The expanding world of small RNAs in plants

Abstract

Plant genomes produce a variety of small RNAs that function in distinct, yet overlapping, genetic and epigenetic silencing pathways. However, the abundance and diversity of small RNA classes varies in different plant species, suggesting co-evolution between environmental adaptations and gene silencing mechanisms. Small RNA biogenesis in plants is well understood, but we are just beginning to uncover their intricate regulation and activity. Here, we discuss the biogenesis of plant small RNAs, such as microRNAs, secondary small-interfering RNAs and heterochromatic small-interfering RNAs, and their diverse cellular and developmental functions, including reproductive transitions, genomic imprinting and paramutation. We also discuss the diversification of small RNA-directed silencing pathways through the expansion of RNA-dependent RNA polymerases, Dicer and Argonaute proteins.

Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima

“…The comparative analysis of sRNA profiles confirms that the extensive differences in gene expression between the Dactylorhiza species are complemented by divergent post‐transcriptional regulations. miRNAs function as negative regulators of gene expression via translational repression or mRNA cleavage (Borges & Martienssen, 2015) and are known to mediate response to genomic or environmental stresses (Ding, Tao, & Zhu, 2013; Ivashuta et al., 2011). From the transcripts that were targeted by miRNAs and/or tasiRNAs, 27.2% were found to be differentially regulated between the two orchid species, with deviating post‐transcriptional regulation of metabolism (e.g., nucleic acids, aromatic compounds, tetrapyrrole and alkaloid metabolism targeted in D. fuchsii , and DNA and tetrapyrrole metabolism targeted in D. incarnata ) and binding (Fig.…”

“…For example, accumulating evidence suggests a role for divergent small RNAs (sRNAs) and other regulatory elements in postzygotic reproductive isolation, and the hybrid incompatibility they trigger is predicted to evolve relatively early in the speciation process (Ha, Pang, Agarwal, & Chen, 2008; Hollister et al., 2011; Kitano, Yoshida, & Suzuki, 2013; McManus et al., 2010; Michalak, 2008). Small RNAs, including plant microRNAs (miRNAs), secondary small interfering RNAs (siRNAs) and heterochromatic small interfering RNAs (hetsiRNAs, Borges & Martienssen, 2015), are involved in (post)transcriptional gene regulation, RNA‐directed DNA methylation and chromatin remodelling, playing major roles in the maintenance of genome stability and function (Zhang, 2008). Importantly, regulatory divergence is generally dynamic, potentially exposing phenotypes to natural selection differentially across time and environmental conditions.…”

Uptake and impact of natural diet-derived small RNA in invertebrates: Implications for ecology and agriculture

“…30 In addition, sRNA expression is known to vary significantly between plant tissues in a given species and are highly sensitive to environmental conditions. 42 As an example, miRNAs in wheat were found to be expressed in a tissue-specific manner and this was influenced significantly by abiotic stressors. 43 Plants also possess a number of other sRNA types, which are generated from longer dsRNA precursors, including hairpinderived siRNA, natural antisense siRNA, secondary siRNA, and heterochromatic siRNA.…”

“…43 Plants also possess a number of other sRNA types, which are generated from longer dsRNA precursors, including hairpinderived siRNA, natural antisense siRNA, secondary siRNA, and heterochromatic siRNA. 42,44 The amounts of these have primarily been examined in model organisms, such as Arabidopsis thaliana, and the agriculturally important rice, maize, and soy, so very few conclusions can currently be made about their typical amounts. In addition, the amount of a given food consumed by an animal also varies considerably 45 and both must be considered to meet this first condition.…”

Developmental Defects Mediated by the P1/HC-Pro Potyviral Silencing Suppressor Are Not Due to Misregulation of AUXIN RESPONSE FACTOR 8

“…Eukaryotes have evolved an elaborate network of RNA silencing pathways mediated by small regulatory RNAs (for review, see Axtell et al [2011] and Borges and Martienssen [2015]). These pathways play two major roles in plants.…”