Dataset Information

Interplay between Histone and DNA Methylation Seen through Comparative Methylomes in Rare Mendelian Disorders

ABSTRACT: Genome wide DNA methylation profiling of blood samples from patients with genetic diseases of the epigenetic machineries. The Illumina Infinium HumanMethylation450 and the Infinium MethylationEPIC BeadChips were used to obtain DNA methylation profiles across approximately 450,000 and 850,000 CpGs in whole blood from patients with ICF and overgrowth syndrome. Samples included 1 ICF1, 2 ICFX, 2 TBRS and 2 Luscan-Lumish patients.

ORGANISM(S): Homo sapiens

PROVIDER: GSE167230 | GEO | 2021/05/25

REPOSITORIES: GEO

ACCESS DATA

Similar Datasets

Project description:Immunodeficiency, centromeric instability and facial anomalies syndrome (ICF) is a rare autosomal recessive disease, characterized by severe hypomethylation in pericentromeric regions of chromosomes (1, 16 and 9), marked immunodeficiency and facial anomalies. The majority of ICF patients present mutations in the DNMT3B gene, affecting the DNA methyltransferase activity of the protein. In the present study, we have used the Infinium 450K DNA methylation array to evaluate the methylation level of 450,000 CpGs in lymphoblastoid cell lines and untrasformed fibroblasts derived from ICF patients and healthy donors. Our results demonstrate that ICF-specific DNMT3B variants A603T/STP807ins and V699G/R54X cause global DNA hypomethylation compared to wild-type protein. We identified 181 novel differentially methylated positions (DMPs) including subtelomeric and intrachromosomic regions, outside the classical ICF-related pericentromeric hypomethylated positions. Interestingly, these sites were mainly located in intergenic regions and inside the CpG islands. Among the identified hypomethylated CpG-island associated genes, we confirmed the overexpression of three selected genes, BOLL, SYCP2 and NCRNA00221, in ICF compared to healthy controls, which are normally expressed in germ line and silenced in somatic tissues. In conclusion, this study contributes in clarifying the direct relationship between DNA methylation defect and gene expression impairment in ICF syndrome, identifying novel direct target genes of DNMT3B. A high percentage of the DMPs are located in the subtelomeric regions, indicating a specific role of DNMT3B in methylating these chromosomal sites. Therefore, we provide further evidence that hypomethylation in specific non-pericentromeric regions of chromosomes might be involved in the molecular pathogenesis of ICF syndrome. The detection of DNA hypomethylation at BOLL, SYCP2 and NCRNA00221 may pave the way for the development of specific clinical biomarkers with the aim to facilitate the identification of ICF patients.

Dataset Information

Interplay between Histone and DNA Methylation Seen through Comparative Methylomes in Rare Mendelian Disorders

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure