miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis

The generation of widespread epigenetically activated short interfering RNAs by the targeting of microRNAs to transposon transcripts in Arabidopsis thaliana is shown to be a latent mechanism that only becomes active when the transcripts are epigenetically reactivated, for example, during reprogramming of the germ line. Transposon targeting by plant miRNAs In the model plant Arabidopsis, transposable elements are generally silenced by DNA methylation. Here, Robert Martienssen and colleagues describe an alternative silencing mechanism. Targeting occurs in the absence of DNA methylation, and generates 21-nucleotide short interfering RNAs -- which the authors call 'easiRNA', for epigenetically activated siRNA -- of a type that has been observed previously in pollen grains. Thousands of transposons are targeted by at least 50 microRNAs, most of them conserved in plant evolution. The authors propose that microRNA-directed easiRNA biogenesis specifically targets transposon transcripts when they are epigenetically reactivated during germline reprogramming. In plants, post-transcriptional gene silencing (PTGS) is mediated by DICER-LIKE 1 (DCL1)-dependent microRNAs (miRNAs), which also trigger 21-nucleotide secondary short interfering RNAs (siRNAs) via RNA-DEPENDENT RNA POLYMERASE 6 (RDR6), DCL4 and ARGONAUTE 1 (AGO1).sup.1,2,3, whereas transcriptional gene silencing (TGS) of transposons is mediated by 24-nucleotide heterochromatic (het)siRNAs, RDR2, DCL3 and AGO4 (ref. 4). Transposons can also give rise to abundant 21-nucleotide 'epigenetically activated' small interfering RNAs (easiRNAs) in DECREASED DNA METHYLATION 1 (ddm1) and DNA METHYLTRANSFERASE 1 (met1) mutants, as well as in the vegetative nucleus of pollen grains.sup.5 and in dedifferentiated plant cell cultures.sup.6. Here we show that easiRNAs in Arabidopsis thaliana resemble secondary siRNAs, in that thousands of transposon transcripts are specifically targeted by more than 50 miRNAs for cleavage and processing by RDR6. Loss of RDR6, DCL4 or DCL1 in a ddm1 background results in loss of 21-nucleotide easiRNAs and severe infertility, but 24-nucleotide hetsiRNAs are partially restored, supporting an antagonistic relationship between PTGS and TGS. Thus miRNA-directed easiRNA biogenesis is a latent mechanism that specifically targets transposon transcripts, but only when they are epigenetically reactivated during reprogramming of the germ line. This ancient recognition mechanism may have been retained both by transposons to evade long-term heterochromatic silencing and by their hosts for genome defence.
Author(s): Kate M. Creasey [sup.1] , Jixian Zhai [sup.2] , Filipe Borges [sup.1] , Frederic Van Ex [sup.1] , Michael Regulski [sup.1] , Blake C. Meyers [sup.2] , Robert A. [...]