MicroRNA Locus Expression Analysis with Phylogenetic Relationship Based on MicroRNA Control from High Throughput Sequencing Data

High throughput sequencing technology is widely applied to discover and profile microRNAs (miRNAs) to gain insights into the biogenesis and function of miRNAs. In the study, we developed an approach for comparing relative expression levels of different miRNAs based on suitable endogenous miRNA control and their locus in the genome, miRNA group (such as miRNA cluster and miRNA family), and phylogenetic relationship between corresponding precursor sequences. According to the approach, we analyzed miR-17-92 cluster and miR-17 family in mouse NIH3T3 cells from high throughput sequencing data using SOLIDTM system. Expression analysis of miR-17-92 cluster and miR-17 (mir-17) family showed evident diversity although some miRNAs were transcribed as a single polycistronic transcript. Combining locus on chromosome and phylogenetic relationship between precursors, different expression levels of these miRNAs might imply complex regulatory networks with gene locus and provide evolutionary and functional implication in miRNA biogenesis, especially for comparing miRNA expression profiles under varying conditions or between mutants and wild type. Our studies show that expression comparison of miRNAs correlated with locus, miRNA group, and phylogenetic relationship, can reveal important insights into the biogenesis, evolution, and function of miRNAs.