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A histone H3 methyltransferase controls DNA methylation in Neurospora crassa

Abstract

DNA methylation is involved in epigenetic processes such as X-chromosome inactivation, imprinting and silencing of transposons. We have demonstrated previously that dim-2 encodes a DNA methyltransferase that is responsible for all known cytosine methylation in Neurospora crassa. Here we report that another Neurospora gene, dim-5, is required for DNA methylation, as well as for normal growth and full fertility. We mapped dim-5 and identified it by transformation with a candidate gene. The mutant has a nonsense mutation in a SET domain of a gene related to histone methyltransferases that are involved in heterochromatin formation in other organisms. Transformation of a wild-type strain with a segment of dim-5 reactivated a silenced hph gene, apparently by ‘quelling’ of dim-5. We demonstrate that recombinant DIM-5 protein specifically methylates histone H3 and that replacement of lysine 9 in histone H3 with either a leucine or an arginine phenocopies the dim-5 mutation. We conclude that DNA methylation depends on histone methylation.

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Figure 1: Growth deficiencies of dim-5 strains.
Figure 2: DNA methylation defect of dim-5 strains.
Figure 3: Identification of dim-5 by genetic mapping and complementation.
Figure 4: Quelling of dim-5 relieves silencing of hph in N644.
Figure 5: DIM-5 is a SET-domain protein.
Figure 6: Histone methyltransferase activity of recombinant DIM-5 protein (rDIM-5).
Figure 7: Reactivation of hph and loss of DNA methylation induced by transformation of a dim+ strain with mutant alleles of histone H3 gene (hH3).

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Acknowledgements

We are grateful to H. Inoue for a gift of Neurospora strain i47. We thank S. Hays for providing the plasmid containing wild-type hH3, and J. Dobosy, M. Freitag, S. Hays, G. Kothe, E. Kouzminova, J. Selker, T. Stevens and P. von Hippel for discussions and comments on the manuscript, and R. Metzenberg, D. Perkins and C. Yanofsky for encouragement. H.T. thanks S. Crosthwaite for inspiration. This study was supported by a grant from the NIH to E.U.S.

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Correspondence to Eric U. Selker.

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Tamaru, H., Selker, E. A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 414, 277–283 (2001). https://doi.org/10.1038/35104508

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