Role of Transposon-Derived Small RNAs in the Interplay between Genomes and Parasitic DNA in Rice

Abstract

RNA silencing is a defense system against “genomic parasites” such as transposable elements (TE), which are potentially harmful to host genomes. In plants, transcripts from TEs induce production of double-stranded RNAs (dsRNAs) and are processed into small RNAs (small interfering RNAs, siRNAs) that suppress TEs by RNA–directed DNA methylation. Thus, the majority of TEs are epigenetically silenced. On the other hand, most of the eukaryotic genome is composed of TEs and their remnants, suggesting that TEs have evolved countermeasures against host-mediated silencing. Under some circumstances, TEs can become active and increase in copy number. Knowledge is accumulating on the mechanisms of TE silencing by the host; however, the mechanisms by which TEs counteract silencing are poorly understood. Here, we show that a class of TEs in rice produces a microRNA (miRNA) to suppress host silencing. Members of the microRNA820 (miR820) gene family are located within CACTA DNA transposons in rice and target a de novo DNA methyltransferase gene, OsDRM2, one of the components of epigenetic silencing. We confirmed that miR820 negatively regulates the expression of OsDRM2. In addition, we found that expression levels of various TEs are increased quite sensitively in response to decreased OsDRM2 expression and DNA methylation at TE loci. Furthermore, we found that the nucleotide sequence of miR820 and its recognition site within the target gene in some Oryza species have co-evolved to maintain their base-pairing ability. The co-evolution of these sequences provides evidence for the functionality of this regulation. Our results demonstrate how parasitic elements in the genome escape the host's defense machinery. Furthermore, our analysis of the regulation of OsDRM2 by miR820 sheds light on the action of transposon-derived small RNAs, not only as a defense mechanism for host genomes but also as a regulator of interactions between hosts and their parasitic elements.

The copy number of rice CACTA DNA transposons carryingMIR820does not correlate withMIR820expression

“…Surprisingly, no expression was detected in W1514 despite the presence of more than 18 copies of MIR820. 7 Accordingly, no cleavage of OsDRM2 by miR820 was detected in W1514 (Fig. 1B).…”

“…1C). 7 The qRT-PCR revealed that the absence of miR820 in W1514 is due to a reduced level of the pre-miR820 transcript, rather than to its reduced processing. This implies that the high copy number of MIR820 in wild rice accession with BB or BBCC genome may cause a stronger MIR820 silencing in these species.…”

“…We also found a dramatic proliferation of CACTA transposons carrying MIR820 in some wild rice accessions, such as BB-and BBCC-genome species. 7 Therefore, we assumed that MIR820 expression would be extremely high in these species.…”

“…7 Therefore, one would assume that once miR820 effectively suppresses OsDRM2, silencing of transposons (including CACTA carrying MIR820) would be released, resulting in an increased transcription of MIR820. This would lead to a feed-forward loop, reinforcing the function of miR820.…”

Co-evolution of plant LTR-retrotransposons and their host genomes

“…It is likely that, during RdDM, double-stranded RNAs (dsRNAs) are processed to produce ~21-24 nt small interfering RNA (siRNAs), which direct de-novo methylation of original genomic locations and trigger epigenetic silencing (Aufsatz et al, 2002). Profi ling of small RNAs in the plant genomes has demonstrated that LTR-RTs are one of the major sources to generate small RNAs (Lu et al, 2005;Nosaka et al, 2012). As illustrated in Fig.…”