Genome-wide survey of rice microRNAs and microRNA-target pairs in the root of a novel auxin-resistant mutant.
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.
Meng
Yijun
Y
State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, 310058 Hangzhou, People's Republic of China.
Huang
Fangliang
F
Shi
Qingyun
Q
Cao
Junjie
J
Chen
Dijun
D
Zhang
Jinwei
J
Ni
Jun
J
Wu
Ping
P
Chen
Ming
M
D001483:Base Sequence; D015152:Blotting, Northern; D016000:Cluster Analysis; D025461:Feedback, Physiological; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D018745:Genome, Plant / Q000235:genetics*; D007210:Indoleacetic Acids / Q000494:pharmacology*; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames / Q000235:genetics; D012275:Oryza / Q000187:drug effects* / Q000235:genetics*; D010641:Phenotype; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000187:drug effects / Q000235:genetics*; D012319:RNA Polymerase II / Q000378:metabolism; D015203:Reproducibility of Results; D020218:Response Elements / Q000235:genetics
D007210:Indoleacetic Acids; D035683:MicroRNAs; D010940:Plant Proteins; D012319:RNA Polymerase II