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CpG methylation is involved in a wide range of biological processes in vertebrates as well as in plants and fungi. To date, three enzymes, Dnmt1, Dnmt3a, and Dnmt3b, are known to have DNA methyltransferase activity in mouse and human. It has been proposed that de novo methylation observed in early embryos is predominantly carried out by the Dnmt3a and Dnmt3b methyltransferases, while Dntm1 is believed to be responsible for maintaining the established methylation patterns upon replication. Analysis of the sites methylated in vivo using the bisulfite genomic sequencing method confirms the previous finding that some regions of the plasmid are much more methylated by Dnmt3a than other regions on the same plasmid. However, the preferred targets of the enzyme cannot be determined due to the presence of other methylases, DNA binding proteins, and chromatin structure. To discern the DNA targets of Dnmt3a without these compounding factors, sites methylated by Dnmt3a in vitro were analyzed. These analyses revealed that the two cDNA strands have distinctly different methylation patterns. Dnmt3a prefers CpG sites on a strand in which it is flanked by pyrimidines over CpG sites flanked by purines in vitro. These findings indicate that, unlike Dnmt1, Dnmt3a most likely methylates one strand of DNA without concurrent methylation of the CpG site on the complementary strand. These findings also indicate that Dnmt3a may methylate some CpG sites more frequently than others, depending on the sequence context. Methylation of each DNA strand independently and with possible sequence preference is a novel feature among the known DNA methyltransferases.CpG methylation is considered to be important for development, X chromosome inactivation, genomic imprinting, and suppression of transposons in mammals. The critical role played by the establishment and maintenance of DNA methylation has been demonstrated by the findings that homozygous disruption of any one of the three known methyltransferases in mice leads to lethality (23,28). It has also been shown that some methyl-CpG binding proteins associate with histone deacetylase and repress transcription (for a review, see reference 6). The importance of this has been exemplified by the recent identification that a human disease, Rett syndrome, is caused by mutations in one of the methyl-CpG binding proteins, MeCP2 (1). Recently, changes in DNA methylation patterns have also been implicated in carcinogenesis (for a review, see reference 18).Three vertebrate genes with known methyltransferase function have been identified, namely, Dnmt1, Dnmt3a, and Dnmt3b (4,27). Dnmt1 has been considered as a maintenance methyltransferase mostly based on its association with the replication foci (22) and its preference for hemimethylated DNA (29,30,37). It has been reported that Dnmt1 is capable of methylating fully unmethylated DNA as well as non-CpG sites in vitro (30,37). Dnmt1 has also been described to have no site preference other than CpGs (37). In Dnmt1 knockout mice, there is still a considerable a...

We conducted a genomewide screen for prostate cancer-susceptibility genes on the basis of data from 98 families from the United States and Canada that had three or more verified diagnoses of prostate cancer among first- and second-degree relatives. We found a statistically significant excess of markers for which affected relatives exhibited modest amounts of excess allele-sharing; however, no single chromosomal region contained markers with excess allele-sharing of sufficient magnitude to indicate unequivocal evidence of linkage. Positive linkage signals of nominal statistical significance were found in two regions (5p-q and 12p) that have been identified as weakly positive in other data sets and in region 19p, which has not been identified previously. All these signals were considerably stronger for analyses restricted to families with mean age at onset below the median than for analyses of families with mean age at onset above the median. The data provided little support for any of the putative prostate cancer-susceptibility genes identified in other linkage studies.

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