Genome-Wide Analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 Pathway inArabidopsisReveals Dependency on miRNA- and tasiRNA-Directed Targeting

Abstract

Posttranscriptional RNA silencing of many endogenous transcripts, viruses, and transgenes involves the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 (RDR6/DCL4)-dependent short interfering RNA (siRNA) biogenesis pathway. Arabidopsis thaliana contains several families of trans-acting siRNAs (tasiRNAs) that form in 21-nucleotide phased arrays through the RDR6/DCL4-dependent pathway and that negatively regulate target transcripts. Using deep sequencing technology and computational approaches, the phasing patterns of known tasiRNAs and tasiRNA-like loci from across the Arabidopsis genome were analyzed in wild-type plants and silencing-defective mutants. Several gene transcripts were found to be routed through the RDR6/DCL4-dependent pathway after initial targeting by one or multiple miRNAs or tasiRNAs, the most conspicuous example of which was an expanding clade of genes encoding pentatricopeptide repeat (PPR) proteins. Interestingly, phylogenetic analysis using Populus trichocarpa revealed evidence for small RNA-mediated regulatory mechanisms within a similarly expanded group of PPR genes. We suggest that posttranscriptional silencing mechanisms operate on an evolutionary scale to buffer the effects of rapidly expanding gene families.

The Rf and Rf-like PPR in higher plants, a fast-evolving subclass of PPR genes

“…[70][71][72][73][74][75][76][77] The reasons for this massive targeting by small regulatory RNA is not understood yet, but such a tight regulation could allow the rapid expansion and diversification of the RFL subfamily with limiting detrimental effects as previously proposed. 76 All in all, the RFL subfamily is most probably more than a means to cope with male sterility, given the rapid expansion of the family and the apparent tight control by micro-RNAs. Identifying RFL functions in distinct species will certainly help to uncover the functionality of this intriguing subgroup of PPR genes.…”

Genome-Wide Characterization of the HD-ZIP IV Transcription Factor Family in Maize: Preferential Expression in the Epidermis

“…It seems unlikely that both motifs are miRNA target sites. Although some plant genes are known to be targets for multiple distinct small RNAs, such examples are not conserved throughout evolution (Axtell et al, 2007;Howell et al, 2007). However, it remains possible that one of the conserved motifs corresponds to a small RNA target site, with the second motif regulating its accessibility.…”

Novel and Recently Evolved MicroRNA Clusters Regulate Expansive F-BOX Gene Networks through Phased Small Interfering RNAs in Wild Diploid Strawberry

“…7). The miR390-TAS3 pathway is one of the most well-characterized pathways in plants and was identified in mosses as well as higher plants (Axtell et al, 2007;Howell et al, 2007). In Arabidopsis, miR390 cleaves TAS3 transcripts using a two-hit mechanism, generating tasiARFs that guide the degradation of transcripts encoding AUXIN RESPONSE FACTOR2 (ARF2), ARF3, and ARF4.…”