psRNATarget: a plant small RNA target analysis server

Dai, Xinbin; Zhao, Patrick Xuechun

doi:10.1093/nar/gkr319

Cited by 1,702 publications

(1,403 citation statements)

References 29 publications

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“…Potential target genes were predicted using the software program psRNATarget (http://plantgrn.noble. org/psRNATarget/) [35].…”

Section: High Throughput Sequencing Annotation and Differential Expmentioning

confidence: 99%

“…6). In order to determine the functions of the predicted novel miRNAs, their targets were predicted using psRNATarget (http://plantgrn.noble.org/psRNATarget/) [35]; ahy-novel-2 putatively targets drought-responsive family protein, and ahy-novel-4 putatively targets disease resistance proteins. Other targets are related to regulatory mechanisms, plant metabolism, and transcription factors (Table A5).…”

Section: Expression Profiles Of Putatively Novel Mirnasmentioning

confidence: 99%

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Characterization of small RNA populations in non-transgenic and aflatoxin-reducing-transformed peanut

et al. 2017

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Power, Imana L.; Dang, Phat M.; Sobolev, Victor S.; Orner, Valerie; Powell, Joseph L.; Lamb, Marshall C.; and Arias, Renée S., "Characterization of small RNA populations in non-transgenic andaflatoxin-reducing-transformed peanut" (2017 t r a c tAflatoxin contamination is a major constraint in food production worldwide. In peanut (Arachis hypogaea L.), these toxic and carcinogenic aflatoxins are mainly produced by Aspergillus flavus Link and A. parasiticus Speare. The use of RNA interference (RNAi) is a promising method to reduce or prevent the accumulation of aflatoxin in peanut seed. In this study, we performed high-throughput sequencing of small RNA populations in a control line and in two transformed peanut lines that expressed an inverted repeat targeting five genes involved in the aflatoxin-biosynthesis pathway and that showed up to 100% less aflatoxin B 1 than the controls. The objective was to determine the putative involvement of the small RNA populations in aflatoxin reduction. In total, 41 known microRNA (miRNA) families and many novel miRNAs were identified. Among those, 89 known and 10 novel miRNAs were differentially expressed in the transformed lines. We furthermore found two small interfering RNAs derived from the inverted repeat, and 39 sRNAs that mapped without mismatches to the genome of A. flavus and were present only in the transformed lines. This information will increase our understanding of the effectiveness of RNAi and enable the possible improvement of the RNAi technology for the control of aflatoxins.

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“…Potential target genes were predicted using the software program psRNATarget (http://plantgrn.noble. org/psRNATarget/) [35].…”

Section: High Throughput Sequencing Annotation and Differential Expmentioning

confidence: 99%

Section: Expression Profiles Of Putatively Novel Mirnasmentioning

confidence: 99%

Characterization of small RNA populations in non-transgenic and aflatoxin-reducing-transformed peanut

et al. 2017

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“…Conservation and phylogenetic analyses were done by the publicly available WebLogo, a sequence logo generator (Larkin et al, 2007), and ClustalW (Crooks et al, 2004) to generate a cladogram tree using neighborjoining clustering, respectively. For data mining in the identification of miRNAs' targets, psRNATarget, a plant small RNA target analysis server available at http:// plantgrn.noble.org/psRNATarget/ (Dai and Zhao, 2011), and RNAhybrid, a miRNA target prediction tool (bibiserv2.cebitec.uni-bielefeld.de/rnahybrid) (Kruger and Rehmsmeier, 2006), were used. The GO database was downloaded from the Gene Ontology website (http:// www.geneontology.org/GO.downloads.shtml) for the confirmation of miRNAs' functions.…”

Section: Bioinformatics Tools Used For Prediction Of Mirnasmentioning

confidence: 99%

Bioinformatics profiling and characterization of potentialmicroRNAs and their targets in the genus Coffea

