Molecular mechanism of action of plant DRM de novo DNA methyltransferases.

Cell. 2014 May 22;157(5):1050-60

Xuehua Zhong ¹ , Jiamu Du ² , Christopher J Hale ¹ , Javier Gallego-Bartolome ³ , Suhua Feng ⁴ ,

Xuehua Zhong ¹ , Jiamu Du ² , Christopher J Hale ¹ , Javier Gallego-Bartolome ³ , Suhua Feng ⁴ , Ajay A Vashisht ⁵ , Joanne Chory ⁶ , James A Wohlschlegel ⁵ , Dinshaw J Patel ⁷ , Steven E Jacobsen ⁸

+ et al

Author information

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.

摘要

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.

原始数据

保存测序数据

Sample name	Organism	Experiment title	Sample type	Library instrument	Attributes
Sample name	Organism	Experiment title	Sample type	Library instrument	age	ecotype	genotype	source name	tissue
131216_DRM2_WT_6	Arabidopsis thaliana	GSM1327038: 131216_DRM2_WT_6; Arabidopsis thaliana; Bisulfite-Seq	Bisulfite-Seq	Illumina HiSeq 2000	2-week old	Columbia	drm2 mutant carrying a DRM2 wildtype transgene	2-week old leaf_DRM2_WT_6	leaf
131216_DRM2_WT_5	Arabidopsis thaliana	GSM1327037: 131216_DRM2_WT_5; Arabidopsis thaliana; Bisulfite-Seq	Bisulfite-Seq	Illumina HiSeq 2000	2-week old	Columbia	drm2 mutant carrying a DRM2 wildtype transgene	2-week old leaf_DRM2_WT_5	leaf
131216_DRM2_WT_1	Arabidopsis thaliana	GSM1327036: 131216_DRM2_WT_1; Arabidopsis thaliana; Bisulfite-Seq	Bisulfite-Seq	Illumina HiSeq 2000	2-week old	Columbia	drm2 mutant carrying a DRM2 wildtype transgene	2-week old leaf_DRM2_WT_1	leaf
131216_DRM2_M5_10	Arabidopsis thaliana	GSM1327035: 131216_DRM2_M5_10; Arabidopsis thaliana; Bisulfite-Seq	Bisulfite-Seq	Illumina HiSeq 2000	2-week old	Columbia	drm2 mutant carrying a DRM2 transgene with 5 mutations in the putative dimerization domain	2-week old leaf_DRM2_M5_10	leaf
131216_DRM2_M5_4	Arabidopsis thaliana	GSM1327034: 131216_DRM2_M5_4; Arabidopsis thaliana; Bisulfite-Seq	Bisulfite-Seq	Illumina HiSeq 2000	2-week old	Columbia	drm2 mutant carrying a DRM2 transgene with 5 mutations in the putative dimerization domain	2-week old leaf_DRM2_M5_4	leaf