DNA methyltransferase

Decitabine (5-aza-deoxycytosine) is an analog of the nucleoside 2 -deoxycytidine. It is believed to exert its antineoplastic effects after phosphorylation and direct incorporation into DNA and by inhibition of the enzyme DNA methyltransferase, causing hypomethylation of DNA and cellular differentiation or apoptosis. DNA hypomethylation is achieved at concentrations below those required to significantly inhibit DNA synthesis, which may promote restoration of function to genes associated with control of cellular differentiation and proliferation. Cytotoxicity in rapidly dividing cells may also result from covalent adducts between DNA methyltransferase and decitabine. 

In higher eukaiyotes, most of the chromosomal DNA carries 5-methyl-cytidine residues located in CpG sequence motives. There is a close correlation between transcriptional inactivation and methylation. On the other hand, considerable evidence shows that regions of DNA that are actively engaged in transcription lack 5-methyl-cytidine nucleotides in CpG motivs. Hence DNA methylation is a means how cells regulate gene expression. DNA methylation which is catalyzed by DNA methyltransferases is the best characterized epigenetic mechanism. 

Cornetta K, Croop J, Dropcho E, Abonour R, Kieran MW, Kreissman S, Reeves L, Erickson LC, Williams DA (2006) A pilot study of dose-intensified procarbazine, CCNU, vincristine for poor prognosis brain tumors utilizing fibronectin-assisted, retroviral-mediated modification of CD34-I- peripheral blood cells with 06-methylguanine DNA methyltransferase. Cancer Gene Ther 13 886-895... 

DIMS was identified as the responsible gene for one of DNA hypomethylation mutants in Neurospora crassa (Tamaru and Selker, 2001). This is the first report that histone (H3K9) methylation regulates DNA methylation. Furthermore, it is reported that this regulation is mediated through the HPl recruitment to the tri-methylated H3K9 loci (Freitag et al, 2004), but it remains to be elucidated whether DNA methylation (DNA methyltransferase) is directly controlled (recruited) by HPl. 

Desaulniers D, Xiao GH, Leingartner K, Chu I, Musicki B, et al. 2005. Comparisons of brain, uterus, and liver mRNA e3q>ression for cytochrome P450s, DNA methyltransferase-1, and catechoTo-methyltransferase in prepubertal female... 

F. D. Araujo, J. D. Knox, S. Ramchandani, R. Pelletier, P. Bigey, G. Price, M. Szyf, and M. Zannis-Hadjopoulos, Identification of initiation sites for DNA replication in the human dnmtl (DNA-methyltransferase) locus. J. Biol. Chem. 274, 9335-9341 (1999). 

Fang, M. Z., Wang, Y., Ai, N., et al. (2003) Tea polyphenol (-)-epigallocatechin-3-gaUate inhibits DNA methyltransferase and reactivates methylation-sdenced genes in cancer ceU lines. Cancer Res. 63, 7563-7570. 

Bonsch, D., Lenz, B., Fiszer, R., Frieling, H., Kornhuber, J., and Bleich, S. (2006) Lowered DNA methyltransferase (DNMT-3b) mRNA expression is associated with genomic DNA hypermethylation in patients with chronic alcoholism. J. Neural Transm. 113, 1299-1304. 

Relationships between histone methylation and DNA methylation and histone acetyation and DNA methylation have been reported [191,314,315], A similar relationship may exist between poly(ADP ribosylated) HI and DNA methylation. Inhibition of poly(ADP-ribose) polymerase with 3-aminobenzamide increases the susceptibility of L929 mouse fibroblast nuclei to be methylated by endogenous DNA methyltransferases [316,317], Further, there is evidence that poly(ADP ribosylation) protects CpG islands located at the 5 end of housekeeping genes from methylation [318], Future studies will likely reveal an interesting dynamic relationship between histone methylation, histone acetylation, and histone poly(ADP-ribosylation). 

Fig. 4. Domain structure of mammalian DNA methyltransferases. (a) The domain structure of the known DNA methyltransferases, depicting the conserved catalytic domain (dark box) and other identified domains. Conserved aminoacid motifs in the catalytic domain are shown in lighter shade of gray. (b) Schematic representation of the reported protein-protein interactions of Dnmtl with a number of regulatory proteins interactions that modulate Dnmtl methyitransferase activity (darker rectangles) or mediate methylation-independent transcriptional repression mechanisms (lighter rectangles). When Dnmtl represses transcription through its enzymatic activity, it has been described to interact with some proteins PCNA [37] and an oncogenic transcription factor PML-RAR [25]. Note that in the case of the PML-RAR transcription factor, histone deacetylase 1 (HDACl) is also bound to the complex. When Dnmtl represses transcription via methylation-independent pathways, it binds to HDACs either directly [34] or indirectly through other proteins the corepressor DMAPl [33], the retinoblastoma protein, and a gene-specific transcription factor [31].

Dnmt3a De novo DNA methyltransferase Adult/Embryo DNMT3a mice die at 4 weeks ES cells from DNMT3a mice are viable and capable of de novo methylation DNMT3a embryos and ES cells exhibit demethylation of centromeric satellite repeats... 

It is clear that we still do not fully understand how the CpG moieties of the CpG islands resist the action of DNA methyltransferases or become vulnerable to it, thus maintaining or losing their characteristic pattern of methylation. More research is definitely needed to answer this intriguing and important question. 

In fact, the cross-talk between histone methylation and DNA methylation has been experimentally demonstrated for the first time in Neurospora [145] (see commentary by Bird [146]) and proved the second scenario. Using the power of Neurospora genetics, Tamaru and Selker [145] have identified a gene which, when mutated, abolishes methylation of all tested DNA sequences. This gene, dim-5, is different from dim-2, the previously identified gene that encodes the only DNA methyltransferase in Neurospora responsible for all known cytosine methylation in this fungus. The dim-5 gene encodes a histone H3 methyltransferase the deduced polypeptide sequence contains a SET domain with sequence similarity to some known histone methyltransferases moreover, the recombinant DIM-5 protein exhibits histone methyltransferase activity in vitro. Additional in vivo experiments... 

So far the major application of IVC has been to select enzymes. Griffiths has used IVC to select DNA methyltransferases and has successfully generated variants that can efficiently modify novel DNA target sequences [38]. This study provides a rare example of a laboratory-produced enzyme with a catalytic efficiency that surpasses that of the wild-type enzyme with the principle substrate. IVC has also... 

Table 4. Chemical structures of natural product Psammaplin A through J, with HD AC and DNA methyltransferase (DNTB) inhibition values. Not tested shown as nt.

In multicellular eukaryotes, DNA methylation is associated with transcriptional silencing [3]. In these organisms, DNA methylation has been observed exclusively on the C5 position of the cytosine ring and is frequently found in CpG-rich regions. This process is attributed to the action of DNA methyltransferases (DNMTs), which utilize the cofactor, S-adenosyl-L-methionine. Approximately half of all human genes have CpG islands in their promoter regions but these stretches of DNA are typically... 

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