title: A unified design space of synthetic stripe-forming networks.
abstract: Synthetic biology is a promising tool to study the function and properties of gene regulatory networks. Gene circuits with predefined behaviours have been successfully built and modelled, but largely on a case-by-case basis. Here we go beyond individual networks and explore both computationally and synthetically the design space of possible dynamical mechanisms for 3-node stripe-forming networks. First, we computationally test every possible 3-node network for stripe formation in a morphogen gradient. We discover four different dynamical mechanisms to form a stripe and identify the minimal network of each group. Next, with the help of newly established engineering criteria we build these four networks synthetically and show that they indeed operate with four fundamentally distinct mechanisms. Finally, this close match between theory and experiment allows us to infer and subsequently build a 2-node network that represents the archetype of the explored design space.
authors.affiliation: 1] EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Yolanda
authors.initials: Y
authors.lastname: Schaerli
authors.affiliation: 1] EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Andreea
authors.initials: A
authors.lastname: Munteanu
authors.affiliation: 1] EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Magüi
authors.initials: M
authors.lastname: Gili
authors.affiliation: 1] EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: James
authors.initials: J
authors.lastname: Cotterell
authors.affiliation: 1] EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona, Spain [3] Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
authors.forename: James
authors.initials: J
authors.lastname: Sharpe
authors.affiliation: 1] EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona, Spain [3] Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
authors.forename: Mark
authors.initials: M
authors.lastname: Isalan
mesh_terms: D001483:Base Sequence; D003001:Cloning, Molecular; D004926:Escherichia coli; D005453:Fluorescence; D053263:Gene Regulatory Networks / Q000235:genetics*; D005818:Genetic Engineering / Q000379:methods*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010957:Plasmids / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D058615:Synthetic Biology / Q000379:methods*