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DNA METHYLTRANSFERASE 1 is involved in mCG and mCCG DNA methylation and is essential for sporophyte development in Physcomitrella patens

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Abstract

DNA methylation has a crucial role in plant development regulating gene expression and silencing of transposable elements. Maintenance DNA methylation in plants occurs at symmetrical mCG and mCHG contexts (m = methylated) and is maintained by DNA METHYLTRANSFERASE 1 (MET1) and CHROMOMETHYLASE (CMT) DNA methyltransferase protein families, respectively. While angiosperm genomes encode for several members of MET1 and CMT families, the moss Physcomitrella patens, serving as a model for early divergent land plants, carries a single member of each family. To determine the function of P. patens PpMET we generated ΔPpmet deletion mutant which lost mCG and unexpectedly mCCG methylation at loci tested. In order to evaluate the extent of mCCG methylation by MET1, we reexamined the Arabidopsis thaliana Atmet1 mutant methylome and found a similar pattern of methylation loss, suggesting that maintenance of DNA methylation by MET1 is conserved through land plant evolution. While ΔPpmet displayed no phenotypic alterations during its gametophytic phase, it failed to develop sporophytes, indicating that PpMET plays a role in gametogenesis or early sporophyte development. Expression array analysis revealed that the deletion of PpMET resulted in upregulation of two genes and multiple repetitive sequences. In parallel, expression analysis of the previously reported ΔPpcmt mutant showed that lack of PpCMT triggers overexpression of genes. This overexpression combined with loss of mCHG and its pleiotropic phenotype, implies that PpCMT has an essential evolutionary conserved role in the epigenetic control of gene expression. Collectively, our results suggest functional conservation of MET1 and CMT families during land plant evolution. A model describing the relationship between MET1 and CMT in CCG methylation is presented.

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Abbreviations

CMT:

CHROMOMETHYLASE

DRM:

DOMAINS REARRANGED METHYLTRANSFERASE

MET1:

DNA METHYLTRANSFERASE

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Acknowledgments

C. N. M and R. Y were supported in part by a matching Tel-Aviv University Deans doctoral fellowship and the Manna foundation. This research was supported by the Israeli Science Foundation Grant #767/09, and by the Israel Korea Program #3-824 financed by the Ministry of Science and Technology, both granted to N.O. Additional support from the German-Israeli Foundation for Scientific Research and Development (GIF I-832-130.12/2004 and I-1008-154.13-2008 to N. O. and R. R.) and by the Excellence Initiative of the German Federal and State Governments (EXC294 to R. R.) is gratefully acknowledged.

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The authors declare that they have no conflict of interest.

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    Authors and Affiliations

    1. Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, 69978, Tel Aviv, Israel

      Rafael Yaari, Chen Noy-Malka, Nitzan Auerbach Gershovitz, Aviva Katz & Nir Ohad

    2. Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany

      Gertrud Wiedemann & Ralf Reski

    3. BIOSS – Centre for Biological Signalling Studies, 79104, Freiburg, Germany

      Ralf Reski

    4. FRIAS – Freiburg Institute for Advances Studies, 79104, Freiburg, Germany

      Ralf Reski & Nir Ohad

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    1. Rafael Yaari
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    Correspondence to Nir Ohad.

    Additional information

    Rafael Yaari and Chen Noy-Malka have contributed equally to this work.

    Transgenic lines described in this study were deposited in the International Moss Stock Center (http://www.moss-stock-center.org/) with the accessions IMSC 40758 (ΔPpmet 5), IMSC 40759 (ΔPpmet 227) and IMSC 40760 (ΔPpmet 262).

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    Yaari, R., Noy-Malka, C., Wiedemann, G. et al. DNA METHYLTRANSFERASE 1 is involved in mCG and mCCG DNA methylation and is essential for sporophyte development in Physcomitrella patens . Plant Mol Biol 88, 387–400 (2015). https://doi.org/10.1007/s11103-015-0328-8

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