Characterization of microRNA expression profiles in normal human tissues

BackgroundMeasuring the quantity of miRNAs in tissues of different physiological and pathological conditions is an important first step to investigate the functions of miRNAs. Matched samples from normal state can provide essential baseline references to analyze the variation of miRNA abundance.ResultsWe provided expression data of 345 miRNAs in 40 normal human tissues, which identified universally expressed miRNAs, and several groups of miRNAs expressed exclusively or preferentially in certain tissue types. Many miRNAs with co-regulated expression patterns are located within the same genomic clusters, and candidate transcriptional factors that control the pattern of their expression may be identified by a comparative genomic strategy. Hierarchical clustering of normal tissues by their miRNA expression profiles basically followed the structure, anatomical locations, and physiological functions of the organs, suggesting that functions of a miRNA could be appreciated by linking to the biologies of the tissues in which it is uniquely expressed. Many predicted target genes of miRNAs that had specific reduced expression in brain and peripheral blood mononuclear cells are required for embryonic development of the nervous and hematopoietic systems based on database search.ConclusionWe presented a global view of tissue distribution of miRNAs in relation to their chromosomal locations and genomic structures. We also described evidence from the cis-regulatory elements and the predicted target genes of miRNAs to support their tissue-specific functional roles to regulate the physiologies of the normal tissues in which they are expressed.

Protocol publication

[…] Genomic sequence of miRNA cluster and the predicted transcription factor binding sites were extracted from the "Cis-element clusters within BlastZ Aligments" option at the GenomeTraFac []. Tissue distribution of selected genes was derived from the GNF database [], in which the expression data from the same tissue types examined in our study were extracted for analyses. Target genes of miRNAs were predicted using the miRanda open-source software [] associated with the miRBase [] with a cutoff p value less than 0.05. The IGTC database [] was used to search the phenotype of mice carrying loss-of-function mutations. […]