Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant

dc.contributor.authorDefoort, Jonas
dc.contributor.authorVan de Peer, Yves
dc.contributor.authorVermeirssen, Vanessa
dc.date.accessioned2019-03-13T14:26:09Z
dc.date.available2019-03-13T14:26:09Z
dc.date.issued2018-06-05
dc.description.abstractGene regulatory networks (GRNs) consist of different molecular interactions that closely work together to establish proper gene expression in time and space. Especially in higher eukaryotes, many questions remain on how these interactions collectively coordinate gene regulation. We study high quality GRNs consisting of undirected protein–protein, genetic and homologous interactions, and directed protein– DNA, regulatory and miRNA–mRNA interactions in the worm Caenorhabditis elegans and the plant Arabidopsis thaliana. Our data-integration framework integrates interactions in composite network motifs, clusters these in biologically relevant, higher-order topological network motif modules, overlays these with gene expression profiles and discovers novel connections between modules and regulators. Similarmodules exist in the integrated GRNs of worm and plant. We show how experimental or computational methodologies underlying a certain data type impact network topology. Through phylogenetic decomposition, we found that proteins of worm and plant tend to functionally interact with proteins of a similar age, while at the regulatory level TFs favor same age, but also older target genes. Despite some influence of the duplication mode difference, we also observe at the motif and module level for both species a preference for age homogeneity for undirected and age heterogeneity for directed interactions. This leads to a model where novel genes are added together to the GRNs in a specific biological functional context, regulated by one or more TFs that also target older genes in the GRNs. Overall, we detected topological, functional and evolutionary properties of GRNs that are potentially universal in all species.en_ZA
dc.description.departmentBiochemistryen_ZA
dc.description.departmentGeneticsen_ZA
dc.description.departmentMicrobiology and Plant Pathologyen_ZA
dc.description.librarianam2019en_ZA
dc.description.sponsorshipEuropean Union Seventh Framework Programme (FP7/2007-2013) under European Research Council Advanced Grant Agreement [322739-DOUBLE-UP]. Funding for open access charge: ERC Advanced Grant Agreement (322739-DOUBLE-UP).en_ZA
dc.description.urihttp://nar.oxfordjournals.orgen_ZA
dc.identifier.citationDefoort, J., Van de Peer, Y. & Vermeirssen, V. 2018, 'Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant', Nucleic Acids Research, vol. 46, no. 13, pp. 6480-6503.en_ZA
dc.identifier.issn0305-1048 (print)
dc.identifier.issn1362-4962 (online)
dc.identifier.other10.1093/nar/gky468
dc.identifier.urihttp://hdl.handle.net/2263/68649
dc.language.isoenen_ZA
dc.publisherOxford University Pressen_ZA
dc.rights© The Author(s) 2018. This is an Open Access article distributed under the terms of a Creative Commons Attribution - NonCommercial Works License (CC BY-NC 3.0).en_ZA
dc.subjectGene regulatory network (GRN)en_ZA
dc.subjectGlucosinolate biosynthesisen_ZA
dc.subjectBiological networksen_ZA
dc.subjectArabidopsis thalianaen_ZA
dc.subjectProtein-protein interactionsen_ZA
dc.subjectChromatin-remodeling complexesen_ZA
dc.subjectTranscription factor networken_ZA
dc.subjectGenome-wide identificationen_ZA
dc.subjectDNA interaction networken_ZA
dc.titleFunction, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and planten_ZA
dc.typeArticleen_ZA

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