Objectives: MicroRNAs (miRNAs) are a class of short, noncoding RNA sequences. In genetics, they are single-stranded RNA molecules which play important roles in the regulation of target genes. Because the transcriptional mechanism of miRNAs is the first, important step of miRNAs biogenesis, we should get a better knowledge about it. We have limited understanding of the transcription of miRNAs so we want to analyze the upstream sequences of miRNA genes to identify putative transcription factor binding sites (TFBS). Methods: We chose four species, including human, chimp, mouse, and rat, to analyze their upstream sequences. Promoter prediction tool, Tmod (Toolbox of Motif Discovery) was employed to search for significant motifs in these sequences. After finding out several significant TFBS, we further identified which motifs are conserved across the four species. Finally, it is found that certain transcription factors (TFs) is responsible for the regulation of miRNA genes, and motifs information are further used for the evolutionary relationship study. Results & Conclusions: It is found that four TFs are conserved across the four species, and we also estimated the significance of their binding motifs in evolution through phylogenetic study.
