Abstract
BackgroundChromatin 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.ResultsWe 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.ConclusionsExpression-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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1032-y) contains supplementary material, which is available to authorized users.
Highlights
Chromatin modifications such as DNA methylation are targeted to transposable elements by small RNAs in a process termed RNA-directed DNA methylation (RdDM)
To identify the regions of the genome targeted by RNA-dependent RNA polymerase 6 (RDR6)-RdDM, we identified differentially methylated regions (DMRs) between all of the genotypes
Aligning the DMRs, we find that the average wild-type Columbia (wt Col) and rdr6 CHH methylation patterns are indistinguishable, demonstrating that RDR6RdDM plays a minor genome-wide role in the Transposable elements (TEs)-silent context (Fig. 1a, replicate data in Additional file 4: Figure S3A)
Summary
Chromatin modifications such as DNA methylation are targeted to transposable elements by small RNAs in a process termed RNA-directed DNA methylation (RdDM). 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 referred to as RDR6-RdDM. Panda et al Genome Biology (2016) 17:170 form of RdDM has been uncovered (reviewed in [2]) This canonical form of RdDM begins with the transcription of the target locus by the RNA polymerase protein Pol IV, a plant-specific Pol II paralog [3], which generates a non-coding RNA that is immediately converted into double-stranded RNA (dsRNA) via RNA-dependent RNA polymerase 2 (RDR2). The Pol V transcript acts as a scaffold for protein assembly, and interaction between AGO4/6 and the Pol V transcript results in the recruitment of the protein DRM2 to methylate the cytosines of the corresponding locus
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