title: In silico evolution of the Drosophila gap gene regulatory sequence under elevated mutational pressure.
abstract: Cis-regulatory sequences are often composed of many low-affinity transcription factor binding sites (TFBSs). Determining the evolutionary and functional importance of regulatory sequence composition is impeded without a detailed knowledge of the genotype-phenotype map.
  
  
  
  We simulate the evolution of regulatory sequences involved in Drosophila melanogaster embryo segmentation during early development. Natural selection evaluates gene expression dynamics produced by a computational model of the developmental network. We observe a dramatic decrease in the total number of transcription factor binding sites through the course of evolution. Despite a decrease in average sequence binding energies through time, the regulatory sequences tend towards organisations containing increased high affinity transcription factor binding sites. Additionally, the binding energies of separate sequence segments demonstrate ubiquitous mutual correlations through time. Fewer than 10% of initial TFBSs are maintained throughout the entire simulation, deemed 'core' sites. These sites have increased functional importance as assessed under wild-type conditions and their binding energy distributions are highly conserved. Furthermore, TFBSs within close proximity of core sites exhibit increased longevity, reflecting functional regulatory interactions with core sites.
  
  
  
  In response to elevated mutational pressure, evolution tends to sample regulatory sequence organisations with fewer, albeit on average, stronger functional transcription factor binding sites. These organisations are also shaped by the regulatory interactions among core binding sites with sites in their local vicinity.
authors.affiliation: Systems Biology and Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, St. Petersburg, 195251, Russia.
authors.forename: Aleksandra A
authors.initials: AA
authors.lastname: Chertkova
authors.affiliation: Molecular and Computational Biology, University of Southern California, Los Angeles, 90089, CA, USA.
authors.forename: Joshua S
authors.initials: JS
authors.lastname: Schiffman
authors.affiliation: Systems Biology and Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, St. Petersburg, 195251, Russia.|Molecular and Computational Biology, University of Southern California, Los Angeles, 90089, CA, USA.
authors.forename: Sergey V
authors.initials: SV
authors.lastname: Nuzhdin
authors.affiliation: Systems Biology and Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, St. Petersburg, 195251, Russia.
authors.forename: Konstantin N
authors.initials: KN
authors.lastname: Kozlov
authors.affiliation: Systems Biology and Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, St. Petersburg, 195251, Russia.
authors.forename: Maria G
authors.initials: MG
authors.lastname: Samsonova
authors.affiliation: Systems Biology and Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, St. Petersburg, 195251, Russia. gursky@math.ioffe.ru.|Theoretical Department, Ioffe Institute, Polytechnicheskaya, 26, St. Petersburg, 194021, Russia. gursky@math.ioffe.ru.
authors.forename: Vitaly V
authors.initials: VV
authors.lastname: Gursky
mesh_terms: D000818:Animals; D001665:Binding Sites; D003198:Computer Simulation; D029721:Drosophila Proteins / Q000235:genetics; D004331:Drosophila melanogaster / Q000196:embryology* / Q000235:genetics*; D019143:Evolution, Molecular; D009154:Mutation; D011485:Protein Binding; D012045:Regulatory Sequences, Nucleic Acid; D012641:Selection, Genetic; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D029721:Drosophila Proteins; D014157:Transcription Factors
keywords: Drosophila development; Evolution; Gap gene regulatory network; Regulatory sequence; Thermodynamic expression model