TY - JOUR T1 - Characterization and Identification of MicroRNA Core Promoters in Four Model Species A1 - Zhou, Xuefeng A1 - Ruan, Jianhua A1 - Wang, Guandong A1 - Zhang, Weixiong Y1 - 2007/03/09 N2 - Author SummaryMicroRNAs are a class of short RNA sequences that have many regulatory functions in complex organisms such as plants and animals. However, our knowledge of the transcriptional mechanisms of microRNA genes is limited. Here, we analyze the upstream sequences of known microRNA genes in four model species, i.e., C. elegans, H. sapiens, A. thaliana, and O. sativa, and compare them with the promoter sequences of protein-coding genes and other classes of RNA genes. This analysis provides genome-wide evidence that microRNA genes have the same type of promoter sequences as protein-coding genes, and therefore are likely transcribed by RNA polymerase II (pol II). Second, we present a novel computational method for promoter prediction, which is then applied to locate the core promoters of known microRNA genes in the four model species. Furthermore, we present an analysis of short DNA motifs that appear frequently in the predicted promoters of microRNA genes, and report several interesting motifs that may have some functional meanings. These results are important for understanding the initiation and regulation of microRNA gene transcription. JF - PLOS Computational Biology JA - PLOS Computational Biology VL - 3 IS - 3 UR - https://doi.org/10.1371/journal.pcbi.0030037 SP - e37 EP - PB - Public Library of Science M3 - doi:10.1371/journal.pcbi.0030037 ER -