Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation

• Published in: Genome Biology 2016-08, Vol.17 (1), p.170-170, Article 170
• Main Authors: Panda, Kaushik, Ji, Lexiang, Neumann, Drexel A, Daron, Josquin, Schmitz, Robert J, Slotkin, R Keith
• Format: Article
• Language: English
• Subjects: Arabidopsis - genetics; Arabidopsis Proteins - genetics; Chromatin; Chromatin - genetics; Deoxyribonucleic acid; DNA; DNA methylation; DNA Methylation - genetics; DNA Transposable Elements - genetics; DNA-directed RNA polymerase; Epigenesis, Genetic - genetics; Epigenetics; Gene Expression Regulation, Plant; Gene Silencing; Genes; Genomes; Investigations; messenger RNA; mutants; Mutation; Proteins; Ribonuclease III - genetics; RNA interference; RNA polymerase; RNA Polymerase II - biosynthesis; RNA Polymerase II - genetics; RNA Replicase - genetics; RNA, Messenger - genetics; RNA, Small Interfering - genetics; RNA, Small Untranslated - genetics; RNA-directed RNA polymerase; RNA-mediated interference; transcription (genetics); Transposition; Transposons
• ISSN: 1474-760X; 1474-7596; 1474-760X
• DOI: 10.1186/s13059-016-1032-y

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.