Bibi¹,

Barozai²,

Din³

2017

Turk J Agric For

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IntroductionMicroRNAs (miRNAs) are an extensive class of noncoding small endogenous RNAs of 18 to 26 nt in length that are derived from self-complementary fold-back structures of longer precursor sequences (pre-miRNAs) and are generated by Dicer-like 1 (DCL1) in plants (Bartel, 2004). Mature miRNAs inhibit gene expression at posttranscriptional levels by either targeting mRNAs for degradation or inhibiting protein translation. Both processes are accomplished by the complementary base pairing of miRNAs to their target mRNA sequences (Ambros, 2004). In plants, for a majority of cases, miRNAs interact with their targets through perfect or near-perfect base pairing and lead to target mRNA degradation (Jones-Rhoades et al., 2006). Increasing evidence has revealed that miRNAs play an important role in a wide range of development processes in plants, including cell proliferation, stress response, metabolism, inflammation, and signal transduction (Ambros, 2004;Jones-Rhoades et al., 2006;Zhang et al., 2007a;Ali et al., 2016) and crosskingdom gene regulation (Barozai and Din, 2017). To date, more than 28,645 miRNAs have been identified from 223 species of plants and animals and deposited in the publicly available database miRBase (Release 21) (Griffiths-Jones et al., 2008). The majority of plant miRNAs have been found in species with fully sequenced genomes including 713 from Oryza sativa, 401 from Populus trichocarpa, 384 from Arabidopsis thaliana, 343 from Solanum tuberosum, 321 from Zea mays, and 241 from Sorghum bicolor (Griffiths-Jones et al., 2008). miRNA-related research is continuously growing and miRNAs, along with their functions, are being identified and elucidated using a wide variety of computational tools and experimental methods including direct cloning, deep sequencing, and other approaches. Comparison of miRNAs across multiple plant species has demonstrated that some miRNAs are highly evolutionary conserved from species to species, such as from mosses to higher flowering eudicots in the plant kingdom (Floyd and Bowman, 2004;Zhang et al., 2006aZhang et al., , 2006b. Conservation of miRNA sequences has provided a powerful strategy for identifying miRNAs in other species. Currently, comparative genome-based homolog searches have been used to identify conserved miRNAs in many plant species, including cotton (

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“…The only stem-loop structure of pre-miRNAs has been selected and used as novel miRNAs of apricot. The miRNA sequences present in stem part used as novel mature miRNAs of apricot and further taken as query to identify their mRNAs (target gene) in human by psRNATarget tool [9]. The detail study of these predicted targets were conducted by Gene Ontology Consortium and Human gene and protein database [10 and 11].…”

Section: Methodsmentioning

confidence: 99%

Untitled

2017

RJLBPCS

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MicroRNAs (miRNAs) are small non-coding post-transcriptionally regulatory RNA, present in both plant and human. The food derived miRNAs have been proved to target genes in human and other animals and regulate their expression at genetic level. Based on this concept, we have computationally identified potential miRNAs of Prunus armeniaca (Apricot) from EST data.After performing different alignments and secondary structure identifications, the 6 (Six) potential miRNAs out of 17686 EST of apricot were identified and they were further subjected against human transcript to find out functional targets. The functional annotation and gene ontology of human target genes were carried out by bioinformatic tools and software. We have noticed that 2 miRNAs of apricot have higher complementarity with 27 human genes and these genes are involved in molecular functions (27%), biological processes (59%) and cellular components (14%).These finding expand the scope of understanding the functions of dietary miRNAs in human and give new insights to the researchers for experimental validation.

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psRNATarget: a plant small RNA target analysis server

Cited by 1,702 publications

References 29 publications

Characterization of small RNA populations in non-transgenic and aflatoxin-reducing-transformed peanut

Characterization of small RNA populations in non-transgenic and aflatoxin-reducing-transformed peanut

Bioinformatics profiling and characterization of potentialmicroRNAs and their targets in the genus Coffea

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