Zhang Wei, Han Zhaoxue, Guo Qingli, Liu Yu, Zheng Yuxian, Wu Fangli, Jin Weibo
College of Life Sciences, Northwest A&F University, Yangling, China.
Institute of Bioengineering, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China.
PLoS One. 2014 Jun 3;9(6):e98958. doi: 10.1371/journal.pone.0098958. eCollection 2014.
Long non-coding RNAs (lncRNAs) represent a class of riboregulators that either directly act in long form or are processed to shorter miRNAs and siRNAs. Emerging evidence shows that lncRNAs participate in stress responsive regulation. In this study, to identify the putative maize lncRNAs responsive to drought stress, 8449 drought responsive transcripts were first uploaded to the Coding Potential Calculator website for classification as protein coding or non-coding RNAs, and 1724 RNAs were identified as potential non-coding RNAs. A Perl script was written to screen these 1724 ncRNAs and 664 transcripts were ultimately identified as drought-responsive lncRNAs. Of these 664 transcripts, 126 drought-responsive lncRNAs were highly similar to known maize lncRNAs; the remaining 538 transcripts were considered as novel lncRNAs. Among the 664 lncRNAs identified as drought responsive, 567 were upregulated and 97 were downregulated in drought-stressed leaves of maize. 8 lncRNAs were identified as miRNA precursor lncRNAs, 62 were classified as both shRNA and siRNA precursors, and 279 were classified as siRNA precursors. The remaining 315 lncRNAs were classified as other lncRNAs that are likely to function as longer molecules. Among these 315 lncRNAs, 10 are identified as antisense lncRNAs and 7 could pair with 17 CDS sequences with near-perfect matches. Finally, RT-qPCR results confirmed that all selected lncRNAs could respond to drought stress. These findings extend the current view on lncRNAs as ubiquitous regulators under stress conditions.
长链非编码RNA（lncRNAs）是一类核糖调节因子，它们要么以长链形式直接发挥作用，要么被加工成较短的微小RNA（miRNAs）和小干扰RNA（siRNAs）。新出现的证据表明，lncRNAs参与应激反应调节。在本研究中，为了鉴定假定的对干旱胁迫有反应的玉米lncRNAs，首先将8449个干旱响应转录本上传到编码潜能计算器网站，以分类为蛋白质编码或非编码RNA，其中1724个RNA被鉴定为潜在的非编码RNA。编写了一个Perl脚本对这1724个非编码RNA进行筛选，最终鉴定出664个转录本为干旱响应lncRNAs。在这664个转录本中，126个干旱响应lncRNAs与已知的玉米lncRNAs高度相似；其余538个转录本被视为新的lncRNAs。在鉴定为干旱响应的664个lncRNAs中，567个在干旱胁迫的玉米叶片中上调，97个下调。8个lncRNAs被鉴定为miRNA前体lncRNAs，62个被归类为短发夹RNA（shRNA）和siRNA前体，279个被归类为siRNA前体。其余315个lncRNAs被归类为其他可能作为较长分子发挥作用的lncRNAs。在这315个lncRNAs中，10个被鉴定为反义lncRNAs，7个可以与17个编码序列（CDS）序列近乎完美匹配。最后，逆转录定量聚合酶链反应（RT-qPCR）结果证实，所有选择的lncRNAs都能对干旱胁迫作出反应。这些发现扩展了目前关于lncRNAs在应激条件下作为普遍存在的调节因子的观点。
