title: A functional selection model explains evolutionary robustness despite plasticity in regulatory networks.
abstract: Evolutionary rewiring of regulatory networks is an important source of diversity among species. Previous evidence suggested substantial divergence of regulatory networks across species. However, systematically assessing the extent of this plasticity and its functional implications has been challenging due to limited experimental data and the noisy nature of computational predictions. Here, we introduce a novel approach to study cis-regulatory evolution, and use it to trace the regulatory history of 88 DNA motifs of transcription factors across 23 Ascomycota fungi. While motifs are conserved, we find a pervasive gain and loss in the regulation of their target genes. Despite this turnover, the biological processes associated with a motif are generally conserved. We explain these trends using a model with a strong selection to conserve the overall function of a transcription factor, and a much weaker selection over the specific genes it targets. The model also accounts for the turnover of bound targets measured experimentally across species in yeasts and mammals. Thus, selective pressures on regulatory networks mostly tolerate local rewiring, and may allow for subtle fine-tuning of gene regulation during evolution.
authors.affiliation: School of Computer Science and Engineering, Hebrew University, Jerusalem, Israel.
authors.forename: Naomi
authors.initials: N
authors.lastname: Habib
authors.forename: Ilan
authors.initials: I
authors.lastname: Wapinski
authors.forename: Hanah
authors.initials: H
authors.lastname: Margalit
authors.forename: Aviv
authors.initials: A
authors.lastname: Regev
authors.forename: Nir
authors.initials: N
authors.lastname: Friedman
mesh_terms: D000818:Animals; D001203:Ascomycota / Q000235:genetics*; D001483:Base Sequence; D017124:Conserved Sequence; D004271:DNA, Fungal / Q000235:genetics; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000378:metabolism; D053263:Gene Regulatory Networks / Q000235:genetics*; D008322:Mammals / Q000235:genetics; D008957:Models, Genetic; D008969:Molecular Sequence Data; D059372:Nucleotide Motifs / Q000235:genetics; D010802:Phylogeny; D011485:Protein Binding; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D012641:Selection, Genetic; D013045:Species Specificity; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D004271:DNA, Fungal; D005656:Fungal Proteins; D014157:Transcription Factors