Computational prediction of miRNAs in Arabidopsis thaliana.

By Alex T. Adai, Cameron Johnson, Sizolwenkosi Mlotshwa, Sarah Archer-Evans, Varun Manocha, Vicki Vance, Venkatesan Sundaresan. Genome Research, 2005

395 citations recorded by the source corpus.

MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression in animals and plants. Comparative genomic computational methods have been developed to predict new miRNAs in worms, flies, and humans. Here, we present a novel single genome approach for the detection of miRNAs in Arabidopsis thaliana. This was initiated by producing a candidate miRNA-target data set using an algorithm called findMiRNA, which predicts potential miRNAs within candidate precursor sequences that have corresponding target sites within transcripts. From this data set, we used a characteristic divergence pattern of miRNA precursor families to select 13 potential new miRNAs for experimental verification, and found that corresponding small RNAs could be detected for at least eight of the candidate miRNAs. Expression of some of these miRNAs appears to be under developmental control. Our results are consistent with the idea that targets of miRNAs encompass a wide range of transcripts, including those for F-box factors, ubiquitin conjugases, Leucine-rich repeat proteins, and metabolic enzymes, and that regulation by miRNAs might be widespread in the genome. The entire set of annotated transcripts in the Arabidopsis genome has been run through find MiRNA to yield a data set that will enable identification of potential miRNAs directed against any target gene.

Subfields: Cancer Research, Plant Science

View Paper: https://www.semanticscholar.org/paper/ffb46cf5760acf41cecd3196a9a5ca3296e4c35e

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Citations in the corpus

Conservation and divergence of plant microRNA genes. (2006, background): “Most miRNAs of dicots (based on Arabidopsis thaliana) have homologs in monocots (primarily based on rice) (Adai et al., 2005; Bonnet et al., 2004a; Jones-Rhoades and Bartel, 2004; Llave et al., 2002; Reinhart et al., 2002; Sunkar and Zhu, 2004; Wang et al., 2004). It is thought that some miRNAs dive”
miREvo: an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments (2012, background): “In fact, the strong phylogenetic conservation has been a wildly-used criterion for the identification of miRNAs, such as in Arabidopsis thaliana [7] and human [8].”
Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA (2005, background): “For individual genes or intergenic regions, we provide links to the FindMiRNA site that can 15 provide supporting data for novel miRNAs (22).”
Novel and Mechanical Stress–Responsive MicroRNAs in Populus trichocarpa That Are Absent from Arabidopsisw⃞ (2005, methodology): “However, the argument that cloning may exclude underexpressed or tissue- or development-specific miRNAs has shifted identification efforts toward computational analyses, which have resulted in a considerably larger number of identified Arabidopsis miRNAs (Bonnet et al., 2004; Wang et al., 2004b; Ada”
Genomics of microRNA. (2006, background): “mature miRNA Seed match, comparative analysis K findMiRNA Arabidopsis [ 107 ]”
Regulation of Phosphate Homeostasis by MicroRNA in Arabidopsis[W] (2005, background): “…has been shown to be regulated by development in a tissue-specific manner or in response to a range of environmental stresses (Reinhart et al., 2002; Jones-Rhoades and Bartel, 2004; Sunkar and Zhu, 2004; Adai et al., 2005; Axtell and Bartel, 2005; Lu et al., 2005a, 2005b; Sunkar et al., 2005).”
Control of Root Cap Formation by MicroRNA-Targeted Auxin Response Factors in Arabidopsisw⃞ (2005, background): “…22 families of miRNAs in Arabidopsis have been identified to date (Reinhart et al., 2002; Bonnet et al., 2004; Jones-Rhoades and Bartel, 2004; Sunkar and Zhu, 2004; Adai et al., 2005); among them, miRNA160 (miR160) has sequence complementarities to a group of ARF genes: ARF10, ARF16, and ARF17.”
Functional diversity of miRNA in plants (2007, background): “The TIR1 auxin receptor is a predicted target of miR393 [18,19].”