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

Autor: Panda K; Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA., Ji L; Institute of Bioinformatics, University of Georgia, Athens, GA, USA., Neumann DA; Department of Genetics, University of Georgia, Athens, GA, USA., Daron J; Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA., Schmitz RJ; Department of Genetics, University of Georgia, Athens, GA, USA., Slotkin RK; Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA. Slotkin.2@OSU.edu.
Jazyk: angličtina
Zdroj: Genome biology [Genome Biol] 2016 Aug 09; Vol. 17 (1), pp. 170. Date of Electronic Publication: 2016 Aug 09.
DOI: 10.1186/s13059-016-1032-y
Abstrakt: Background: 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.
Results: 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.
Conclusions: 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.
Databáze: MEDLINE
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