Regulation of Gene Expression in Plants through miRNA Inactivation

Ivashuta, Sergey; Banks, Isaac R.; Wiggins, B. Elizabeth; Zhang, Yuanji; Ziegler, Todd E.; Roberts, James K.; Heck, Gregory R.

doi:10.1371/journal.pone.0021330

Cited by 74 publications

(80 citation statements)

References 26 publications

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“…Only in miR171_2M transformants, which show a small decrease in miR171 levels, were no dramatic phenotypic differences evident (data not shown). These results confirm previous observations made in model plants 15,24,25 and suggest that decoy-dependent miRNA degradation, along with miRNA sequestration, are conserved mechanisms of miRNA inactivation in plants. While decoy dependent miRNA degradation was shown to be associated with activity of the proteins encoded by the SMALL RNA is not limited to the endogenous miR399 mimic example described, 24,25 which contains a three nucleotide bulge structure.…”

supporting

confidence: 92%

RNA decoys

Banks

Zhang

Wiggins

et al. 2012

Plant Signaling & Behavior

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T he role of non-coding RNAs (ncRNAs), both short and long ncRNAs, in the regulation of gene expression has become evident in recent years. Non-coding RNA-based regulation is achieved through a variety of mechanisms; some are relatively wellcharacterized, while others are much less understood. MicroRNAs (miRNAs), a class of endogenous small RNAs, function as master regulators of gene expression in eukaryotic organisms. A notable, recently discovered role for long ncRNAs is that of miRNA decoys, also referred to as target mimics or sponges, in which long ncRNAs carry a short stretch of sequence sharing homology to miRNAbinding sites in endogenous targets. As a consequence, miRNA decoys are able to sequester and inactivate miRNA function. Engineered miRNA decoys are also efficacious and useful tools for studying gene function. We recently demonstrated that the potential of miRNA decoys to inactivate miRNAs in the model plants Arabidopsis thaliana and Nicotiana benthamiana is dependent on the level of sequence complementarity to miRNAs of interest. The flexibility of the miRNA decoy approach in sequence-dependent miRNA inactivation, backbone choice, ability to simultaneously inactivate multiple miRNAs, and more importantly, to achieve a desirable level of miRNA inactivation, makes it a potentially useful tool for crop improvement. This research addendum reports the functional extension of miRNA decoys from model plants to crops. Furthermore, endogenous miRNA decoys, first described in plants, have been proposed to play a significant RNA decoys:

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supporting

confidence: 92%

RNA decoys

Banks

Zhang

Wiggins

et al. 2012

Plant Signaling & Behavior

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“…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.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2017

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The orchid family is the largest in the angiosperms, but little is known about the molecular basis of the significant variation they exhibit. We investigate here the transcriptomic divergence between two European terrestrial orchids, Dactylorhiza incarnata and Dactylorhiza fuchsii, and integrate these results in the context of their distinct ecologies that we also document. Clear signals of lineage‐specific adaptive evolution of protein‐coding sequences are identified, notably targeting elements of biotic defence, including both physical and chemical adaptations in the context of divergent pools of pathogens and herbivores. In turn, a substantial regulatory divergence between the two species appears linked to adaptation/acclimation to abiotic conditions. Several of the pathways affected by differential expression are also targeted by deviating post‐transcriptional regulation via sRNAs. Finally, D. incarnata appears to suffer from insufficient sRNA control over the activity of RNA‐dependent DNA polymerase, resulting in increased activity of class I transposable elements and, over time, in larger genome size than that of D. fuchsii. The extensive molecular divergence between the two species suggests significant genomic and transcriptomic shock in their hybrids and offers insights into the difficulty of coexistence at the homoploid level. Altogether, biological response to selection, accumulated during the history of these orchids, appears governed by their microenvironmental context, in which biotic and abiotic pressures act synergistically to shape transcriptome structure, expression and regulation.

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“…In addition, besides IPS1-based miRNA target mimicry and STTM methods, several other techniques, such as transcriptional gene silencing of miRNA gene promoters (Vaistij et al, 2010), artificial miRNA-directed silencing of miRNA precursors (Eamens et al, 2011), and miRNA decoy (Ivashuta et al, 2011), have successfully been used to investigate miRNA/target interactions in transgenic plants. Given the performance of VbMS by TRV-based expression of miRNA target mimics, these miRNAsilencing approaches can be widely adapted to VbMS to elucidate small RNA functions in plants.…”

Section: Discussionmentioning

confidence: 99%