ArticleNucleic acids research2017
Integrative FourD omics approach profiles the target network of the carbon storage regulatory system.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Modeling binding of the conserved Csr/Rsm protein family across species of the γ-proteobacteria reveals niche-specific adaptation of the post-transcriptional regulon.bioRxiv : the preprint server for biology · 2026Article
- Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs.Nucleic acids research · 2025Article
- Integrated Transcriptomic and Proteomic Analyses Reveal CsrA-Mediated Regulation of Virulence and Metabolism inMicroorganisms · 2025Article
- Concentration-Dependent CsrA Regulation of theACS synthetic biology · 2025Article
- Article
- Thermodynamic modeling of RsmA - mRNA interactions capture novel direct binding across theFrontiers in molecular biosciences · 2025Article
- Rewiring native post-transcriptional global regulators to achieve designer, multi-layered genetic circuits.Nature communications · 2024Article
- Multitier regulation of theJournal of bacteriology · 2024Article
- The Post-Transcriptional Regulatory Protein CsrA Amplifies Its Targetome through Direct Interactions with Stress-Response Regulatory Hubs: The EvgA and AcnA Cases.Microorganisms · 2024Article
- CsrA Shows Selective Regulation of sRNA-mRNA Networks.bioRxiv : the preprint server for biology · 2023Article
- Identification and Regulatory Roles of a New Csr Small RNA from Arctic Pseudoalteromonas fuliginea BSW20308 in Temperature Responses.Microbiology spectrum · 2023Article
- CsrA selectively modulates sRNA-mRNA regulator outcomes.Frontiers in molecular biosciences · 2023Article
- Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria.Science (New York, N.Y.) · 2022Article
- Article
- RNP-Based Control Systems for Genetic Circuits in Synthetic Biology Beyond CRISPR.Methods in molecular biology (Clifton, N.J.) · 2022Review
- The International Society of RNA Nanotechnology and Nanomedicine (ISRNN): The Present and Future of the Burgeoning Field.ACS nano · 2021Article
- Genome-Wide Analysis of Targets for Post-Transcriptional Regulation by Rsm Proteins inFrontiers in molecular biosciences · 2021Article
- The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches.Frontiers in molecular biosciences · 2021Review
- Uncovering Transcriptional Regulators and Targets of sRNAs Using an Integrative Data-Mining Approach: H-NS-Regulated RseX as a Case Study.Frontiers in cellular and infection microbiology · 2021Article
- CsrA-Mediated Translational Activation ofmBio · 2020Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Multi-target regulators represent a largely untapped area for metabolic engineering and anti-bacterial development. These regulators are complex to characterize because they often act at multiple levels, affecting proteins, transcripts and metabolites. Therefore, single omics experiments cannot profile their underlying targets and mechanisms. In this work, we used an Integrative FourD omics approach (INFO) that consists of collecting and analyzing systems data throughout multiple time points, using multiple genetic backgrounds, and multiple omics approaches (transcriptomics, proteomics and high throughput sequencing crosslinking immunoprecipitation) to evaluate simultaneous changes in gene expression after imposing an environmental stress that accentuates the regulatory features of a network. Using this approach, we profiled the targets and potential regulatory mechanisms of a global regulatory system, the well-studied carbon storage regulatory (Csr) system of Escherichia coli, which is widespread among bacteria. Using 126 sets of proteomics and transcriptomics data, we identified 136 potential direct CsrA targets, including 50 novel ones, categorized their behaviors into distinct regulatory patterns, and performed in vivo fluorescence-based follow up experiments. The results of this work validate 17 novel mRNAs as authentic direct CsrA targets and demonstrate a generalizable strategy to integrate multiple lines of omics data to identify a core pool of regulator targets.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.