Computational identification of novel microRNAs and targets in Brassica napus

Abstract

MicroRNAs (miRNAs) are a newly discovered class of non-protein-coding small RNAs with roughly 22 nucleotidelong. Increasing evidence has shown that miRNAs play multiple roles in biological processes, including development, cell proliferation and apoptosis and stress responses. In this research, several approaches were combined to make computational prediction of potential miRNAs and their targets in Brassica napus. We used previously known miRNAs from Arabidopsis, rice and other plant species against both expressed sequence tags (EST) and genomic survey sequence (GSS) databases to search for potential miRNAs in B. napus. A total of 21 potential miRNAs were detected following a range of strict filtering criteria. Using these potential miRNA sequences, we could further blast the mRNA database and found 67 potential targets in this species. According to the mRNA target information provided by NCBI (http:// www.ncbi.nlm.nih.gov/), most of the target mRNAs appeared to be involved in plant growth, development and stress responses. To validate the prediction of miRNAs in B. napus, we performed a RT-PCR based assay of mature miRNA expression. Five miRNAs were identified in response to auxin, cadmium stress and phosphate starvation. So far, little is known about experimental or computational identification of miRNA in B. napus species. To improve efficiency for blast search, we developed an implementation (miRNAassist) that can identify homologs of miRNAs and their targets, with high sensitivity and specificity. The program is allowed to be run on Windows Operation System platform. miRNAassist is freely available if required.

Arabidopsis Ribosomal Proteins RPL23aA and RPL23aB Are Differentially Targeted to the Nucleolus and Are Disparately Required for Normal Development

“…First, mutants in miRNA biogenesis (dcl1, hyl1, hen1, arg1) have a range of severe pleiotropic symptoms consistent with disrupted auxin responses, including altered leaf morphology, reduced stature, aberrant gynoecium patterning, decreased apical dominance, atypical phyllotaxis, and irregular vasculature (Bohmert et al, 1998;Jacobsen et al, 1999;Lu and Fedoroff, 2000;Chen et al, 2002). Secondly, several experimentally and computationally determined targets of miRNAs are involved in the auxin response, including TIR1, a component of the SCF TIR complex; NAC1/NAM, an auxin signal transducer; and ARF6, ARF8, ARF10, ARF16, and ARF17 (Bonnet et al, 2004;Vazquez et al, 2004;Xie et al, 2007; for review, see Eckardt, 2005;Mallory and Vaucheret, 2006). How then are miRNA-mediated processes dependent on translational status?…”

Identification of Potential microRNAs and Their Targets in Brassica rapa L.

“…These 2 methods have been used to identify hundreds of miRNAs in several plant species, including the model plant Arabidopsis thaliana (AlvesJunior et al, 2009;Buhtz et al, 2008;Jagadeeswaran et al, 2009;Jin et al, 2008;Klevebring et al, 2009;Song et al, 2009;Sunkar et al, 2005;2008;Szittya et al, 2008;Xie et al, 2007;Zhang et al, 2006b;2007a;2008). Recently, many miRNAs have been shown to regulate a wide range of biological functions of plants.…”

Prediction of potential novel microRNAs in soybean when in symbiosis

“…Despite the current knowledge of miRNAs involved in the regulation of nodulation, activity during the initial stages (e.g., the regulation of homeostasis and auxin signaling process) and nodule maturation (e.g., the nitrogen fixation process) (Subramanian et al, 2008;Wang et al, In silico identification of miRNAs 2009; Li et al, 2010), their functions are still not fully understood. Computational strategies have proven to be successful, highly effective, and important in identifying new miRNAs, as shown by the studies of Qiu et al (2007), Xie et al (2007), and Lu and Yang (2010), among others, where new miRNAs and target genes were identified by in silico analysis based on expressed sequence tags of Gossypium hirsutum, Brassica napus, and Vigna unguiculata, respectively. Our study performed an in silico analysis of miRNAs and their target genes present in a subtractive library of soybean roots inoculated with the Bradyrhizobium japonicum strain CPAC 15 obtained in a previous study (Barros de Carvalho et al, 2013).…”