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. 2007 Mar 9;3(3):e37.
doi: 10.1371/journal.pcbi.0030037. Epub 2007 Jan 9.

Characterization and identification of microRNA core promoters in four model species

Xuefeng Zhou  1 , Jianhua Ruan, Guandong Wang, Weixiong Zhang
Affiliations

Characterization and identification of microRNA core promoters in four model species

Xuefeng Zhou et al. PLoS Comput Biol. .

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.

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Conflict of interest statement

Competing interests. The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. The Distribution of the Distances between Putative Promoters and MicroRNA Hairpins
The horizontal axis shows the positions of putative promoters with respect to the corresponding microRNA hairpins and the vertical axis shows the percentage of microRNA genes that have putative promoters at the specified positions.
Figure 2
Figure 2. Significant Conserved Motifs Discovered in the Putative Promoters of the Four Species
(A) The number of microRNA genes that contain the corresponding motifs in their upstream. (B) Expected frequencies of the corresponding motifs. (C) Z-scores obtained by Monte Carlo Simulations (see the section Motif Analysis).
Figure 3
Figure 3. The Distributions of CT Repeats
The first group to the left of the figure shows the distributions of CT repeats in the genomes of the four species studied, estimated by a Monte Carlo simulation. The subsequent groups show the distributions of CT repeats in the upstream of microRNA hairpins. The vertical axis is the percentage of microRNA genes and randomly sampled sequences that contain CT repeats (see text).
Figure 4
Figure 4. Significant Species-Specific Motifs Discovered in the Putative Promoters of MicroRNA Genes in Four Species.
(A–C) The same as in Figure 2.
See this image and copyright information in PMC

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