Identification of homologous microRNAs in 56 animal genomes

Abstract

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.

Identification and characterization of the microRNAs and their targets in Salmo salar

“…Majority (55%, i.e., 56 out of 102) of the miRNAs are 22 nt in length, followed by 21 nt (19.6%), 20 nt (11.8%), 23 nt (7.8%), 25 nt (3%), 24 nt (2%) and 19 nt (1%). The mature and pre-miRNA lengths are similar to previous reports in other animal and plant species (Barozai et al, 2008;Li et al, 2010). The 37 newly identified miRNA sequences in S. salar are perfectly (100%) matched, 38 have a difference of 1 to 2 and 27 have a difference of 3-4 nucleotides with the corresponding homologue miRNAs.…”

“…1. Similar findings were given by a number of researchers in plants and animals (Barozai et al, 2008;Li et al, 2010;Qiu et al, 2007;Zhang et al, 2007). Table 1 summarizes the novel identified S. salar miRNAs, reference miRNAs, the minimum free folding energies (mfe), pre-miRNA length, mature miRNAs, mature sequence arm, E-value, mature sequence length, source EST, Table 1 Characterization of the novel identified S. salar miRNAs.…”

Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics

“…Noncoding RNA genes are as widespread as they are diverse , are transcribed from both strands of the genome, and may well exceed protein-coding genes in terms of their number [Fejes-Toth et al, 2009;Washietl et al, 2005] Seila et al, 2008;Taft et al, 2009]. Thus, more than 700 microRNA genes have already been identified in the human genome with many more probably awaiting discovery (miRBase; http://www.mirbase.org/cgi-bin/mirna_summary.pl?org5hsa) [Li et al, 2010b]. In total, at least 1,500 nonprotein-coding RNA genes have already been annotated in the human genome reference sequence with up to 5,000 more predicted by homology-based methods [Griffiths-Jones, 2007] (see Ensembl, database version 56.37a).…”

Aberrant hypermethylation ofmiR-9genes in gastric cancer

“…miR-9 is a highly conserved miRNA found in insects and primates. 22 In humans, there are three independent miR-9 gene loci, miR-9-1, miR-9-2 and miR-9-3, which are located at chromosomes 1, 5 and 15, respectively. According to the miRBase definition, these three loci encode the same mature miR-9 sequences, while the hairpin precursors are varied.…”