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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 de...

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Autores principales: Banerjee, Ayushman Kumar, Mal, Chittabrata
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7672285/
https://www.ncbi.nlm.nih.gov/pubmed/33241156
http://dx.doi.org/10.1016/j.heliyon.2020.e05496
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author Banerjee, Ayushman Kumar
Mal, Chittabrata
author_facet Banerjee, Ayushman Kumar
Mal, Chittabrata
author_sort Banerjee, Ayushman Kumar
collection PubMed
description 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.
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spelling pubmed-76722852020-11-24 Underpinning miRNA-miRNA co-functional interaction patterns in the metabolism of Oryza sativa by genome-scale network analysis Banerjee, Ayushman Kumar Mal, Chittabrata Heliyon Research Article 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. Elsevier 2020-11-12 /pmc/articles/PMC7672285/ /pubmed/33241156 http://dx.doi.org/10.1016/j.heliyon.2020.e05496 Text en © 2020 The Authors http://creativecommons.org/licenses/by/4.0/ This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Research Article
Banerjee, Ayushman Kumar
Mal, Chittabrata
Underpinning miRNA-miRNA co-functional interaction patterns in the metabolism of Oryza sativa by genome-scale network analysis
title Underpinning miRNA-miRNA co-functional interaction patterns in the metabolism of Oryza sativa by genome-scale network analysis
title_full Underpinning miRNA-miRNA co-functional interaction patterns in the metabolism of Oryza sativa by genome-scale network analysis
title_fullStr Underpinning miRNA-miRNA co-functional interaction patterns in the metabolism of Oryza sativa by genome-scale network analysis
title_full_unstemmed Underpinning miRNA-miRNA co-functional interaction patterns in the metabolism of Oryza sativa by genome-scale network analysis
title_short Underpinning miRNA-miRNA co-functional interaction patterns in the metabolism of Oryza sativa by genome-scale network analysis
title_sort underpinning mirna-mirna co-functional interaction patterns in the metabolism of oryza sativa by genome-scale network analysis
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7672285/
https://www.ncbi.nlm.nih.gov/pubmed/33241156
http://dx.doi.org/10.1016/j.heliyon.2020.e05496
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