title: Genome-wide identification of endogenous RNA-directed DNA methylation loci associated with abundant 21-nucleotide siRNAs in Arabidopsis.
abstract: In Arabidopsis, the 24-nucleotide (nt) small interfering RNAs (siRNAs) mediates RNA-directed DNA methylation (RdDM) and transcriptional gene silencing (TGS) of transposable elements (TEs). In the present study, we examined genome-wide changes in DNA methylation and siRNA accumulation in Arabidopsis induced by expression of the Cucumber mosaic virus silencing suppressor protein 2b known to directly bind to both the 21/24-nt siRNAs as well as their associated Argonaute proteins. We demonstrated a genome-wide reduction of CHH and CHG methylation in the 2b-transgenic plants. We found that 2b suppressed RdDM not only at the previously annotated loci directed by 24-nt siRNAs but also a new set of loci associated with 21/22-nt siRNAs. Further analysis showed that the reduced methylation of TEs and coding genes targeted by 21/22-nt siRNAs was associated with sequestration of the duplex siRNAs by the 2b protein but not with changes in either siRNA production or transcription. Notably, we detected both the deletion and/or the transposition of multicopy TEs associated with 2b-induced hypomethylation, suggesting potential TE reactivation. We propose that the silencing of many TEs in Arabidopsis is controlled by the 24- and 21-nt endogenous siRNAs analogous to Drosophila TE silencing by PIWI-interacting RNAs and siRNAs.
authors: State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
authors: Jian-Hua
authors: JH
authors: Zhao
authors: State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
authors: Yuan-Yuan
authors: YY
authors: Fang
authors: State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
authors: Cheng-Guo
authors: CG
authors: Duan
authors: State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
authors: Rong-Xiang
authors: RX
authors: Fang
authors: Department of Plant Pathology and Microbiology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA.
authors: Shou-Wei
authors: SW
authors: Ding
authors: State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
authors: Hui-Shan
authors: HS
authors: Guo
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D060565:Argonaute Proteins / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D020868:Gene Silencing / Q000502:physiology; D018745:Genome, Plant / Q000235:genetics*; D055106:Genome-Wide Association Study / Q000379:methods; D009711:Nucleotides / Q000235:genetics*; D030821:Plants, Genetically Modified / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics*
chemical_list: D029681:Arabidopsis Proteins; D060565:Argonaute Proteins; D004251:DNA Transposable Elements; D009711:Nucleotides; D018749:RNA, Plant; D034741:RNA, Small Interfering