Molecular mechanism of action of plant DRM de novo DNA methyltransferases

Xuehua Zhong; Jiamu Du; Christopher J Hale; Javier Gallego-Bartolome; Suhua Feng; Ajay A Vashisht; Joanne Chory; James A Wohlschlegel; Dinshaw J Patel; Steven E Jacobsen

doi:10.1016/j.cell.2014.03.056

Molecular mechanism of action of plant DRM de novo DNA methyltransferases

Cell. 2014 May 22;157(5):1050-60. doi: 10.1016/j.cell.2014.03.056.

Authors

Affiliations

¹ Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
² Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
³ Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
⁴ Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute and Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA.
⁵ Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
⁶ Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
⁷ Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA. Electronic address: pateld@mskcc.org.
⁸ Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute and Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address: jacobsen@ucla.edu.

Abstract

DNA methylation is a conserved epigenetic gene-regulation mechanism. DOMAINS REARRANGED METHYLTRANSFERASE (DRM) is a key de novo methyltransferase in plants, but how DRM acts mechanistically is poorly understood. Here, we report the crystal structure of the methyltransferase domain of tobacco DRM (NtDRM) and reveal a molecular basis for its rearranged structure. NtDRM forms a functional homodimer critical for catalytic activity. We also show that Arabidopsis DRM2 exists in complex with the small interfering RNA (siRNA) effector ARGONAUTE4 (AGO4) and preferentially methylates one DNA strand, likely the strand acting as the template for RNA polymerase V-mediated noncoding RNA transcripts. This strand-biased DNA methylation is also positively correlated with strand-biased siRNA accumulation. These data suggest a model in which DRM2 is guided to target loci by AGO4-siRNA and involves base-pairing of associated siRNAs with nascent RNA transcripts.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Sequence
Arabidopsis / enzymology*
Arabidopsis / metabolism
Arabidopsis Proteins / metabolism
Argonaute Proteins / metabolism
Catalytic Domain
Methyltransferases / chemistry
Methyltransferases / metabolism*
Models, Molecular
Molecular Sequence Data
Nicotiana / enzymology*
Nicotiana / metabolism

Substances

AGO4 protein, Arabidopsis
Arabidopsis Proteins
Argonaute Proteins
Methyltransferases
DRM1 protein, Arabidopsis
DRM2 protein, Arabidopsis

Abstract

Publication types

MeSH terms

Substances

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