Abstract
MicroRNAs (miRNAs) are a class of small (∼22 nucleotides) non-coding RNAs that post-transcriptionally regulate gene expression by interacting with target mRNAs. A majority of miRNAs is located within intronic or exonic regions of protein-coding genes (host genes), and increasing evidence suggests a functional relationship between these miRNAs and their host genes. Here, we introduce miRIAD, a web-service to facilitate the analysis of genomic and structural features of intragenic miRNAs and their host genes for five species (human, rhesus monkey, mouse, chicken and opossum). miRIAD contains the genomic classification of all miRNAs (inter- and intragenic), as well as classification of all protein-coding genes into host or non-host genes (depending on whether they contain an intragenic miRNA or not). We collected and processed public data from several sources to provide a clear visualization of relevant knowledge related to intragenic miRNAs, such as host gene function, genomic context, names of and references to intragenic miRNAs, miRNA binding sites, clusters of intragenic miRNAs, miRNA and host gene expression across different tissues and expression correlation for intragenic miRNAs and their host genes. Protein–protein interaction data are also presented for functional network analysis of host genes. In summary, miRIAD was designed to help the research community to explore, in a user-friendly environment, intragenic miRNAs, their host genes and functional annotations with minimal effort, facilitating hypothesis generation and in-silico validations.Database URL: http://www.miriad-database.org
Highlights
Amongst regulatory mechanisms of gene expression in eukaryotes, microRNAs have established a central role in the past two decades [1]
Additional complex information is provided, such as the visualization of intragenic miRNAs within their host genes and positioning along the isoforms, expression correlation between intragenic miRNAs and their host genes, intragenic miRNAs binding to their own host genes and intragenic miRNAs binding to genes that are directly interacting with their host genes
The past miRBase release 11 (April 2008) had around 47% of intragenic miRNAs [3], and this proportion increased to 53% in the miRBase 19 (August 2012) and to 57% in the miRBase [20]. miRIAD was created to help dealing with the challenges of unraveling the functional relationships between miRNAs and their host genes
Summary
Amongst regulatory mechanisms of gene expression in eukaryotes, microRNAs (miRNAs) have established a central role in the past two decades [1]. These 22-nt short singlestranded RNA molecules guide the RNA-induced silencing complex to modulate the expression of target mRNAs [2]. A substantial number of these intragenic miRNAs are co-transcribed, and co-regulated with their host genes [4, 5, 7]. Recent evidence suggests a functional linkage between intragenic miRNAs and their hosts on multiple levels, including direct and indirect interaction [8,9,10]
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