ArticleNature communications2023
Robustness and innovation in synthetic genotype networks.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Graph-based representations in modern protein science.The Biochemical journal · 2026Review
- Transcription Factor Promiscuity Drives Regulatory Rewiring and Evolvability in Gene Networks in Bacteria.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Design of CRISPRi-Based Synthetic Gene Circuits in Bacteria.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Tuning evolvability via plasmid copy number and regulatory architecture.Nature communications · 2025Article
- Intracellularly coupled oscillators for synthetic biology.Nature communications · 2025Review
- Hif-1 responsive IFFLs to explain specific transcriptional responses to cycling hypoxia in cancers.NPJ systems biology and applications · 2025Article
- A tool for modeling gene regulatory networks (GRN_modeler) and its applications to synthetic biology.Molecular systems biology · 2025Article
- Evolvability in vertebrate segmentation.Seminars in cell & developmental biology · 2025Review
- Emergent dynamics of cellular decision making in multi-node mutually repressive regulatory networks.Journal of the Royal Society, Interface · 2025Article
- Engineering intercellular communication using M13 phagemid and CRISPR-based gene regulation for multicellular computing in Escherichia coli.Nature communications · 2025Article
- A direct experimental test of Ohno's hypothesis.eLife · 2025Article
- Bioengineering hybrid artificial life.Frontiers in bioinformatics · 2025Review
- Morphogens in the evolution of size, shape and patterning.Development (Cambridge, England) · 2024Review
- Open-endedness in synthetic biology: A route to continual innovation for biological design.Science advances · 2024Review
- Synthetic Gene Circuits Combining CRISPR Interference and CRISPR Activation inACS synthetic biology · 2023Article
- Environment-dependent epistasis increases phenotypic diversity in gene regulatory networks.Science advances · 2023Article
- Mutation bias and the predictability of evolution.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2023Review
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genotype networks are sets of genotypes connected by small mutational changes that share the same phenotype. They facilitate evolutionary innovation by enabling the exploration of different neighborhoods in genotype space. Genotype networks, first suggested by theoretical models, have been empirically confirmed for proteins and RNAs. Comparative studies also support their existence for gene regulatory networks (GRNs), but direct experimental evidence is lacking. Here, we report the construction of three interconnected genotype networks of synthetic GRNs producing three distinct phenotypes in Escherichia coli. Our synthetic GRNs contain three nodes regulating each other by CRISPR interference and governing the expression of fluorescent reporters. The genotype networks, composed of over twenty different synthetic GRNs, provide robustness in face of mutations while enabling transitions to innovative phenotypes. Through realistic mathematical modeling, we quantify robustness and evolvability for the complete genotype-phenotype map and link these features mechanistically to GRN motifs. Our work thereby exemplifies how GRN evolution along genotype networks might be driving evolutionary innovation.
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Registered trials
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