Identification of maize long non-coding RNAs responsive to drought stress

PLoS One. 2014 Jun 3;9(6):e98958. doi: 10.1371/journal.pone.0098958. eCollection 2014.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Computational Biology
  • Databases, Genetic
  • Down-Regulation
  • Droughts
  • MicroRNAs / analysis
  • Plant Leaves / genetics
  • Plant Leaves / metabolism
  • Plant Roots / genetics
  • Plant Roots / metabolism
  • RNA, Long Noncoding / metabolism*
  • RNA, Small Interfering / chemistry
  • RNA, Small Interfering / metabolism
  • Real-Time Polymerase Chain Reaction
  • Up-Regulation
  • Zea mays / genetics*
  • Zea mays / growth & development
  • Zea mays / metabolism

Substances

  • MicroRNAs
  • RNA, Long Noncoding
  • RNA, Small Interfering

Grant support

This work was supported by the Natural Science Foundation of China (grant No. 31000913, 31372075 and 31201268), and the website is http://isisn.nsfc.gov.cn/egrantweb/. This work was also supported by the Fundamental Research Funds for the Central Universities (grant No. QN2011095), the website is http://www.dost.moe.edu.cn/dostmoe/. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.