Characterization and Identification of MicroRNA Core Promoters in Four Model Species

By Xuefeng Zhou, Jianhua Ruan, Guandong Wang, Weixiong Zhang. PLoS Comput. Biol., 2007

339 citations recorded by the source corpus.

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.

Subfields: Cancer Research, Plant Science

View Paper: https://www.semanticscholar.org/paper/58fe69e19a08edbb752d942fc869fb858f1535ec

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Citations in the corpus

A microRNA DNA methylation signature for human cancer metastasis (2008, methodology): “The CpG Island Searcher Program (36) was used to determine which miRNAs were embedded in a CpG island, because it has been predicted that 90% of the human miRNA promoters are located 1,000 bp upstream of the mature miRNA (37).”
MicroRNAs in development and disease. (2011, methodology): “For that purpose, computational tools were developed for prediction of miRNA core promoters (271, 715).”
Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells (2008, background): “Previous strategies to identify the 50 ends of primary miRNAs have been hampered because they relied on isolation of transient primary miRNA transcript, required knowledge of the specific cell type in which each given miRNA is transcribed, or focused only on potential start sites proximal to mature ”