02. Bioinformatic hunting of microRNAs
Abstract
MicroRNAs (miRNAs) are endogenous, small, noncoding RNAs of 18-25 nucleotides in length that negatively
regulate their complementary messenger-RNAs at the post transcriptional level. Presently there are three approaches
for miRNA identification. Two approaches i.e. bioinformatic and small RNA library construction and sequencing
are examples of reverse genetics approach. In these two approaches researchers try to find miRNAs in the known
genotypes (sequences). A third approach called the classical approach is example of forward genetics in which
researchers determine the unknown genotype (miRNA sequence) of a known phenotype. The miRNAs have shown
both evolutionarily converged nature (conserved miRNAs) from species to species within the same kingdom and
species specific expression (species specific miRNAs). Majority of the miRNA genes are observed as conserved
miRNAs as orthologs. This conserved nature of majority of miRNAs becomes an important logical tool for
bioinformatics discovery of miRNAs in other species. Identification of miRNAs by using bioinformatic tools is now
a commonplace and of the most widely used methods and it has facilitated the prediction of new miRNAs in both
plant and animal systems. This is largely used due to its low cost and high efficiency. In 2001 the 1st release of
miRBases (an online repository of miRNAs) contained only 218 miRNA entries and now its latest release 20
(released in June 2013) contains 24521 entries. The bioinformatics hunting of miRNAs has also a reasonable
contribution in identification of new miRNAs. Around 25% of entries in miRBase (across all species) are predicted
computationally. Likewise in Plant MicroRNA Database (PMRD) within the total 8433 miRNAs, 1297 of them are
experimentally demonstrated and 7136 of them are from computational predictions . This review is aimed at
describing the bioinformatic resources used in miRNA identification. Furthermore, the limitations of these resources
are also described.
Keywords: Bioinformatics, Comparative genomics, MicroRNA
