Computational Identification of MicroRNAs and Their Targets from Finger Millet (Eleusine coracana).

MicroRNAs are endogenous small RNAs regulating intrinsic normal growth and development of plant. Discovering miRNAs, their targets and further inferring their functions had become routine process to comprehend the normal biological processes of miRNAs and their roles in plant development. In this study, we used homology-based analysis with available expressed sequence tag of finger millet (Eleusine coracana) to predict conserved miRNAs. Three potent miRNAs targeting 88 genes were identified. The newly identified miRNAs were found to be homologous with miR166 and miR1310. The targets recognized were transcription factors and enzymes, and GO analysis showed these miRNAs played varied roles in gene regulation. The identification of miRNAs and their targets is anticipated to hasten the pace of key epigenetic regulators in plant development.

Identification of microRNAs and their targets in Finger millet by high throughput sequencing.

MicroRNAs are short non-coding RNAs which play an important role in regulating gene expression by mRNA cleavage or by translational repression. The majority of identified miRNAs were evolutionarily conserved; however, others expressed in a species-specific manner. Finger millet is an important cereal crop; nonetheless, no practical information is available on microRNAs to date. In this study, we have identified 95 conserved microRNAs belonging to 39 families and 3 novel microRNAs by high throughput sequencing. For the identified conserved and novel miRNAs a total of 507 targets were predicted. 11 miRNAs were validated and tissue specificity was determined by stem loop RT-qPCR, Northern blot. GO analyses revealed targets of miRNA were involved in wide range of regulatory functions. This study implies large number of known and novel miRNAs found in Finger millet which may play important role in growth and development.

Identification and Characterization of High Temperature Stress Responsive Novel miRNAs in French Bean (Phaseolus vulgaris).

MicroRNAs are important gene regulators controlling almost all biological and metabolic functions. They elicit their regulatory response through modulation of their target gene expression. In this study, we identified eight novel microRNAs (miRNAs) belonging to four miRNA families and one miR* sequence from the French bean genome which responded to high temperature. The precursor miRNAs varied in length and showed conserved signatures of RNA polymerase II transcripts in their upstream regions. Promoter region analysis indicated the prevalence of MYB and WRKY binding sites emphasizing auto-inhibition of miRNA biogenesis. The genomic organization study revealed the presence of 150 putative regulatory motifs of which 41 are unique. Common motifs shared by miRNAs involved in more than one abiotic stresses were also identified. Further, the miRNA validation was carried out by stem-loop real-time PCR, and the results emphasize that the differential expression of miRNAs confers stress tolerance. Functional analysis revealed that most of the targets represent transcription factors. The results obtained would provide new insights to the complex regulatory mechanism employing small non-coding regulatory RNAs toward stress adaptation.