Computational Analysis of Drought Stress-Associated miRNAs and miRNA Co-Regulation Network in Physcomitrella patens

• Published in: Genomics, proteomics & bioinformatics proteomics & bioinformatics, 2011-04, Vol.9 (1-2), p.37-44
• Main Authors: Wan, Ping, Wu, Jun, Zhou, Yuan, Xiao, Junshu, Feng, Jie, Zhao, Weizhong, Xiang, Shen, Jiang, Guanglong, Chen, Jake Y.
• Format: Article
• Language: English
• Subjects: Bioinformatics; co-regulation network; Computer applications; Computer programs; drought; Drought resistance; drought stress; drought tolerance; genes; Internet; microRNA; miRNA; Physcomitrella patens; prediction; proteomics; 合作; 小分子RNA; 小立碗藓; 干旱胁迫; 生物学性状; 计算; 调控网络
• ISSN: 1672-0229; 2210-3244
• DOI: 10.1016/S1672-0229(11)60006-5

miRNAs are non-coding small RNAs that involve diverse biological processes. Until now, little is known about their roles in plant drought resistance. Physcomitrella patens is highly tolerant to drought; however, it is not clear about the basic biology of the traits that contribute P. patens this important character. In this work, we discovered 16 drought stress-associated miRNA (DsAmR) families in P. patens through computational analysis. Due to the possible discrepancy of expression periods and tissue distributions between potential DsAmRs and their targeting genes, and the existence of false positive results in computational identification, the prediction results should be examined with further experimental validation. We also constructed an miRNA co-regulation network, and identified two network hubs, miR902a-5p and miR414, which may play important roles in regulating drought-resistance traits. We distributed our results through an online database named ppt-miRBase, which can be accessed at http://bioinfor.cnu.edu.cn/ppt_miRBase/index.php. Our methods in finding DsAmR and miRNA co-regulation network showed a new direction for identifying miRNA functions.