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

Jonas Defoort (UGent) , Yves Van de Peer (UGent) and Vanessa Vermeirssen (UGent)
(2018) NUCLEIC ACIDS RESEARCH. 46(13). p.6480-6503
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Abstract
Gene 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 Ara-bidopsis 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. Similar modules 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.
Keywords
PROTEIN-PROTEIN INTERACTION, CHROMATIN-REMODELING COMPLEXES, TRANSCRIPTION FACTOR NETWORK, GENOME-WIDE IDENTIFICATION, DNA, INTERACTION NETWORK, C. ELEGANS, CAENORHABDITIS-ELEGANS, ARABIDOPSIS-THALIANA, BIOLOGICAL NETWORKS, GLUCOSINOLATE BIOSYNTHESIS

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Chicago
Defoort, Jonas, Yves Van de Peer, and Vanessa Vermeirssen. 2018. “Function, Dynamics and Evolution of Network Motif Modules in Integrated Gene Regulatory Networks of Worm and Plant.” Nucleic Acids Research 46 (13): 6480–6503.
APA
Defoort, 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, 46(13), 6480–6503.
Vancouver
1.
Defoort J, Van de Peer Y, Vermeirssen V. Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant. NUCLEIC ACIDS RESEARCH. 2018;46(13):6480–503.
MLA
Defoort, Jonas, Yves Van de Peer, and Vanessa Vermeirssen. “Function, Dynamics and Evolution of Network Motif Modules in Integrated Gene Regulatory Networks of Worm and Plant.” NUCLEIC ACIDS RESEARCH 46.13 (2018): 6480–6503. Print.
@article{8575754,
  abstract     = {Gene 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 Ara-bidopsis 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. Similar modules 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.},
  author       = {Defoort, Jonas and Van de Peer, Yves and Vermeirssen, Vanessa},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  keywords     = {PROTEIN-PROTEIN INTERACTION,CHROMATIN-REMODELING COMPLEXES,TRANSCRIPTION FACTOR NETWORK,GENOME-WIDE IDENTIFICATION,DNA,INTERACTION NETWORK,C. ELEGANS,CAENORHABDITIS-ELEGANS,ARABIDOPSIS-THALIANA,BIOLOGICAL NETWORKS,GLUCOSINOLATE BIOSYNTHESIS},
  language     = {eng},
  number       = {13},
  pages        = {6480--6503},
  title        = {Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant},
  url          = {http://dx.doi.org/10.1093/nar/gky468},
  volume       = {46},
  year         = {2018},
}

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