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Open Access Highly Accessed Research article

Target mimics: an embedded layer of microRNA-involved gene regulatory networks in plants

Yijun Meng1*, Chaogang Shao2, Huizhong Wang1 and Yongfeng Jin3*

Author affiliations

1 College of Life and Environmental Sciences, Hangzhou Normal University, Xuelin Street 16#, Xiasha, Hangzhou, 310036, P. R. China

2 College of Life Sciences, Huzhou Teachers College, Huzhou, 313000, P. R. China

3 Institute of Biochemistry, College of Life Sciences, Zhejiang University, Zijingang Campus, Yu Hang Tang Road 866#, Hangzhou, 310058, P. R. China

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Citation and License

BMC Genomics 2012, 13:197  doi:10.1186/1471-2164-13-197

Published: 21 May 2012

Abstract

Background

MicroRNAs (miRNAs) play an essential role in gene regulation in plants. At the same time, the expression of miRNA genes is also tightly controlled. Recently, a novel mechanism called “target mimicry” was discovered, providing another layer for modulating miRNA activities. However, except for the artificial target mimics manipulated for functional studies on certain miRNA genes, only one example, IPS1 (Induced by Phosphate Starvation 1)—miR399 was experimentally confirmed in planta. To date, few analyses for comprehensive identification of natural target mimics have been performed in plants. Thus, limited evidences are available to provide detailed information for interrogating the questionable issue whether target mimicry was widespread in planta, and implicated in certain biological processes.

Results

In this study, genome-wide computational prediction of endogenous miRNA mimics was performed in Arabidopsis and rice, and dozens of target mimics were identified. In contrast to a recent report, the densities of target mimic sites were found to be much higher within the untranslated regions (UTRs) when compared to those within the coding sequences (CDSs) in both plants. Some novel sequence characteristics were observed for the miRNAs that were potentially regulated by the target mimics. GO (Gene Ontology) term enrichment analysis revealed some functional insights into the predicted mimics. After degradome sequencing data-based identification of miRNA targets, the regulatory networks constituted by target mimics, miRNAs and their downstream targets were constructed, and some intriguing subnetworks were further exploited.

Conclusions

These results together suggest that target mimicry may be widely implicated in regulating miRNA activities in planta, and we hope this study could expand the current understanding of miRNA-involved regulatory networks.

Keywords:
Target mimic; Network; Subnetwork; MicroRNA; Degradome; Arabidopsis (Arabidopsis thaliana); Rice (Oryza sativa)