miRviewer: a multispecies microRNA homologous viewer

Abstract

Background: MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression via binding to the 3' ends of mRNAs. MiRNAs have been associated with many cellular events ascertaining their central role in gene regulation. In order to better understand miRNAs of interest it is of utmost importance to learn about the genomic conservation of these genes.

Findings: The miRviewer web-server, presented here, encompasses all known miRNAs of currently fully annotated animal genomes in a visual 'birds-eye' view representation. miRviewer provides a graphical outlook of the current miRNA world together with sequence alignments and secondary structures of each miRNA. As a test case we experimentally examined the expression of several miRNAs in various animals.

Conclusions: miRviewer completes the homologous miRNA space with hundreds of unreported miRNAs and is available at: http://people.csail.mit.edu/akiezun/miRviewer.

Figure 1

A partial screenshot of miRviewer's main entry page. Species are indicated on the X-axis while miRNAs are on the Y-axis. Level of conservation is indicated in shades of green and numerical values are indicated on top. Current sorting is human centric and is ordered by most to least conserved miRNAs. A dot at the center of each box indicates the presence of the miRNA in miRbase [6]. Lack of such dot indicates the identification of the miRNA gene through miRNAminer [7].

Figure 2

A screenshot of miR-98a multiple alignment in different organisms. Though this magnification does not allow reading the exact sequences, it does allow viewing each row representing miR-98a from a different animal. Mature (blue), mutation (red) and all other sequences (gray) are indicated (also see text). On the right are links to miRbase, genomic locations on UCSC Genome Browser [9] and Ensembl [8]. Below the alignments, conservation of the pre-miRNA sequence is plotted.

Figure 3

A partial screenshot of known and novel miR-21 secondary structures. This view, presented alongside (to the right) of the sequence alignment (presented in Figure 2) allows viewing the predicted secondary structure (based on RNAfold, http://www.tbi.univie.ac.at/RNA) of a specific miRNA among the various organisms. The three letter abbreviations represent the animal and the negative numbers indicate the folding energy (delta G).

Figure 4

Confirmation of the expression of two novel miRNAs, miR-101 and miR-16, in monkey (marmoset), rabbit and dolphin. PCR was used to amplify expressed miRNAs based on presence in miRviewer. Amplified fragments were stained and separated in Agarose gel then excised and sequenced for confirmation (Additional file 1: Figure S1). These miRNAs were identified as part of a very large set of homologous miRNAs using the miRNAminer tool [7] all of which are presented in miRviewer.