DNA Hypermethylation in Drosophila melanogaster Causes Irregular Chromosome Condensation and Dysregulation of Epigenetic Histone Modifications

Abstract

The level of genomic DNA methylation plays an important role in development and disease. In order to establish an experimental system for the functional analysis of genome-wide hypermethylation, we overexpressed the mouse de novo methyltransferase Dnmt3a in Drosophila melanogaster. These flies showed severe developmental defects that could be linked to reduced rates of cell cycle progression and irregular chromosome condensation. In addition, hypermethylated chromosomes revealed elevated rates of histone H3-K9 methylation and a more restricted pattern of H3-S10 phosphorylation. The developmental and chromosomal defects induced by DNA hypermethylation could be rescued by mutant alleles of the histone H3-K9 methyltransferase gene Su(var)3-9. This mutation also resulted in a significantly decreased level of genomic DNA methylation. Our results thus uncover the molecular consequences of genomic hypermethylation and demonstrate a mutual interaction between DNA methylation and histone methylation.Aberrant DNA methylation patterns are one of the most consistent hallmarks of cancer (31). Many of the epigenetic aberrations that occur during tumorigenesis can be related to ectopic hypermethylation (4). While the analysis by various experimental systems of reduced levels of DNA methylation has helped to define the role of DNA methylation, the functional consequences of DNA hypermethylation remain unclear. DNA methylation is catalyzed by a class of enzymes called DNA methyltransferases (7). During early mammalian embryogenesis, de novo methyltransferases catalyze the methylation of previously unmethylated cytosine residues. During later stages, DNA methylation patterns are copied postreplicatively from the parental strand to the daughter strand (29). This step requires a functionally specialized DNA methyltransferase that has been termed the maintenance methyltransferase. To date, there are four known mammalian DNA methyltransferase genes. Dnmt1 encodes an enzyme with maintenance methyltransferase activity (8,22), while the closely related genes Dnmt3a and Dnmt3b encode de novo methyltransferases (26,39,48). The function of the fourth gene, Dnmt2, remains enigmatic (16,49,65).Disruption of DNA methyltransferase activity proved that DNA methylation was essential for proper development of mice (35), frogs (59), and plants (18,54). The analysis of corresponding DNA hypomethylation phenotypes identified a role for DNA methylation in the regulation of gene activity (28, 59), control of foreign DNA elements (42, 63), and genome stability (14). Similar conclusions have been reached from the analysis of ICF (immunodeficiency, centromeric instability, facial anomalies) syndrome patients. These patients lack the majority of DNMT3B methyltransferase activity (23,48,64) and show striking chromosome aberrations that have been attributed to the demethylation and concomitant decondensation of pericentromeric satellite DNA (57). Together, these results suggest that DNA methylation might influence yet undefined aspects of higher-order chrom...

A Dnmt2-like protein mediates DNA methylation inDrosophila

“…Consistent with results from other organisms (Jackson et al, 2002;Tamaru and Selker, 2001) this revealed an unambiguous reduction in DNA methylation (Fig. 1F) and confirmed that DNA methylation in Drosophila interacts with histone H3-K9 methylation (Weissmann et al, 2003). Finally, we also incubated wild-type embryos with the (cytosine-5) DNA methyltransferase inhibitor 5-azacytidine.…”

“…Studies in Neurospora and Arabidopsis have shown that mutations in Su(var)3-9 histone H3-K9 methyltransferase homologues result in reduced levels of DNA methylation (Jackson et al, 2002;Tamaru and Selker, 2001). In addition, we have shown recently that DNA hypermethylation phenotypes in Drosophila can be rescued by mutations in the Su(var)3-9 gene (Weissmann et al, 2003), which suggested a preservation of this phenomenon in flies. The Drosophila Su(var)3-9 gene has been shown to encode a major histone H3-K9 methyltransferase activity in fly embryos (Schotta et al, 2002).…”

Evolution of Gene Sequence in Response to Chromosomal Location

“…Several lines of indirect evidence support this proposal. First, excessive DNA methylation, produced by expression of a mouse DNA methylase in Drosophila, produces general heterochromatin-like phenotypes that are relieved by a suppressor-of-variegation mutation (Weissmann et al 2003). This suggests that DNA methylation might play an important role in the formation of heterochromatin.…”

The rise and fall of genomic methylation in cancer

“…[51][52][53] Although the exact molecular events involved remain to be determined, it is believed that the link between genomic methylation and heterochromatin stability is correlated with Suv39 HMTase. 60 This connection is attractive given the recent study by Selker and co-workers that trimethH3K9 is a mark for DNA methylation and provides a functional link between these epigenetic pathways. 61 Although covalent histone modifications are crucial for regulating genomic methylation patterns in Neurospora, there seem to be exceptional differences in plants and mammals; for example, DNA methylation is dispensable in Neurospora.…”