title: Construction of microRNA- and microRNA*-mediated regulatory networks in plants.
abstract: The critical biological roles of microRNAs (miRNAs) have been well recognized. However, knowledge on the regulatory activities of miRNA*s is limited. Although several studies pointed to the capacity of this small RNA species to repress target genes in animals, few related analyses were performed in plants. Here, we set out to uncover the repressive effects of miRNA*s on their targets in both Arabidopsis and rice. Systemic identification of miRNA*s was performed through secondary structure-based predictions and expression level-based verification. The targets of the miRNA*s were predicted and further filtered based on degradome sequencing data, resulting in comprehensive miRNA*--target lists with high reliability. Besides, comprehensive miRNA--target lists were also obtained. The phenomenon that one transcript was targeted by two or more miRNA(*)s was observed, which was defined as co-regulation. Finally, comprehensive miRNA- and miRNA*-mediated regulatory networks were constructed. Further investigation of some specific subnetworks implied the utility of these networks for biologists. This study could broaden the current understanding of miRNA gene-mediated regulation in plants.
authors.affiliation: Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China.
authors.forename: Yijun
authors.initials: Y
authors.lastname: Meng
authors.forename: Chaogang
authors.initials: C
authors.lastname: Shao
authors.forename: Lingfeng
authors.initials: L
authors.lastname: Gou
authors.forename: Yongfeng
authors.initials: Y
authors.lastname: Jin
authors.forename: Ming
authors.initials: M
authors.lastname: Chen
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D018506:Gene Expression Regulation, Plant; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012275:Oryza / Q000235:genetics*; D010944:Plants / Q000235:genetics
chemical_list: D035683:MicroRNAs; C559759:Mirn156 microRNA, Arabidopsis