Beckwith-Wiedemann Syndrome study with ChIP_Seq (NGS), WGS data on dbGaP (7 participants)

phs002408 — The Role of CTCF in the Organization of the Centromeric 11p15 Imprinted    Domain Interactome

<p>Beckwith-Wiedemann Syndrome (BWS) is the most common human imprinting disorder and comprises a spectrum of overgrowth phenotypes. While approximately 35% of BWS cases are caused by isolated loss of methylation (LOM) at the human imprinting center 2 (IC2) on chromosome 11p15, only around 5% of patients develop BWS due to structural alterations to the IC2 domain. In this study, we identify a BWS-causing 7.6 kB familial deletion within the IC2 domain by performing Whole Genome Sequencing (WGS) on patient-derived human fibroblasts. Using a chromatin conformation capture technique, Capture C, on 3 control fibroblast samples, 3 BWS LOM fibroblast samples, and the single familial deletion sample, we investigate how the domain interactome changes in BWS patients. We find that high-strength interactions occur within the IC2 domain between the 5’ end of <a href="https://www.ncbi.nlm.nih.gov/gene/3784">KCNQ1</a>, KCNQ1 intron 2, and the 5’ end of <a href="https://www.ncbi.nlm.nih.gov/gene/1028">CDKN1C</a> in the control profile that are largely abrogated in the BWS samples, but some lower frequency contacts between the imprinting control region (ICR), KCNQ1 intron 2, and the 5’ end of CDKN1C are unaffected. We conclude that the strong KCNQ1-CDKN1C interactions are important in maintaining the domain imprint.</p>