The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome

Abstract

DNA methylation is an important regulator of genetic information in species ranging from bacteria to humans. DNA methylation appears to be critical for mammalian development because mice nullizygous for a targeted disruption of the DNMT1 DNA methyltransferase die at an early embryonic stage. No DNA methyltransferase mutations have been reported in humans until now. We describe here the first example of naturally occurring mutations in a mammalian DNA methyltransferase gene. These mutations occur in patients with a rare autosomal recessive disorder, which is termed the ICF syndrome, for immunodeficiency, centromeric instability, and facial anomalies. Centromeric instability of chromosomes 1, 9, and 16 is associated with abnormal hypomethylation of CpG sites in their pericentromeric satellite regions. We are able to complement this hypomethylation defect by somatic cell fusion to Chinese hamster ovary cells, suggesting that the ICF gene is conserved in the hamster and promotes de novo methylation. ICF has been localized to a 9-centimorgan region of chromosome 20 by homozygosity mapping. By searching for homologies to known DNA methyltransferases, we identified a genomic sequence in the ICF region that contains the homologue of the mouse Dnmt3b methyltransferase gene. Using the human sequence to screen ICF kindreds, we discovered mutations in four patients from three families. Mutations include two missense substitutions and a 3-aa insertion resulting from the creation of a novel 3 splice acceptor. None of the mutations were found in over 200 normal chromosomes. We conclude that mutations in the DNMT3B are responsible for the ICF syndrome.DNA methylation ͉ somatic cell complementation ͉ consanguinity ͉ RNA splicing

Epigenetic changes in virus-associated human cancers

“…Similarly, cell culture studies have demonstrated an important role for DNMT3A in cancer cell survival [21]. ICF syndrome, a rare disorder characterized by immunodeficiency, centromeric instability, and facial abnormalities, is caused by germ-line mutations in dnmt3b [22,23]. Interestingly, mouse embryo fibroblasts deficient of DNMT3B are resistant to transformation by SV40 large T antigen and contain active Ras oncogenes [24], suggesting that epigenetic and genetic mechanisms likely act in concert during cellular transformation.…”

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).…”

A Method to Detect DNA Methyltransferase I Gene Transcription In Vitro in Aging Systems

“…Morphological data suggested that cells were arrested in interphase, and this was supported by biochemical analysis that indicated cells had not entered M-phase (9). Dnmt1 −/− and Dnmt3b −/− mutations in mice result in embryonic death while mice with mutations Dnmt1,3a −/− die at approx 4 wk of age (10,11). A study investigating DNMT activity in human systems showed that overall maintenance methylation decreased during cellular senescence of WI-38 fibroblasts and that combined de novo methylation initially decreased but later increased as these cells aged (12).…”