Computational Identification, Characterization and Analysis of Conserved miRNAs and their Targets in Amborella Trichopoda

Hajieghrari B Farrokhi N

doi:10.4172/2153-0602.1000168

Abstract

MicroRNAs (miRNAs) are single stranded non-coding endogenous small RNAs of about 22 nucleotides, which are directly involved in regulating gene expression at post transcriptional level. miRNAs play key roles in development and response to biotic and abiotic stresses. Homology searches allow identification of new miRNAs due to their relative high conservation in plant species. Here, miRNAs were identified for Amborella trichopoda. Known and unique plant miRNAs from miRBase were BLAST-searched against Expressed Sequence Tag (EST) and Genomic Survey Sequence (GSS) in A. trichopoda. All candidate sequences with appropriate fold back structure were screened by a series of miRNA filtering criteria. Finally, we identified and analysed conservation of 5 potential conserved miRNAs belonging to 5 miRNA gene families from ESTs as well 82 newly identified miRNAs dependant 39 miRNA families from GSSs. Potential target genes of identified miRNAs were identified based on their sequence complementarities to the respective miRNAs using psRNATarget against scaffold assignment of A. trichopoda genome sequences. Totally, 1219 target sites in A. trichopoda genome were identified. From which, 941 (77.19%) were predicted to be the subject of miRNA cleavage and 278 (22.81%) scaffolds were regulated via translational repression of mRNA. From the predicted miRNAs, 18 had no target sequence in A.trichopoda.

Highlights

Micro RNAs are a class of endogenous, single-stranded, non-protein-coding small RNAs that negatively regulate expression of varieties of protein-coding genes at post transcriptional level
A.trichopoda Expressed Sequence Tag (EST) and Genomic Survey Sequence (GSS) were obtained from the relevant databases, which were available at nucleotide database of the National Center for Biotechnology Information (NCBI)
All found A.trichopoda sequences were in Micro RNAs (miRNAs) gene families

Summary

Introduction

Micro RNAs (miRNAs) are a class of endogenous, single-stranded, non-protein-coding small RNAs that negatively regulate expression of varieties of protein-coding genes at post transcriptional level. This ancient evolutionary mechanism controls the expression by both targeting and cleavage of complementary mRNA, or in some cases by translational repression [1]. The single-stranded mature miRNA is assembled into the ARGONAUTE 1 (Ago1) associated RNA-induced silencing complex (RISC) [13]. This complex is capable of binding to the complementary sequence of an mRNA molecule; the binding can be partial or complete. An mRNA target can be regulated by multiple miRNAs [14]

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Conclusion