from the study of Beckwith–Wiedemann syndrome and Silver–Russell syndrome cases

Abstract

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 into two domains with independent imprinting control regions (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 the maintenance of genomic imprinting and with the SRS phenotype. The second is a 160 kb duplication also inverted and in cis, but resulting in the imprinting alteration of the centromeric domain. It includes the centromeric ICR (ICR2) and the most 5′ 20 kb of the non-coding 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 kb duplication carried discordant DNA methylation on the maternal chromosome and supported the hypothesis that the ICR2 sequence is not sufficient for establishing imprinted methylation and some other property, possibly orientation-dependent, is needed. Furthermore, the 1.2 Mb duplication demonstrated that all features are present for correct imprinting at ICR2 when this is duplicated and inverted within the entire cluster. In the individuals maternally inheriting the 160 kb duplication, ICR2 hypomethylation led to the expression of a truncated KCNQ1OT1 transcript and to down-regulation of CDKN1C. We demonstrated by chromatin RNA immunopurification 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 non-coding RNA.

(Epi)genotype–phenotype correlations in Beckwith–Wiedemann syndrome

“…The following molecular anomalies were identified: 190 IC2-LoM (184 epigenetic anomalies, 5 already published cases with familial IC2 duplications 21 and 1 IC2 deletion), 87 UPD carriers, 31 IC1-GoM (21 already published cases 22,23 including one IC1 duplication, one translocation, 11 familial microdeletions [24][25][26] ), 10 CDKN1C variants (all unrelated cases, 9 maternally inherited). None of the patients tested was positive for genome-wide UPD.…”

Familial 1.3-Mb 11p15.5p15.4 Duplication in Three Generations Causing Silver-Russell and Beckwith-Wiedemann Syndromes

“…There are at least 13 studies reporting maternally inherited duplications as a cause of SRS. Most of such rearrangements involve ICR1 and ICR2 and are usually caused by unbalanced translocations, but duplication of the whole ICR2 as well as partial duplication of ICR1 can also cause SRS [Fisher et al, 2002;Eggermann et al, 2005;Schonherr et al, 2007;South et al, 2008;Bliek et al, 2009;Cardarelli et al, 2010;Eggermann et al, 2010;Bonaldi et al, 2011;Demars et al, 2011;Begemann et al, 2012;Chiesa et al, 2012;Hu et al, 2013;Brown et al, 2014].…”

Looking for CDKN1C enhancers

“…These regions may also be involved in imprinting control, as they are included in two maternal duplications ( Figure 1) associated with ICR2 hypomethylation and BWS. 12,13 Intriguingly, region 3 also harbors strong binding sites for CTCF (Supplementary Figure 1), which have been shown to interact with other CTCF binding sequences near CDKN1C, possibly forming higher-order chromatin structures or insulators that may be disrupted by the duplication and result in ICR2 imprinting alteration. 14 In conclusion, by integrating information on chromosome rearrangements and chromatin features, we have identified three sequences meeting the features predicted for CDKN1C enhancers that help explain the phenotypes associated with different 11p15.5 deletions.…”