title: Characterization and identification of microRNA core promoters in four model species.
abstract: MicroRNAs are short, noncoding RNAs that play important roles in post-transcriptional gene regulation. Although 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 Caenorhabditis elegans, Homo sapiens, Arabidopsis thaliana, and Oryza sativa. We show that most known microRNA genes in these four species have the same type of promoters as protein-coding genes have. To further characterize the promoters of microRNA genes, we developed a novel promoter prediction method, called common query voting (CoVote), which is more effective than available promoter prediction methods. Using this new method, we identify putative core promoters of most known microRNA genes in the four model species. Moreover, we characterize the promoters of microRNA genes in these four species. We discover many significant, characteristic sequence motifs in these core promoters, several of which match or resemble the known cis-acting elements for transcription initiation. Among these motifs, some are conserved across different species while some are specific to microRNA genes of individual species.
authors.affiliation: Department of Computer Science and Engineering, Washington University in Saint Louis, Saint Louis, Missouri, United States of America.
authors.forename: Xuefeng
authors.initials: X
authors.lastname: Zhou
authors.forename: Jianhua
authors.initials: J
authors.lastname: Ruan
authors.forename: Guandong
authors.initials: G
authors.lastname: Wang
authors.forename: Weixiong
authors.initials: W
authors.lastname: Zhang
mesh_terms: D000818:Animals; D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics*; D017124:Conserved Sequence; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity
chemical_list: D035683:MicroRNAs