ArticleNature methods2021
Persistence and plasticity in bacterial gene regulation.
Article in Nature methods, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed, 63 citations in OpenAlex.
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- Transcription Factor Promiscuity Drives Regulatory Rewiring and Evolvability in Gene Networks in Bacteria.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- From binding to networks: methods for identifying transcription factor targets in plant systems.Frontiers in plant science · 2026Review
- The Algorithm for Reversible Jump Inference of Motifs.bioRxiv : the preprint server for biology · 2025Article
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- Unveiling a pervasive DNA adenine methylation regulatory network in the early-diverging fungus Rhizopus microsporus.Nature communications · 2025Article
- Predicting input signals of transcription factors in Escherichia coli.Molecular systems biology · 2025Article
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- How Klebsiella pneumoniae controls its virulence.PLoS pathogens · 2025Review
- Using DNA affinity purification sequencing (DAP-seq) to identifyMicrobiology resource announcements · 2025Article
- A binding agreement.Nature plants · 2025Article
- Recruitment, rewiring and deep conservation in flowering plant gene regulation.Nature plants · 2025Article
- Genome mining based on transcriptional regulatory networks uncovers a novel locus involved in desferrioxamine biosynthesis.PLoS biology · 2025Article
- Genome-resolved metatranscriptomics unveils distinct microbial functionalities across aggregate sizes in aerobic granular sludge.Environmental science and ecotechnology · 2025Article
- Symmetric adenine methylation is an essential DNA modification in the early-diverging fungus Rhizopus microsporus.Nature communications · 2025Article
- Genomic epidemiology and phylodynamics of Acinetobacter baumannii bloodstream isolates in China.Nature communications · 2025Article
- Transcriptional mechanism by which IS5 activates the fucAO operon in Escherichia coli.Nucleic acids research · 2025Article
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Authors and funding
11 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Organisms orchestrate cellular functions through transcription factor (TF) interactions with their target genes, although these regulatory relationships are largely unknown in most species. Here we report a high-throughput approach for characterizing TF-target gene interactions across species and its application to 354 TFs across 48 bacteria, generating 17,000 genome-wide binding maps. This dataset revealed themes of ancient conservation and rapid evolution of regulatory modules. We observed rewiring, where the TF sensing and regulatory role is maintained while the arrangement and identity of target genes diverges, in some cases encoding entirely new functions. We further integrated phenotypic information to define new functional regulatory modules and pathways. Finally, we identified 242 new TF DNA binding motifs, including a 70% increase of known Escherichia coli motifs and the first annotation in Pseudomonas simiae, revealing deep conservation in bacterial promoter architecture. Our method provides a versatile tool for functional characterization of genetic pathways in prokaryotes and eukaryotes.
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