A unified design space of synthetic stripe-forming networks

Yolanda Schaerli, Andreea Munteanu, Magüi Gili, James Cotterell, James Sharpe () and Mark Isalan ()
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Yolanda Schaerli: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG)
Andreea Munteanu: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG)
Magüi Gili: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG)
James Cotterell: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG)
James Sharpe: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG)
Mark Isalan: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG)

Nature Communications, 2014, vol. 5, issue 1, 1-10

Abstract: 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: 2014
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DOI: 10.1038/ncomms5905

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