title: Topological characteristics of target genes regulated by abiotic-stress-responsible miRNAs in a rice interactome network.
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.
authors.affiliation: School of Science, Anhui Agricultural University, Hefei, 230036, China.
authors.forename: Linzhong
authors.initials: L
authors.lastname: Zhang
authors.affiliation: College of Information and Computer Science, Anhui Agricultural University, Hefei, 230036, China.
authors.forename: Hongdong
authors.initials: H
authors.lastname: Xuan
authors.affiliation: College of Life Sciences, Inner Mongolia University, Hohhot, 010021, China.
authors.forename: Yongchun
authors.initials: Y
authors.lastname: Zuo
authors.affiliation: College of Information and Computer Science, Anhui Agricultural University, Hefei, 230036, China.
authors.forename: Gaojian
authors.initials: G
authors.lastname: Xu
authors.affiliation: School of Science, Anhui Agricultural University, Hefei, 230036, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Wang
authors.affiliation: School of Agronomy, Anhui Agricultural University, Hefei, 230036, China.
authors.forename: Youhong
authors.initials: Y
authors.lastname: Song
authors.affiliation: School of Science, Anhui Agricultural University, Hefei, 230036, China. zhangshihua@ahau.edu.cn.|State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China. zhangshihua@ahau.edu.cn.
authors.forename: Shihua
authors.initials: S
authors.lastname: Zhang
mesh_terms: D030541:Databases, Genetic; D055864:Droughts; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006358:Hot Temperature; D035683:MicroRNAs / Q000096:biosynthesis / Q000235:genetics*; D012275:Oryza / Q000235:genetics* / Q000254:growth & development; D018749:RNA, Plant / Q000235:genetics; D054712:Salinity; D013312:Stress, Physiological / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant
keywords: Abiotic stress; Rice; Target gene; Topological analysis; miRNA
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