Characterization of the Promoters of MicroRNA Genes: A Genome-Scale Analysis on Three Model Species∗

MicroRNAs are short, noncoding RNAs and play important roles in post-transcriptional gene regulation. Al-though many functions of microRNAs in plants and animals have been revealed in recent years, the transcriptional mechanism of microRNA genes is not well understood. To elucidate the transcriptional regulation of microRNA genes, we study and characterize, in a genome scale, the promoters of intergenic microRNA genes in Caenorhab-ditis elegans, Homo sapiens and Arabidopsis thaliana. Specifically, we show that the known microRNA genes in these species have the same type of promoters as the class-II genes. To further characterize the promoters of miRNA genes, we develop a promoter prediction approach, Query-Ranked Frequent Rule (QRFR), which is spe-cific for miRNA genes. With this new approach, we identify putative core promoters of most known microRNA genes. Moreover, we discover some characteristic sequence motifs in the putative core promoters, several of which match or resemble the known cis-acting motifs for transcription initiation.