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KMID : 0381120160380040377
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Genes and Genomics
2016 Volume.38 No. 4 p.377 ~ p.387
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Genomic identification of microRNA promoters and their cis-acting elements in Populus
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Chen Min
Wei Ming
Dong Zhanghui
Bao Hai
Wang Yanwei
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Abstract
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MicroRNAs (miRNAs) are non-coding single-stranded RNAs of appropriately 21 nucleotides in length that negatively regulate post-transcriptional processes in plants and animals. In recent years, while an increasing number of miRNAs has been identified in various species, little is known regarding the specific transcriptional regulation of miRNAs in Populus. In this investigation, 368 miRNAs belonging to 37 miRNA families in Populus were analyzed to identify promoter regions and predict the distribution patterns of core promoter elements [TATA boxes and transcription start sites (TSSs)], as well as main cis-acting elements through a bioinformatics approach. A total of 368 precursor miRNA (pre-miRNA) gene loci belonging to 213 unique miRNAs were detected. We identified 229 promoters and further predicted 121 TSSs and TATA boxes for 139 pre-miRNAs. The conserved motifs, base composition and the average free energy profiles in the neighboring regions of TSSs were further analyzed. In addition, 101 types of cis-acting elements, such as anaerobic induction elements, abscisic acid-response elements, and MYB binding sites, were predicted in the predicted promoter regions of the pre-miRNAs. The data obtained in our investigation may aid in the analysis of specific upstream sequences of pre-miRNAs for differential expression and further our understanding of the molecular biology of miRNAs in Populus.
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KEYWORD
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Populus, miRNAs, Promoter, Cis-acting elements
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