Planta

, Volume 230, Issue 5, pp 883–898 | Cite as

Genome-wide survey of rice microRNAs and microRNA–target pairs in the root of a novel auxin-resistant mutant

  • Yijun Meng
  • Fangliang Huang
  • Qingyun Shi
  • Junjie Cao
  • Dijun Chen
  • Jinwei Zhang
  • Jun Ni
  • Ping Wu
  • Ming Chen
Original Article

Abstract

Auxin is one of the central hormones in plants, and auxin response factor (ARF) is a key regulator in the early auxin response. MicroRNAs (miRNAs) play an essential role in auxin signal transduction, but knowledge remains limited about the regulatory network between miRNAs and protein-coding genes (e.g. ARFs) involved in auxin signalling. In this study, we used a novel auxin-resistant rice mutant with plethoric root defects to investigate the miRNA expression patterns using microarray analysis. A number of miRNAs showed reduced auxin sensitivity in the mutant compared with the wild type, consistent with the auxin-resistant phenotype of the mutant. Four miRNAs with significantly altered expression patterns in the mutant were further confirmed by Northern blot, which supported our microarray data. Clustering analysis revealed some novel auxin-sensitive miRNAs in roots. Analysis of miRNA duplication and expression patterns suggested the evolutionary conservation between miRNAs and protein-coding genes. MiRNA promoter analysis suggested the possibility that most plant miRNAs might share the similar transcriptional mechanisms with other non-plant eukaryotic genes transcribed by RNA polymerase II. Auxin response elements were proved to be more frequently present in auxin-related miRNA promoters. Comparative analysis of miRNA and protein-coding gene expression datasets uncovered many reciprocally expressed miRNA–target pairs, which could provide some hints for miRNA downstream analysis. Based on these findings, we also proposed a feedback circuit between miRNA(s) and ARF(s). The results presented here could serve as the basis for further in-depth studies of plant miRNAs involved in auxin signalling.

Keywords

Auxin response element Auxin response factor Auxin signalling Microarray MicroRNA–target pairs Rice root 

Abbreviations

α-NAA

α-Naphthalene acetic acid

ARF

Auxin response factor

AuxRE

Auxin response element

EMS

Ethyl methanesulfonate

GO

Gene Ontology

IAA

3-Indole acetic acid

MiRNA

MicroRNA

MT

osaxr mutant

osaxr

Oryza sativa auxin resistant

TF

Transcription factor

TSS

Transcription start site

WT

Wild type

Supplementary material

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Supplementary material 1 (TXT 362 kb)
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Supplementary material 11 (DOC 67 kb)

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Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Yijun Meng
    • 1
  • Fangliang Huang
    • 1
  • Qingyun Shi
    • 2
  • Junjie Cao
    • 2
  • Dijun Chen
    • 1
    • 2
  • Jinwei Zhang
    • 1
  • Jun Ni
    • 1
  • Ping Wu
    • 1
  • Ming Chen
    • 1
    • 2
  1. 1.State Key Laboratory of Plant Physiology and Biochemistry, College of Life SciencesZhejiang UniversityHangzhouPeople’s Republic of China
  2. 2.Department of Bioinformatics, College of Life SciencesZhejiang UniversityHangzhouPeople’s Republic of China

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