Abstract
BackgroundMicroRNAs (miRNAs) are small, non-coding RNA molecules that play a key role in gene regulation in both plants and animals. MicroRNA biogenesis involves the enzymatic processing of a primary RNA transcript. The final step is the production of a duplex molecule, often designated as miRNA:miRNA*, that will yield a functional miRNA by separation of the two strands. This miRNA will be incorporated into the RNA-induced silencing complex, which subsequently will bind to its target mRNA in order to suppress its expression. The analysis of miRNAs is still a developing area for computational biology with many open questions regarding the structure and function of this important class of molecules. Here, we present StarSeeker, a simple tool that outputs the putative miRNA* sequence given the precursor and the mature sequences.ResultsWe evaluated StarSeeker using a dataset consisting of all plant sequences available in miRBase (6992 precursor sequences and 8496 mature sequences). The program returned a total of 15,468 predicted miRNA* sequences. Of these, 2650 sequences were matched to annotated miRNAs (~ 90% of the miRBase-annotated sequences). The remaining predictions could not be verified, mainly because they do not comply with the rule requiring the two overhanging nucleotides in the duplex molecule.ConclusionsThe expression pattern of some miRNAs in plants can be altered under various abiotic stress conditions. Potential miRNA* molecules that do not degrade can thus be detected and also discovered in high-throughput sequencing data, helping us to understand their role in gene regulation.
Highlights
MicroRNAs are small, non-coding RNA molecules that play a key role in gene regulation in both plants and animals
MicroRNAs are small, non-coding RNA molecules that play a key role in post-transcriptional gene regulation in plants, animals and some viruses
Natsidis et al J of Biol Res-Thessaloniki (2018) 25:11 the functional miRNA by separation of the two clones. This miRNA will be incorporated into the RNA-induced silencing complex (RISC), which subsequently will bind to its target mRNA in order to suppress its expression
Summary
MicroRNAs (miRNAs) are small, non-coding RNA molecules that play a key role in gene regulation in both plants and animals. MicroRNAs are small, non-coding RNA molecules that play a key role in post-transcriptional gene regulation in plants, animals and some viruses. They are usually 21–24 nucleotides long and regulate a diversity of cellular processes such as growth, development, differentiation and apoptosis. MicroRNAs are produced through enzymatic processing of a primary RNA transcript, which can originate either from its own gene, usually found in intergenic regions across the whole genome, or from an intron of a protein-coding gene [2] This transcript is called primary miRNA (pri-miRNA) and it is processed into a ~ 70 nucleotide-long precursor miRNA (pre-miRNA) by the enzyme Drosha. This RNA is the miRNA:miRNA* duplex and it will give
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