Three novel DNMT3B mutations in Japanese patients with ICF syndrome

Abstract

ICF syndrome is a rare autosomal recessive disorder characterized by immunodeficiency, centromeric instability, and facial anomalies. It is caused by mutations in a de novo DNA methyltransferase gene, DNMT3B. We here report the first three Japanese cases of ICF syndrome from two unrelated families. All patients had typical facial dysmorphism and immunoglobulin A (IgA) deficiency, but none of them had apparent mental retardation. Cytogenetic analysis of peripheral blood lymphocytes showed chromosomal abnormalities, including multiradial configurations and a stretching of the pericentromeric heterochromatin of chromosomes 1 and 16. Hypomethylation of classical satellite 2 DNA was also observed. Mutation analyses of DNMT3B revealed three novel mutations: patient 1 from the first family was a compound heterozygote for a nonsense mutation (Q42Term) and a missense mutation (R832Q); patients 2 and 3 from the second family were both homozygous for a missense mutation (S282P). The R832Q mutation occurred within the conserved methyltransferase domain, and thus may affect the enzyme activity directly. The S282P mutation, on the other hand, occurred close to the PWWP domain, which is presumably involved in protein-protein interaction. This is the first missense mutation mapped to the N-terminal half of the protein, suggesting that the region plays an important role in the regulation of the DNMT3B enzyme.

Chromatin Targeting of de Novo DNA Methyltransferases by the PWWP Domain

“…A recently identified missense mutation (S282P) in two patients falls within the PWWP domain (23). The homozygous patients exhibited all typical features including loss of methylation in the classical satellite 2 DNA but had no apparent mental retardation.…”

“…The four mutations found in the N-terminal region are either nonsense or frameshift mutations, which would terminate the protein synthesis completely. One most recently identified missense mutation close to the N terminus (S282P, homozygous) is of great interest because it falls into the PWWP domain (23). We suspected that this point mutation might lead to deficiency in genomic methylation in patients due to the loss of chromatin targeting capacity of the affected DNMT3B enzyme.…”

“…The PWWP domain is essential for chromatin targeting. An ICF missense mutation located in this domain (23) causes the loss of chromatin targeting ability, which is suggested to contribute to the deficiency in DNA methylation in ICF patients. Collectively our findings underscore the importance of PWWP-mediated chromatin targeting for the function of DNA methyltransferases and provide a framework for future study of regulation of DNA methylation in development and pathogenesis.…”

Cancer cells express aberrant DNMT3B transcripts encoding truncated proteins

“…Dnmt1À/À embryonic stem cells display extensive demethylation of endogenous retroviral DNA (Li et al, 1992), and murine embryonic stem cells lacking Dnmt3b demonstrate hypomethylation of minor satellite sequences (Okano et al, 1999). Patients with a rare autosomal recessive syndrome, the immunodeficiency, centromere instability, facial anomalies (ICF) syndrome, have germline mutations in the DNMT3B gene (Hansen et al, 1999;Xu et al, 1999;Shirohzu et al, 2002), and lymphocytes from affected individuals display hypomethylation of repetitive DNA sequences. Furthermore, mice expressing Dnmt3b alleles similar to those found in ICF syndrome are small with abnormal craniofacial development and hypomethylation of repetitive elements, suggesting that these alleles encode hypomorphic proteins (Ueda et al, 2006).…”

Diverse Domains of (Cytosine-5)-DNA Methyltransferases: Structural and Functional Characterization

“…However, such mutants are catalytically active since they are able to methylate DNA in other regions [121]. In humans, S282P point mutation in the PWWP domain of Dnmt3b causes the ICF syndrome [124]. In this case, the disease is likely to be caused by the enzyme improper distribution in nuclei rather than by its insufficient catalytic activity.…”