An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation (original) (raw)

• Letter
• Published: 21 April 2010
• Hai-Liang Liu1,2 na1,
• Lucia Daxinger3 na1 nAff11,
• Olga Pontes4 na1,
• Xinjian He1,5,
• Weiqiang Qian1,
• Huixin Lin1,
• Mingtang Xie1,
• Zdravko J. Lorkovic6,
• Shoudong Zhang1,5,
• Daisuke Miki1,
• Xiangqiang Zhan1,5,
• Dominique Pontier7,
• Thierry Lagrange7,
• Hailing Jin8,
• Antonius J. M. Matzke3,
• Marjori Matzke3,
• Craig S. Pikaard9 &
• …
• Jian-Kang Zhu1,5

Nature volume 465, pages 106–109 (2010)Cite this article

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Abstract

DNA methylation is an important epigenetic mark in many eukaryotes1,2,3,4,5. In plants, 24-nucleotide small interfering RNAs (siRNAs) bound to the effector protein, Argonaute 4 (AGO4), can direct de novo DNA methylation by the methyltransferase DRM2 (refs 2, 4–6). Here we report a new regulator of RNA-directed DNA methylation (RdDM) in Arabidopsis: RDM1. Loss-of-function mutations in the RDM1 gene impair the accumulation of 24-nucleotide siRNAs, reduce DNA methylation, and release transcriptional gene silencing at RdDM target loci. RDM1 encodes a small protein that seems to bind single-stranded methyl DNA, and associates and co-localizes with RNA polymerase II (Pol II, also known as NRPB), AGO4 and DRM2 in the nucleus. Our results indicate that RDM1 is a component of the RdDM effector complex and may have a role in linking siRNA production with pre-existing or de novo cytosine methylation. Our results also indicate that, although RDM1 and Pol V (also known as NRPE) may function together at some RdDM target sites in the peri-nucleolar siRNA processing centre, Pol II rather than Pol V is associated with the RdDM effector complex at target sites in the nucleoplasm.

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Change history

• 06 May 2010

Reference 23 was updated to reflect a change in the title.

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Acknowledgements

This work was supported by National Institutes of Health grants (J.-K.Z.), Austrian Fonds zur Förderung der wissenschaftlichen Forschung (M.M. and Z.J.L.), National Science Foundation Career Award (H.J.), Edward Mallinckrodt Foundation Award (O.P.), and Agence Nationale de la Recherche (T.L.). We thank E. Richards for his gift of methylated DNA oligonucleotides, B. Stevenson for technical assistance and T. Kanno for discussions.

Author information

Author notes

1. Lucia Daxinger
   Present address: Present address: Division of Genetics and Population Health, Queensland Institute of Medical Research, QLD 4006, Herston, Australia.,
2. Zhihuan Gao, Hai-Liang Liu, Lucia Daxinger and Olga Pontes: These authors contributed equally to this work.

Authors and Affiliations

1. Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA,
   Zhihuan Gao, Hai-Liang Liu, Xinjian He, Weiqiang Qian, Huixin Lin, Mingtang Xie, Shoudong Zhang, Daisuke Miki, Xiangqiang Zhan & Jian-Kang Zhu
2. School of life science and technology, Tongji University, Shanghai 200092, China
   Hai-Liang Liu
3. Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
   Lucia Daxinger, Antonius J. M. Matzke & Marjori Matzke
4. Biology Department, Washington University, St Louis, Missouri 63130, USA,
   Olga Pontes
5. Center for Plant Stress Genomics and Technology, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
   Xinjian He, Shoudong Zhang, Xiangqiang Zhan & Jian-Kang Zhu
6. Max F. Perutz Laboratory, Medical University of Vienna, 1030 Vienna, Austria
   Zdravko J. Lorkovic
7. LGDP, CNRS/IRD/Université de Perpignan, UMR 5096, 66860 Perpignan, France,
   Dominique Pontier & Thierry Lagrange
8. Institute for Integrative Genome Biology and Department of Plant Pathology and Microbiology, University of California, Riverside, California 92521, USA,
   Hailing Jin
9. Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA,
   Craig S. Pikaard

Authors

1. Zhihuan Gao
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2. Hai-Liang Liu
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3. Lucia Daxinger
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4. Olga Pontes
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5. Xinjian He
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6. Weiqiang Qian
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7. Huixin Lin
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8. Mingtang Xie
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9. Zdravko J. Lorkovic
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10. Shoudong Zhang
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11. Daisuke Miki
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12. Xiangqiang Zhan
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13. Dominique Pontier
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14. Thierry Lagrange
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15. Hailing Jin
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16. Antonius J. M. Matzke
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17. Marjori Matzke
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18. Craig S. Pikaard
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19. Jian-Kang Zhu
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Contributions

Z.G., H.-L.L, X.H., W.Q., H.L., M.X., S.Z., D.M., and X.Z. contributed Figs 1, 2, 3b–d, Supplementary Figs 1–6 and 9–12, and Supplementary Table 2. L.D, Z.J.L., A.J.M. and M.M. contributed the rdm1-4 allele (Supplementary Fig. 5) and data on its characterization (Supplementary Fig. 7). O.P. and C.S.P contributed Fig. 4, Supplementary Fig. 8 and Supplementary Table 1. D.P and T.L. contributed Fig. 3a. J.-K.Z designed the experiments and wrote the paper together with Z.G., H.J., O.P., C.S.P. and M.M.

Corresponding author

Correspondence toJian-Kang Zhu.

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The authors declare no competing financial interests.

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Supplementary Information

This file contains Supplementary Figures S1-S12 with legends, Supplementary Tables S1-S2 and References. (PDF 1869 kb)

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Gao, Z., Liu, HL., Daxinger, L. et al. An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation.Nature 465, 106–109 (2010). https://doi.org/10.1038/nature09025

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• Received: 16 November 2009
• Accepted: 22 March 2010
• Published: 21 April 2010
• Issue Date: 06 May 2010
• DOI: https://doi.org/10.1038/nature09025

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Editorial Summary

RNA-directed DNA methylation in Arabidopsis

Small interfering RNAs (siRNAs) are important regulators of gene expression in the plant model Arabidopsis, and intriguingly the vast majority of the small RNAs involved are generated from methylated regions of the genome. A previously unknown protein termed RdDM (for regulator of RNA-directed DNA methylation) has now been identified in Arabidopsis, throwing more light on the interactions of epigenetics, DNA methylation and small RNAs in plants. RDM1 is a novel methyl DNA-binding protein that binds to single-stranded methylated DNA: the many methyl DNA-binding proteins known previously in plants and animals bind only to double-stranded methylated DNA. RDM1 interacts with complexes of the effector protein Argonaute 4 (AGO4) with siRNAs to direct de novo DNA methylation and gene silencing.