title: Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation.
abstract: Chromatin modifications such as DNA methylation are targeted to transposable elements by small RNAs in a process termed RNA-directed DNA methylation (RdDM). In plants, canonical RdDM functions through RNA polymerase IV to reinforce pre-existing transposable element silencing. Recent investigations have identified a "non-canonical" form of RdDM dependent on RNA polymerase II expression to initiate and re-establish silencing of active transposable elements. This expression-dependent RdDM mechanism functions through RNAi degradation of transposable element mRNAs into small RNAs guided by the RNA-dependent RNA polymerase 6 (RDR6) protein and is therefore referred to as RDR6-RdDM.
  
  
  
  We performed whole-genome MethylC-seq in 20 mutants that distinguish RdDM mechanisms when transposable elements are either transcriptionally silent or active. We identified a new mechanism of expression-dependent RdDM, which functions through DICER-LIKE3 (DCL3) but bypasses the requirement of both RNA polymerase IV and RDR6 (termed DCL3-RdDM). We found that RNA polymerase II expression-dependent forms of RdDM function on over 20 % of transcribed transposable elements, including the majority of full-length elements with all of the domains required for autonomous transposition. Lastly, we find that RDR6-RdDM preferentially targets long transposable elements due to the specificity of primary small RNAs to cleave full-length mRNAs.
  
  
  
  Expression-dependent forms of RdDM function to critically target DNA methylation to full-length and transcriptionally active transposable elements, suggesting that these pathways are key to suppressing mobilization. This targeting specificity is initiated on the mRNA cleavage-level, yet manifested as chromatin-level silencing that in plants is epigenetically inherited from generation to generation.
authors: Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA.
authors: Kaushik
authors: K
authors: Panda
authors: Institute of Bioinformatics, University of Georgia, Athens, GA, USA.
authors: Lexiang
authors: L
authors: Ji
authors: Department of Genetics, University of Georgia, Athens, GA, USA.
authors: Drexel A
authors: DA
authors: Neumann
authors: Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA.
authors: Josquin
authors: J
authors: Daron
authors: Department of Genetics, University of Georgia, Athens, GA, USA.
authors: Robert J
authors: RJ
authors: Schmitz
authors: Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA. Slotkin.2@OSU.edu.
authors: R Keith
authors: 0000-0001-9582-3533
authors: RK
authors: Slotkin
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D029681:Arabidopsis Proteins / Q000235:genetics*; D002843:Chromatin / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics*; D044127:Epigenesis, Genetic / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing; D012319:RNA Polymerase II / Q000096:biosynthesis / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics; D058727:RNA, Small Untranslated / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics*; D043244:Ribonuclease III / Q000235:genetics*
chemical_list: D029681:Arabidopsis Proteins; D002843:Chromatin; D004251:DNA Transposable Elements; D012333:RNA, Messenger; D034741:RNA, Small Interfering; D058727:RNA, Small Untranslated; D012319:RNA Polymerase II; C514575:RDR6 protein, Arabidopsis; D012324:RNA-Dependent RNA Polymerase; C519654:DCL3 protein, Arabidopsis; D043244:Ribonuclease III
keywords: Cytosine methylation; Decrease in DNA methylation 1 (DDM1); MethylC-seq; Methylome; RNA interference (RNAi); RNA-directed DNA methylation (RdDM); Small interfering RNA (siRNA); TE-active context; TE-silent context; Transposable element (TE)