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Review
. 2016 Jan 8;44(1):24-44.
doi: 10.1093/nar/gkv1221. Epub 2015 Nov 17.

Bioinformatic tools for microRNA dissection

Most Mauluda Akhtar  1 , Luigina Micolucci  2 , Md Soriful Islam  3 , Fabiola Olivieri  4 , Antonio Domenico Procopio  4
Affiliations
Review

Bioinformatic tools for microRNA dissection

Most Mauluda Akhtar et al. Nucleic Acids Res. .

Abstract

Recently, microRNAs (miRNAs) have emerged as important elements of gene regulatory networks. MiRNAs are endogenous single-stranded non-coding RNAs (~22-nt long) that regulate gene expression at the post-transcriptional level. Through pairing with mRNA, miRNAs can down-regulate gene expression by inhibiting translation or stimulating mRNA degradation. In some cases they can also up-regulate the expression of a target gene. MiRNAs influence a variety of cellular pathways that range from development to carcinogenesis. The involvement of miRNAs in several human diseases, particularly cancer, makes them potential diagnostic and prognostic biomarkers. Recent technological advances, especially high-throughput sequencing, have led to an exponential growth in the generation of miRNA-related data. A number of bioinformatic tools and databases have been devised to manage this growing body of data. We analyze 129 miRNA tools that are being used in diverse areas of miRNA research, to assist investigators in choosing the most appropriate tools for their needs.

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Figures

Figure 1.
Figure 1.
Figure illustrates the complexity of large data sets and the need for bioinformatic tools.
Figure 2.
Figure 2.
Biogenesis and clinical implications of microRNAs (miRNAs). MiRNA genes are typically transcribed by RNA polymerase II and III and produce primary miRNA (pri-miRNA). Next pri-miRNA is processed to precursor miRNA (pre-miRNA) hairpin structure in the nucleus by the Drosha/Pasha complex and transported into the cytoplasm by Exportin 5. Pre-miRNA is further processed by Dicer-TRBP (TAR RNA binding protein) into a miRNA:miRNA* duplex. After being separated, the mature miRNA loaded into the Argonaute 2 (Ago 2) containing RNA-induced silencing complexes (RISCs). Once the miRISC is assembled, the miRNA drives it to silence target mRNA via mRNA cleavage, translational repression or deadenylation. At present two strategies are used for miRNA-based therapeutics in the management of cancer: (i) inhibition of miRNA function for oncomiRs includes miRNA sponges, antisense antimiRs and miRNA masks, (ii) Restoration of miRNA function for tumor suppressive miRNAs includes miRNA mimics and expression vectors.
Figure 3.
Figure 3.
Schematic overview of currently available bioinformatic tools classified according to the main purpose for which they are being used. Sample tools are presented for each category.
See this image and copyright information in PMC

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