Computational Identification of Micro RNAs and Their Transcript Target(s) in Field Mustard (Brassica rapa L.)

Document Type: Research Paper

Authors

1 Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, IRAN

2 Department of Biotechnology Engineering, Faculty of Energy Engineering and New Technologies Shahid Beheshti University

3 Departments of Biophysics and Bioinformatics laboratories, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, IRAN

4 Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, IRAN

Abstract

Background: Micro RNAs (miRNAs) are a pivotal part of non-protein-coding endogenous small RNA molecules that regulate the genes involved in plant growth and development, and respond to biotic and abiotic environmental stresses posttranscriptionally.
Objective: In the present study, we report the results of a systemic search for identifi cation of new miRNAs in B. rapa using homology-based ESTs (Expressed Sequence Tags) analysis and considering a series of fi ltration criteria.
Materials and Methods: Plant mature miRNA sequences were searched in non-protein coding ESTs registered in NCBI EST database. Zuker RNA folding algorithm was used to generate the secondary structures of the ESTs. Potential sequences were candidate as miRNA genes and characterized evolutionarily only and if only they fi t some described criteria. Also, the web tool psRNATarget was applied to predict candidate B. rapa miRNA targets.
Results: In this study, 10 novel miRNAs from B. rapa belonging to 6 miRNA families were identifi ed using EST-based homology analysis by considering a series of fi ltration criteria. All potent miRNAs appropriate fold back structure. Several potential targets with known/unknown functions for these novel miRNAs were identifi ed. The target genes mainly encode transcription factors, enzymes, DNA binding proteins, disease resistance proteins, carrier proteins and other biological processes.
Conclusions: MicroRNA having diverse functions in plant species growth, development and evolution by post transcriptionally regulating the levels of specifi c transcriptome so by eff ecting on their translation products. Research in miRNA led to the identifi cation of many miRNAs and their regulating genes from diverse plant species.

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