Underpinning miRNA-miRNA co-functional interaction patterns in the metabolism of Oryza sativa by genome-scale network analysis

MicroRNA (miRNA) is a class of non-coding small RNAs, which post-transcriptionally regulate a large number of genes and are now known to be important regulators in a wide variety of biological processes including metabolism. Thus, for better understanding these complex biological networks, and to derive their significance and inter-dependency, a systems biology approach enables us to explore and draw vital insights into these molecular network architectures. In this study, we aimed to understand the significance of synergistic miRNA-miRNA interactions in rice by constructing and analysing metabolic networks. The construction of the network involves target gene prediction of experimentally verified miRNAs of rice and then appending associated metabolic pathways to the network. A genome-scale miRNA-miRNA co-functional network (MFSN) is constructed based on co-regulatory interactions among the miRNAs and common target genes by applying transformational procedures. The analysis of the extracted MFSN modules identifies co-regulated target genes that are associated with corresponding interconnected metabolic pathways such as VALDEG-PWY (L-valine degradation I pathway was found to be targeted by multiple miRNA families, such as osa-miR812, osa-miR818, osa-miR821, and osa-miR5799 families while another pathway that was found to be associated with multiple miRNA families was PWY-6952 (glycerophosphodiester degradation pathway), PWY-6952 was found to be targeted by osa-miR812, osa-miR11344 and osa-miR5801 families. Such extensive study will help in systematically elucidating the regulatory networks in metabolism of rice, which in turn can be utilised to devise strategies for crop improvement and novel cultivar development.