A unified design space of synthetic stripe-forming networks
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Published version
Author(s)
Type
Journal Article
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.
Date Issued
2014-09-23
Date Acceptance
2014-08-02
Citation
Nature Communications, 2014, 5, pp.1-10
ISSN
2041-1723
Publisher
Nature Publishing Group
Start Page
1
End Page
10
Journal / Book Title
Nature Communications
Volume
5
Copyright Statement
© 2014 The Authors. This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license
holder to reproduce the material. To view a copy of this license, visit http://
creativecommons.org/licenses/by-nc-sa/4.0/
holder to reproduce the material. To view a copy of this license, visit http://
creativecommons.org/licenses/by-nc-sa/4.0/
Identifier
https://www.nature.com/articles/ncomms5905
Subjects
Science & Technology
Multidisciplinary Sciences
Science & Technology - Other Topics
ESCHERICHIA-COLI
GENE-EXPRESSION
CIRCUITS
PRINCIPLES
TRANSCRIPTION
COMPUTATION
PROTEIN
GATES
Base Sequence
Cloning, Molecular
Escherichia coli
Fluorescence
Gene Regulatory Networks
Genetic Engineering
Models, Genetic
Molecular Sequence Data
Plasmids
Reverse Transcriptase Polymerase Chain Reaction
Sequence Analysis, DNA
Synthetic Biology
Escherichia coli
Cloning, Molecular
Genetic Engineering
Reverse Transcriptase Polymerase Chain Reaction
Sequence Analysis, DNA
Base Sequence
Plasmids
Fluorescence
Models, Genetic
Molecular Sequence Data
Gene Regulatory Networks
Synthetic Biology
Article Number
4905
Date Publish Online
2014-09-23