title: Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network.
abstract: Gene duplication results in two identical paralogs that diverge through mutation, leading to loss or gain of interactions with other biomolecules. Here, we comprehensively characterize such network rewiring for C. elegans transcription factors (TFs) within and across four newly delineated molecular networks. Remarkably, we find that even highly similar TFs often have different interaction degrees and partners. In addition, we find that most TF families have a member that is highly connected in multiple networks. Further, different TF families have opposing correlations between network connectivity and phylogenetic age, suggesting that they are subject to different evolutionary pressures. Finally, TFs that have similar partners in one network generally do not in another, indicating a lack of pressure to retain cross-network similarity. Our multiparameter analyses provide unique insights into the evolutionary dynamics that shaped TF networks.
authors.affiliation: University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors.forename: John S
authors.initials: JS
authors.lastname: Reece-Hoyes
authors.forename: Carles
authors.initials: C
authors.lastname: Pons
authors.forename: Alos
authors.initials: A
authors.lastname: Diallo
authors.forename: Akihiro
authors.initials: A
authors.lastname: Mori
authors.forename: Shaleen
authors.initials: S
authors.lastname: Shrestha
authors.forename: Sreenath
authors.initials: S
authors.lastname: Kadreppa
authors.forename: Justin
authors.initials: J
authors.lastname: Nelson
authors.forename: Stephanie
authors.initials: S
authors.lastname: Diprima
authors.forename: Amelie
authors.initials: A
authors.lastname: Dricot
authors.forename: Bryan R
authors.initials: BR
authors.lastname: Lajoie
authors.forename: Philippe Souza Moraes
authors.initials: PS
authors.lastname: Ribeiro
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Weirauch
authors.forename: David E
authors.initials: DE
authors.lastname: Hill
authors.forename: Timothy R
authors.initials: TR
authors.lastname: Hughes
authors.forename: Chad L
authors.initials: CL
authors.lastname: Myers
authors.forename: Albertha J M
authors.initials: AJ
authors.lastname: Walhout
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics*; D029742:Caenorhabditis elegans Proteins / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D019143:Evolution, Molecular; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D014157:Transcription Factors / Q000378:metabolism / Q000502:physiology*
chemical_list: D029742:Caenorhabditis elegans Proteins; D014157:Transcription Factors