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The methylated component of the Neurospora crassa genome

Abstract

Cytosine methylation is common, but not ubiquitous, in eukaryotes. Mammals1 and the fungus Neurospora crassa2,3 have about 2–3% of cytosines methylated. In mammals, methylation is almost exclusively in the under-represented CpG dinucleotides, and most CpGs are methylated1 whereas in Neurospora, methylation is not preferentially in CpG dinucleotides and the bulk of the genome is unmethylated4. DNA methylation is essential in mammals5 but is dispensable in Neurospora3,6, making this simple eukaryote a favoured organism in which to study methylation. Recent studies indicate that DNA methylation in Neurospora depends on one DNA methyltransferase, DIM-2 (ref. 6), directed by a histone H3 methyltransferase, DIM-5 (ref. 7), but little is known about its cellular and evolutionary functions. As only four methylated sequences have been reported previously in N. crassa, we used methyl-binding-domain agarose chromatography8 to isolate the methylated component of the genome. DNA sequence analysis shows that the methylated component of the genome consists almost exclusively of relics of transposons that were subject to repeat-induced point mutation—a genome defence system that mutates duplicated sequences9.

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Figure 1: Fractionation of Neurospora DNA on a methylated-DNA-binding column.
Figure 2: Verification of DNA methylation in genomic DNA regions.
Figure 3: Comparison of DNA methylation in Oak Ridge (OR), Mauriceville (M) and dim strains of N. crassa.
Figure 4: Methylation of sequences with extreme RIP indices.

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Acknowledgements

We thank F. K. Selker and C. B. Matsen for help with computer analyses; T. Wolfe for technical assistance; G. Mannhaupt for providing some accession numbers; and J. Galagan for comments on the manuscript. E.U.S. acknowledges the hospitality of the Bird laboratory when he initiated this project while on sabbatical, and is thankful to D. Macleod, R. Meehan and F. Antequera for their advice. This work was supported by a US Public Health Service grant to E.U.S. from the National Institutes of Health, and a Senior International Fellowship from the Fogarty International Center of the National Institutes of Health.

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Correspondence to Eric U. Selker.

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Selker, E., Tountas, N., Cross, S. et al. The methylated component of the Neurospora crassa genome. Nature 422, 893–897 (2003). https://doi.org/10.1038/nature01564

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