Exploring the unique function of imprinting control centers in the PWS/AS-responsible region: finding from array-based methylation analysis in cases with variously sized microdeletions

Keiko MatsubaraEmail author,
Masatsune Itoh,
Kenji Shimizu,
Shinji Saito,
Keisuke Enomoto,
Kazuhiko Nakabayashi,
Kenichiro Hata,
Kenji Kurosawa,
Tsutomu Ogata,
Maki Fukami and
Masayo KagamiEmail author

Clinical Epigenetics201911:36

https://doi.org/10.1186/s13148-019-0633-1

Received: 28 December 2018
Accepted: 14 February 2019
Published: 28 February 2019

Abstract

Background

Human 15q11–13 is responsible for Prader-Willi syndrome (PWS) and Angelman syndrome (AS) and includes several imprinted genes together with bipartite elements named AS-IC (imprinting center) and PWS-IC. These concertedly confer allele specificity on 15q11–13. Here, we report DNA methylation status of 15q11–13 and other autosomal imprinted differentially methylated regions (iDMRs) in cases with various deletions within the PWS/AS-responsible region.

Methods

We performed array-based methylation analysis and examined the methylation status of CpG sites in 15q11–13 and in 71 iDMRs in six cases with various microdeletions, eight cases with conventional deletions within 15q11–13, and healthy controls.

Results

We detected 89 CpGs in 15q11–13 showing significant methylation changes in our cases. Of them, 14 CpGs in the SNORD116s cluster presented slight hypomethylation in the PWS cases and hypermethylation in the AS cases. No iDMRs at regions other than 15q11–13 showed abnormal methylation.

Conclusions

We identified CpG sites and regions in which methylation status is regulated by AS-IC and PWS-IC. This result indicated that each IC had unique functions and coordinately regulated the DNA methylation of respective alleles. In addition, only aberrant methylation at iDMRs in 15q11–13 leads to the development of the phenotypes in our cases.