Identification of cold-inducible microRNAs in plants by transcriptome analysis

Xuefeng Zhou, Guandong Wang, Keita Sutoh, Jian Kang Zhu, Weixiong Zhang

Research output: Contribution to journalArticlepeer-review

287 Scopus citations

Abstract

MicroRNAs are ~ 21-nt long, non-coding RNAs that play critical roles in post-transcriptional gene regulation. Even though a large number of miRNAs have been identified, annotating their functions remains a challenge. We develop a computational, transcriptome-based approach to annotating stress-inducible microRNAs in plants. With this approach, we find that nineteen microRNA genes of eleven microRNA families in Arabidopsis thaliana are up-regulated by cold stress. Our experiments validate that among the eleven microRNAs, eight are differentially induced and three are constantly expressed under low temperature. Our result expands the number of cold-inducible microRNAs from four to eight. A promoter analysis further reveals that the cold-responsive microRNA genes contain many known stress-related cis-regulatory elements in their promoters. Our analysis also indicates that many signaling pathways, such as auxin pathways, may be affected by cold-inducible microRNAs. Our approach can be applied to plant microRNAs responding to other abiotic and biotic stresses. The research demonstrates that machine learning methods, augmented by wet-lab analysis, hold a great promise for functional annotation of microRNAs.

Original languageEnglish
Pages (from-to)780-788
Number of pages9
JournalBiochimica et Biophysica Acta - Gene Regulatory Mechanisms
Volume1779
Issue number11
DOIs
StatePublished - Nov 2008

Keywords

  • MicroRNAs
  • Post-transcriptional regulation
  • Stress response
  • Transcriptome modeling
  • cis-elements

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