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

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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.

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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

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Acknowledgments

This study is supported by 973 Program (2005CB120901), NSFC (30771326), 863 Program (2008AA10Z125), and Program for NCET.

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Authors and Affiliations

  1. State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, 310058, Hangzhou, People’s Republic of China

    Yijun Meng, Fangliang Huang, Dijun Chen, Jinwei Zhang, Jun Ni, Ping Wu & Ming Chen

  2. Department of Bioinformatics, College of Life Sciences, Zhejiang University, 310058, Hangzhou, People’s Republic of China

    Qingyun Shi, Junjie Cao, Dijun Chen & Ming Chen

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  1. Yijun Meng
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  2. Fangliang Huang
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  3. Qingyun Shi
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  4. Junjie Cao
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  6. Jinwei Zhang
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  7. Jun Ni
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  8. Ping Wu
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  9. Ming Chen
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Correspondence to Ming Chen.

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Meng, Y., Huang, F., Shi, Q. et al. Genome-wide survey of rice microRNAs and microRNA–target pairs in the root of a novel auxin-resistant mutant. Planta 230, 883–898 (2009). https://doi.org/10.1007/s00425-009-0994-3

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  • DOI: https://doi.org/10.1007/s00425-009-0994-3

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