Genomic identification of microRNA promoters and their cis-acting elements in Populus

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• 作者：Min Chen ; Ming Wei ; Zhanghui Dong ; Hai Bao ; Yanwei Wang
• 关键词：Populus ; miRNAs ; Promoter ; Cis ; acting elements
• 刊名：Genes & Genomics
• 出版年：2016
• 出版时间：April 2016
• 年：2016
• 卷：38
• 期：4
• 页码：377-387
• 全文大小：2,306 KB
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• 作者单位：Min Chen (1) (2) (3)
  Ming Wei (1) (2) (3)
  Zhanghui Dong (4)
  Hai Bao (1) (2) (3)
  Yanwei Wang (1) (2) (3)
  
  1. National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083, People’s Republic of China
  2. Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, 100083, People’s Republic of China
  3. College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, People’s Republic of China
  4. Shijiazhuang Scientific Institute of Agriculture, Shijiazhuang, 050041, People’s Republic of China
  
• 刊物主题：Microbial Genetics and Genomics; Plant Genetics & Genomics; Animal Genetics and Genomics; Human Genetics;
• 出版者：Springer Netherlands
• ISSN：2092-9293

文摘

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.