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- Title
Characterization and Identification of MicroRNA Core Promoters in Four Model Species.
- Authors
Zhou, Xuefeng; Ruan, Jianhua; Wang, Guandong; Zhang, Weixiong
- 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.
- Subjects
NON-coding RNA; PROMOTERS (Genetics); GENETIC regulation; GENETIC transcription; CAENORHABDITIS elegans; HUMAN beings; ARABIDOPSIS thaliana; RICE
- Publication
PLoS Computational Biology, 2007, Vol 3, Issue 3, p0412
- ISSN
1553-734X
- Publication type
Article
- DOI
10.1371/journal.pcbi.0030037