microRNA (miRNA) are a class of small endogenous non-coding RNA that are mainly negative transcriptional and post-transcriptional regulators in both plants and animals. Recent studies have shown that miRNA are involved in different types of cancer and other diseases such as autism and Alzheimer’s that are yet to be fully understood.
Functional ~22nt mature miRNAs are excised from longer hairpin-like sequences that are known as miRNA genes (see the illustrations below).
The central repository for miRNA research, miRBase (release 19, dated
August 2012), contains 21,264 validated miRNA genes expressing 25,141 mature miRNA in 193 species.
About 73% (15,554) of the miRNA genes at miRBase have been assigned into 1,543 miRNA families based on their
sequence and structural properties.
miRNAVISA is a web-based tool that allows customized interrogation and comparisons of miRNA families for hypotheses generation, and comparison of the per-species chromosomal distribution of miRNA genes in different families.
Technological improvements have resulted in increased discovery of new microRNAs (miRNAs) and refinement and enrichment of existing miRNA families. Elucidating function of miRNAs and their influence on biochemical pathways and diseases is, however, challenging. miRNA families are important because they suggest a common sequence or structure configuration in sets of genes that hint to a shared function. However, exploratory tools to enhance investigation of the functions of family-specific miRNA genes are lacking.
We have developed, miRNAVISA, a user-friendly tool that allows customized interrogation and comparisons of miRNA families for hypotheses generation, inter-species comparisons, and intra-species comparison of the chromosomal distribution of miRNA genes in different families. The design and implementation of the miRNAVISA system is targeted for use by both the biological and computational scientists.
Biological investigations that are enabled by miRNAVISA may include, but are not limited to, the following.
Our study demonstrates the generation of hypotheses using miRNAVISA in seven species. Our results unveil a subclass of miRNA that may be regulated by genomic imprinting. Further, the results suggest that miRNA families may not only be species-specific, but can also be chromosome- and/or strand-specific.