Volume 26, No 1, Jan 2016
ISSN: 1001-0602
EISSN: 1748-7838 2018
impact factor 17.848*
(Clarivate Analytics, 2019)
Volume 26 Issue 1, January 2016: 66-82
ORIGINAL ARTICLES
Dicer-independent RNA-directed DNA methylation in Arabidopsis
Dong-Lei Yang1,3,*, Guiping Zhang1,*, Kai Tang2, Jingwen Li1, Lan Yang1, Huan Huang1, Heng Zhang1 and Jian-Kang Zhu1,2
1Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
2Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47906, USA
3Current address: National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
Correspondence: Jian-Kang Zhu, Tel: +86-21-57078201; Fax: +86-21-54924107(jkzhu@sibs.ac.cn)
RNA-directed DNA methylation (RdDM) is an important de novo DNA methylation pathway in plants. Small interfering RNAs (siRNAs) generated by Dicers from RNA polymerase IV (Pol IV) transcripts are thought to guide sequence-specific DNA methylation. To gain insight into the mechanism of RdDM, we performed whole-genome bisulfite sequencing of a collection of Arabidopsis mutants, including plants deficient in Pol IV (nrpd1) or Dicer (dcl1/2/3/4) activity. Unexpectedly, of the RdDM target loci that required Pol IV and/or Pol V, only 16% were fully dependent on Dicer activity. DNA methylation was partly or completely independent of Dicer activity at the remaining Pol IV- and/or Pol V-dependent loci, despite the loss of 24-nt siRNAs. Instead, DNA methylation levels correlated with the accumulation of Pol IV-dependent 25-50 nt RNAs at most loci in Dicer mutant plants. Our results suggest that RdDM in plants is largely guided by a previously unappreciated class of Dicer-independent non-coding RNAs, and that siRNAs are required to maintain DNA methylation at only a subset of loci.
10.1038/cr.2015.145
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