Abstract
A great number of microRNAs (miRNAs) have been identified in responding and acting in gene regulatory networks associated with plant tolerance to abiotic stress conditions, such as drought, salinity, and high temperature. The topological exploration of target genes regulated by abiotic-stress-responsible miRNAs (ASRmiRs) in a network facilitates to discover the molecular basis of plant abiotic stress response. This study was based on the staple food rice (Oryza sativa) in which ASRmiRs were manually curated. After having compared the topological properties of target genes (stress-miR-targets) with those (non-stress-miR-targets) not regulated by ASRmiRs in a rice interactome network, we found that stress-miR-targets exhibited distinguishable topological properties. The interaction probability analysis and k-core decomposition showed that stress-miR-targets preferentially interacted with non-stress-miR-targets and located at the peripheral positions in the network. Our results indicated an obvious topological distinction between the two types of genes, reflecting the specific mechanisms of action of stress-miR-targets in rice abiotic stress response. Also, the results may provide valuable clues to elucidate molecular mechanisms of crop response to abiotic stress.
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Acknowledgments
The research was supported by the National Natural Science Foundation of China (grant no. 31301248) and the Science Research Foundation of Anhui Provincial Colleges (grant no. KJ2013Z075).
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Linzhong Zhang and Hongdong Xuan contributed equally to this work.
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Zhang, L., Xuan, H., Zuo, Y. et al. Topological characteristics of target genes regulated by abiotic-stress-responsible miRNAs in a rice interactome network. Funct Integr Genomics 16, 243–251 (2016). https://doi.org/10.1007/s10142-016-0481-4
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DOI: https://doi.org/10.1007/s10142-016-0481-4