Tissue Specific DNA Methylation Patterns: Biochemistry of Formation and Possible Role

Abstract

It is now well established that tissue specific DNA methylation patterns exist in vertebrates. A long list of gene sequences exhibiting tissue specific expression have been studied in the past 8 years with respect to their methylation pattern (for recent review, see Razin and Szyf, 1984). Investigators took advantage of the restriction enzymes HpaII (CCGG) and HhaI (GCGC) that are inactive when the internal cytosine residue in their recognition site is methylated. Cleaving the genomic DNA with one of these enzymes, blotting and hybridizing with the appropriate labeled probes allowed the establishment of the state of methylation of each of these specific sites in a given gene sequence (Bird and Southern, 1978). The results of such an analysis represent the methylation pattern of the given sequence since methylation of higher eukaryotic DNA occurs exclusively at cytosine residues in CpG sequences. In most studies, when the pattern of methylation of a tissue specific gene has been correlated with the expression of the gene, an inverse correlation has been found (Yisraeli and Szyf, 1984). Many genes are under-methylated in the tissue of expression as compared to the extent of their methylation in other tissues. It should, however, be noted that in about 20% of the genes studied, no such correlation is found. Keeping in mind that the HpaII and HhaI recognition sequences constitute a subset of the CpG sites in the DNA and represent only about 10% of the CpGs, it is not altogether surprising that some exceptions are found to the rule correlating gene expression with undermethylation of the gene. In fact, the correlation found in most genes is overwhelming and indicates that patterns of methylation of CCGG and GCGC sites represent quite faithfully the pattern of methylation of CpGs. This compilation of data strongly supports the ten year old theory, independently put forward by Riggs (1975) and Holliday and Pugh (1978), that DNA methylation in higher organisms is associated with differentiation.