Abnormal methylation pattern in constitutive and facultative (X inactive chromosome) heterochromatin of ICF patients

Abstract

We have investigated the distribution of DNA methylation in chromosomes and nuclei of normal individuals and ICF (Immunodeficiency, Centromeric instability and Facial abnormalities) syndrome patients, using 5-methylcytosine monoclonal antibody. In this syndrome, DNA digestion with methyl-sensitive enzymes has previously shown a specific hypomethylation of classical satellites located in constitutive heterochromatin. The chromosome methylation pattern confirms this hypomethylation showing in addition a clear undermethylation of facultative heterochromatin (X inactive chromosome). Antibodies give, in normal and ICF chromosomes, a non-uniform labeling of euchromatin, generating a weak R-like banding pattern on chromosomes. This pattern reflects an unequal distribution of DNA methylation over the genome disclosing another aspect of chromosome organization. The breakpoints of chromosome rearrangements and the heterochromatin stretchings observed in ICF patients were analyzed by means of in situ hybridization. These chromosome modifications involve hypomethylated classical DNA satellite sequences. The underlying hypomethylation, associated with an abnormal chromatin organization, may predispose to chromosome instability.

DNA methylation, methyltransferases, and cancer

“…These regions are normally heavily methylated in somatic cells but ICF patients demonstrate a marked hypomethylation of these regions (Jeanpierre et al, 1993;Tagarro et al, 1994), indicating that DNA methylation may be essential for proper centromere structure and stability. Repetitive elements elsewhere in the genome, including a subtelomeric repeat (Kondo et al, 2000), and single copy sequences on the inactive X chromosome (Hansen et al, 2000;Miniou et al, 1994) have also been shown to undergo hypomethylation in ICF cells. In contrast to the drastic hypomethylation of satellite 2 and 3 sequences, overall genomic 5-methylcytosine levels in ICF versus normal lymphoblastoid cell lines (LCLs) was unchanged (a result likely in¯uenced by cell culture), and primary ICF brain tissue showed only a 7% decrease in 5-methylcytosine content (Tuck-Muller et al, 2000).…”

“…For example, V(D)J recombination is reduced more than 100-fold when the recombination substrate is methylated (Hsieh and Lieber, 1992). In addition, Dnmt1 knockout ES cells exhibit a 10-fold increased mutation rate involving gene rearrangements (Chen et al, 1998), and individuals with ICF syndrome or cultured cells treated with 5-azaCdR show increased numbers of chromosomal translocations (Ji et al, 1997;Miniou et al, 1994).…”

Role of DNMT3B in the regulation of early neural and neural crest specifiers

“…21,23 Although global levels of DNA methylation are only slightly reduced in ICF patients, 24 pericentromeric satellite repeat sequences on chromosomes 1, 9 and 16 are highly decondensed and hypomethylated. 15,[25][26][27][28][29] Other non-satellite repeat regions 30 and a number of genes on inactive X chromosome in female ICF patients [31][32][33][34][35] are also hypomethylated. However, in-depth genome-wide analyses of the methylation effects of DNMT3B deficiency have not been previously performed.…”

The rise and fall of genomic methylation in cancer

“…17,18 Somewhat analogous to tumour development models, alterations in the methylation pattern may predispose cells to chromosomal instability with abnormal changes in chromatin organization. 19 Perhaps, one of the most fascinating features of genomic hypomethylation are the changes in DNA stability and chromatin undercondensation. 20 The knockout of DNMT3b in embryonic stem cells promotes genome-wide destabilization.…”

“…17,18 Somewhat analogous to tumour development models, alterations in the methylation pattern may predispose cells to chromosomal instability with abnormal changes in chromatin organization. 19 Perhaps, one of the most fascinating features of …”