Addressing the Role of microRNAs in Reprogramming Leaf Growth during Drought Stress in Brachypodium distachyon

Bertolini, Edoardo; Verelst, Wim; Horner, David S.; Gianfranceschi, L.; Piccolo, Viviana; Inzé, Dirk; Pè, Mario Enrico; Mica, Erica

doi:10.1093/mp/sss160

Cited by 80 publications

(63 citation statements)

References 109 publications

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“…Our analysis uncovered a total of 81 new miRNA precursors of conserved and non-conserved miRNAs. These confirmed 11 conserved and five non-conserved miRNA precursors that were recently reported [42]. In addition, evidence that miR162-mediated DCL1 regulation may not function in Brachypodium was presented.…”

Section: Discussionsupporting

confidence: 86%

Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon

et al. 2013

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BackgroundThe wild grass Brachypodium distachyon has emerged as a model system for temperate grasses and biofuel plants. However, the global analysis of miRNAs, molecules known to be key for eukaryotic gene regulation, has been limited in B. distachyon to studies examining a few samples or that rely on computational predictions. Similarly an in-depth global analysis of miRNA-mediated target cleavage using parallel analysis of RNA ends (PARE) data is lacking in B. distachyon.ResultsB. distachyon small RNAs were cloned and deeply sequenced from 17 libraries that represent different tissues and stresses. Using a computational pipeline, we identified 116 miRNAs including not only conserved miRNAs that have not been reported in B. distachyon, but also non-conserved miRNAs that were not found in other plants. To investigate miRNA-mediated cleavage function, four PARE libraries were constructed from key tissues and sequenced to a total depth of approximately 70 million sequences. The roughly 5 million distinct genome-matched sequences that resulted represent an extensive dataset for analyzing small RNA-guided cleavage events. Analysis of the PARE and miRNA data provided experimental evidence for miRNA-mediated cleavage of 264 sites in predicted miRNA targets. In addition, PARE analysis revealed that differentially expressed miRNAs in the same family guide specific target RNA cleavage in a correspondingly tissue-preferential manner.ConclusionsB. distachyon miRNAs and target RNAs were experimentally identified and analyzed. Knowledge gained from this study should provide insights into the roles of miRNAs and the regulation of their targets in B. distachyon and related plants.

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Section: Discussionsupporting

confidence: 86%

Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon

et al. 2013

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“…Similar kind of up regulation of miR162 under drought was reported in cotton and Brachypodium (Bertolinia et al, 2013). Up regulation of miR162 under salt stress was has also been reported in roots of Vigna unguiculata (Paul et al, 2011).…”

Section: Targets Of Mirnas Identified In This Studysupporting

confidence: 78%

Comparative miRNAome Analysis Revealed Numerous Conserved and Novel Drought Responsive miRNAs in Cotton (<i>Gossypium spp.</i>)

Boopathi

Sathish²,

Kavitha³

et al. 2016

cgg

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Negative regulations of gene expression by endogenous, non-coding miRNAs have been shown to play important role in abiotic stress responses in plants. However, limited knowledge is available on water stress responsive miRNAs in cotton. In this study, differentially expressed drought responsive miRNAs and their targets were identified under natural field conditions th rough high-throughput small RNA sequencing by comparing leaf samples of drought tolerant Gossypium hirsutum cv. KC3 and drought susceptible G. barbadense cv. Suvin. Totally four small RNA libraries were constructed and sequenced by employing ion proton TM technology. Altogether, there were 39 407 089 reads with a mean read length of 22 nt. In KC3, there were 5 138 unique miRNA reads that were differentially expressed with at least two folds under water stressed conditions. In contrast, Suvin have sho wn 8 469 unique miRNA reads that were differentially expressed with minimum of two folds under water stressed conditions. Comparison of miRNAs expressed under water stressed conditions between KC3 and Suvin, have resulted 7 494 miRNA reads and interestingly majority of them were down regulated with at least two folds. Besides identify ing large numbers of novel miRNAs, several abiotic stress responsive conserved miRNAs were also noticed. Of particular interest were miR750, miR2, miR14, miR276, miR279, miRbantam and miR5176 that were highly down regulated in KC3 under water stress conditions. Strikingly, miR2 and miR-bantam were previously shown to target pre-apoptotic genes in biological systems. Further, the identified miRNAs were also targeting different classes of dehydrogenases, protein kinases and transcription factors. Our results revealed for the first time that there were large numbers of water stress related miRNAs that might be sequentially and/or complexly involved in gene regulation that confers drought tolerance in cotton under field conditions and they have enormous potential in elucidating the molecular mechanism of miRNA based gene regulation and more importantly in genetic improvement of drought tolerance in cotton. Further, this is the first report on experimentally identifying miRNAs in G. barbadense.

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“…Of these, miR1435 and miR7714 have been experimentally validated in rice (Sunkar et al 2008) and Brachypodium distachyon (Bertolini et al 2013), close relatives of wheat, and experimental evidence for miR5024 exists in Arabidopsis (Breakfield et al 2012), suggesting that these are genuine miRNAs with potential roles on drought tolerance. A majority of putative stress-related miRNAs identified in this study (15 out of 20) were reported only in one or two species to date, while two others (miR444 and miR437) were included in this study, which may account for their contrasting drought responses.…”

Section: Discussionmentioning

confidence: 99%

Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress

Akpınar

Kantar

Budak

2015

Funct Integr Genomics

107

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MicroRNAs, small regulatory molecules with significant impacts on the transcriptional network of all living organisms, have been the focus of several studies conducted mostly on modern wheat cultivars. In this study, we investigated miRNA repertoires of modern durum wheat and its wild relatives, with differing degrees of drought tolerance, to identify miRNA candidates and their targets involved in drought stress response. Root transcriptomes of Triticum turgidum ssp. durum variety Kızıltan and two Triticum turgidum ssp. dicoccoides genotypes TR39477 and TTD-22 under control and drought conditions were assembled from individual RNA-Seq reads and used for in silico identification of miRNAs. A total of 66 miRNAs were identified from all species, across all conditions, of which 46 and 38 of the miRNAs identified from modern durum wheat and wild genotypes, respectively, had not been previously reported. Genotype- and/or stress-specific miRNAs provide insights into our understanding of the complex drought response. Particularly, miR1435, miR5024, and miR7714, identified only from drought-stress roots of drought-tolerant genotype TR39477, can be candidates for future studies to explore and exploit the drought response to develop tolerant varieties.

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Addressing the Role of microRNAs in Reprogramming Leaf Growth during Drought Stress in Brachypodium distachyon

Cited by 80 publications

References 109 publications

Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon

Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon

Comparative miRNAome Analysis Revealed Numerous Conserved and Novel Drought Responsive miRNAs in Cotton (<i>Gossypium spp.</i>)

Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress

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