In plants, post-transcriptional gene silencing (PTGS) is mediated by DICER-LIKE1 (DCL1)-dependent miRNAs, that also trigger 21-nt secondary siRNA via RNA DEPENDENT RNA POLYMERASE6 (RDR6), DCL4, and ARGONAUTE1 (AGO1)1–3, while transcriptional gene silencing (TGS) of transposons is mediated by 24-nt heterochromatic (het)siRNA RDR2, DCL3 and AGO44. Transposons can also give rise to abundant 21-nt “epigenetically activated” small interfering RNAs (easiRNAs) in DECREASE IN DNA METHYLATION1 (ddm1) and DNA METHYLTRANSFERASE1 (met1) mutants, as well as in the vegetative nucleus of pollen grains5, and in dedifferentiated plant cell cultures6. Here we show that easiRNAs resemble secondary siRNAs, in that thousands of transposon transcripts are specifically targeted by more than fifty miRNAs for cleavage and processing by RDR6. Loss of RDR6, DCL4 or DCL1 in a ddm1 background results in loss of 21-nt easiRNA, and severe infertility, but 24-nt hetsiRNA 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 germline. This ancient recognition mechanism may have been retained both by transposons to evade long-term heterochromatic silencing, and by their hosts for genome defence.

No abstract

Heterochromatin is composed of transposable elements (TEs) and other repeats and was once considered to be a wasteland of redundant genetic material and potentially harmful TE. Therefore, the reprogramming of heterochromatin and subsequent reactivation of TE in the immature seed and pollen is paradoxical in plants. Recent studies have shown that reactivation of TE occurs specifically in germline companion cells, the vegetative nucleus (VN) in pollen (Slotkin et al. 2009) and the endosperm in seed (Gehring et al. 2009). In the ovule, ARGONAUTE 9 (AGO9) not only has a role in silencing TE in the egg cell but also in preventing the formation of multiple asexual gametophytes (Olmedo-Monfil et al. 2010). We propose that reprogramming of heterochromatin in germline companion cells reveals TE in a controlled manner to expose them within the germline and, by the production of small interfering RNA (siRNA), ensures TE silencing in the next generation. We also propose that the mechanisms evolved to silence TE may actually promote sexual reproduction by inhibiting the formation of asexual gametes.