Identification of homologous microRNAs in 56 animal genomes

Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan.
Genomics (Impact Factor: 2.28). 03/2010; 96(1):1-9. DOI: 10.1016/j.ygeno.2010.03.009
Source: PubMed


MicroRNAs (miRNAs) are endogenous non-protein-coding RNAs of approximately 22 nucleotides. Thousands of miRNA genes have been identified (computationally and/or experimentally) in a variety of organisms, which suggests that miRNA genes have been widely shared and distributed among species. Here, we used unique miRNA sequence patterns to scan the genome sequences of 56 bilaterian animal species for locating candidate miRNAs first. The regions centered surrounding these candidate miRNAs were then extracted for folding and calculating the features of their secondary structure. Using a support vector machine (SVM) as a classifier combined with these features, we identified an additional 13,091 orthologous or paralogous candidate pre-miRNAs, as well as their corresponding candidate mature miRNAs. Stem-loop RT-PCR and deep sequencing methods were used to experimentally validate the prediction results in human, medaka and rabbit. Our prediction pipeline allows the rapid and effective discovery of homologous miRNAs in a large number of genomes.

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Available from: Sung-Chou Li, May 23, 2014
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    • "They negatively regulate gene expression through sequence-specific interactions with the 3′ untranslated regions (UTRs) of target mRNAs and thereby cause translational repression or mRNA destabilization [8,9]. Since the discovery of the founding members of the miRNA family, lin-4 and let-7 in Caenorhabditis elegans in 1993 [10-12], many endogenously encoded miRNAs have been identified in mammals, plants, insects, worms, and viruses through plasmid vector cloning, northern blotting, microarray assay and sequencing technology in recent years [13-15]. Currently, 21264 mature miRNAs from 193 species have been discovered and deposited in the public available miRNA database miRBase (Release 19.0, June 2013) [16]. "
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    BMC Genomics 11/2013; 14(1):754. DOI:10.1186/1471-2164-14-754 · 3.99 Impact Factor
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    • "4). Shown in color are the purported occurrences of these miRNAs in these taxa according to Li et al. (2010) "
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    ABSTRACT: microRNAs (miRNAs) are a key component of gene regulatory networks and have been implicated in the regulation of virtually every biological process found in multicellular eukaryotes. What makes them interesting from a phylogenetic perspective is the high conservation of primary sequence between taxa, their accrual in metazoan genomes through evolutionary time, and the rarity of secondary loss in most metazoan taxa. Despite these properties, the use of miRNAs as phylogenetic markers has not yet been discussed within a clear conceptual framework. In this review we highlight five properties of miRNAs that underlie their utility in phylogenetics: 1) The processes of miRNA biogenesis enables the identification of novel miRNAs without prior knowledge of sequence; 2) The continuous addition of miRNA families to metazoan genomes through evolutionary time; 3) The low-level of secondary gene loss in most metazoan taxa; 4) The low substitution rate in the mature miRNA sequence; and 5) The small probability of convergent evolution of two miRNAs. Phylogenetic analyses using both Bayesian and parsimony methods on a eumetazoan miRNA dataset highlight the potential of miRNAs to become an invaluable new tool, especially when used as an additional line of evidence, to resolve previously intractable nodes within the tree of life.
    Molecular Biology and Evolution 08/2013; 30(11). DOI:10.1093/molbev/mst133 · 9.11 Impact Factor
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    • "we annotated to zebrafish Danio rerio as the least distant species from Salmonids (Davidson et al., 2010) as was done in a previous study on Atlantic cod (Gadus morhua; Johansen et al., 2011). miRBase was used since it is a reliable source for miRNA alignment between conserved species (Li et al., 2010). Sequence data were hence aligned to the Danio rerio danrer6 genome reference allowing for two base mismatches in the identification of known miRNAs. "
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