PsRobot: a web-based plant small RNA meta-analysis toolbox

Wu, Hua‐Jun; Ma, Yingke; Chen, Tong; Wang, Meng; Wang, Xiu‐Jie

doi:10.1093/nar/gks554

Cited by 440 publications

(347 citation statements)

References 45 publications

(62 reference statements)

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“…Similar to the initial computational prediction of miR5200a targets in wheat and barley (see Supplemental Figures 4A and 4B online), using psROBOT sRNA analysis toolbox (Wu et al, 2012), we identified two B. distachyon FT-like genes (Bradi2g07070 and Bradi1g48830), which were previously annotated as FTL1 and FTL2 (Higgins et al, 2010), as miR5200a targets (Figure 1C;see Supplemental Figures 4C and 4D online). Further validation through 59 RNA ligase-mediated RACE showed that both FTL1 and FTL2 mRNAs could be cleaved at miR5200 target sites in vivo, suggesting that these two FTs are bona fide miR5200 target genes ( Figure 1C).…”

Section: Mir5200 Targets Ft Orthologous Genes and Accumulates In Leavessupporting

confidence: 55%

Regulation of FLOWERING LOCUS T by a MicroRNA in Brachypodium distachyon

Liu

et al. 2013

The Plant Cell

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ORCID IDs: 0000-0003-4953-7258 (L.W.); 0000-0002-3377-4040 (L.M.).The highly conserved florigen gene FLOWERING LOCUS T (FT) functions at the core of the flowering pathways. Extensive studies have examined the transcriptional regulation of FT; however, other layers of FT regulation remain unclear. Here, we identified miR5200 a Pooideae-specific microRNA that is expressed in leaves and targets Brachypodium distachyon FT orthologs for mRNA cleavage. miR5200 was abundantly expressed in plants grown under short-day (SD) conditions but was dramatically repressed in plants transferred to long-day (LD) conditions. We also found that the epigenetic chromatin status, specifically the levels of histone methylation marks, at miR5200 precursor loci changed in response to daylength. Moreover, artificial interruption of miR5200 activity by target mimicry in B. distachyon altered flowering time in SD but not in LD conditions, suggesting that miR5200 functions in photoperiod-mediated flowering time regulation. Together, these findings illustrate a posttranscriptional regulation mechanism of FT and provide insights into understanding of the multiple concerted pathways for flowering time control in plants.

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Section: Mir5200 Targets Ft Orthologous Genes and Accumulates In Leavessupporting

confidence: 55%

Regulation of FLOWERING LOCUS T by a MicroRNA in Brachypodium distachyon

Liu

et al. 2013

The Plant Cell

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“…All primers are shown in Supplemental Table S4. Target genes of miRNAs in N. benthamiana were predicted by psRobot (Wu et al, 2012).…”

Section: Transient Agroinfiltration Assay In Nicotiana Benthamianamentioning

confidence: 99%

Widespread Long Noncoding RNAs as Endogenous Target Mimics for MicroRNAs in Plants

Wang

et al. 2013

Plant Physiology

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359

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Target mimicry is a recently identified regulatory mechanism for microRNA (miRNA) functions in plants in which the decoy RNAs bind to miRNAs via complementary sequences and therefore block the interaction between miRNAs and their authentic targets. Both endogenous decoy RNAs (miRNA target mimics) and engineered artificial RNAs can induce target mimicry effects. Yet until now, only the Induced by Phosphate Starvation1 RNA has been proven to be a functional endogenous microRNA target mimic (eTM). In this work, we developed a computational method and systematically identified intergenic or noncoding gene-originated eTMs for 20 conserved miRNAs in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). The predicted miRNA binding sites were well conserved among eTMs of the same miRNA, whereas sequences outside of the binding sites varied a lot. We proved that the eTMs of miR160 and miR166 are functional target mimics and identified their roles in the regulation of plant development. The effectiveness of eTMs for three other miRNAs was also confirmed by transient agroinfiltration assay.

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“…Target predictions were performed using psRobot_tar in psRobot [32] and through alignment with the U. pumila transcriptome (SRA database, SRP080724). The following criteria were then used to identify potential miRNA targets: (1) no more than four mismatches between the mature miRNA and its potential target site; (2) no more than one mismatch at nucleotide positions 1-9; (3) no more than two consecutive mismatches; and (4) no mismatches at positions 10 and 11 [30,33,34].…”

Section: Prediction Of Mirna Target Genesmentioning

confidence: 99%

Identification and Target Prediction of MicroRNAs in Ulmus pumila L. Seedling Roots under Salt Stress by High-Throughput Sequencing

Zhu¹,

Yang²,

Liu³

et al. 2016

Forests

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MicroRNAs (miRNAs) are a class of endogenous small RNAs with important roles in plant growth, development, and environmental stress responses. Ulmus pumila L., a deciduous broadleaved tree species of northern temperate regions, is widely distributed in central and northern Asia and has important economic and ecological value. With the spread and aggravation of soil salinization, salt stress has become a major abiotic stress affecting the normal growth and development of U. pumila. However, the influence of salt stress on U. pumila miRNA expression has not been investigated. To identify miRNAs and predict their target mRNA genes under salt stress, three small RNA libraries were generated and sequenced from roots of U. pumila seedlings treated with various concentrations of NaCl corresponding to no salt stress, light short-term salt stress, and medium-heavy long-term salt stress. Integrative analysis identified 254 conserved miRNAs representing 29 families and 49 novel miRNAs; 232 potential targets of the miRNAs were also predicted. Expression profiling of miRNAs between libraries was performed, and the expression of six miRNAs was validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Our findings provide an overview of potential miRNAs and corresponding targets involved in regulating U. pumila salt defense responses. These results lay the foundation for further research into molecular mechanisms involved in salt stress resistance in U. pumila and other Ulmaceae species.

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PsRobot: a web-based plant small RNA meta-analysis toolbox

Cited by 440 publications

References 45 publications

Regulation of FLOWERING LOCUS T by a MicroRNA in Brachypodium distachyon

Regulation of FLOWERING LOCUS T by a MicroRNA in Brachypodium distachyon

Widespread Long Noncoding RNAs as Endogenous Target Mimics for MicroRNAs in Plants

Identification and Target Prediction of MicroRNAs in Ulmus pumila L. Seedling Roots under Salt Stress by High-Throughput Sequencing

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