ArticleNucleic acids research2011
Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 181 papers.
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Who cites it
181 citing papers in PubMed, 315 citations in OpenAlex.
- Disentangling polymer confinement from specific-folding interactions reveals the drivers of Escherichia coli chromosome organization.Nucleic acids research · 2026Article
- ShapeME: A Tool and Web Front-end for De Novo Discovery of Structural Motifs Underpinning Protein-DNA Interactions.Journal of molecular biology · 2026Article
- Acquired mutations in transcriptional regulatorAntimicrobial agents and chemotherapy · 2026Article
- The adaptive landscapes of three globaleLife · 2026Article
- The Absence of E. coli Nucleoid-Associated Protein FIS at Low Temperature Leads to an Adaptation Response That Causes a Shift Towards Genome Compaction in Small Rods.Molecular microbiology · 2026Article
- A plasmid-encoded H-NS protein selectively binds its own plasmid.bioRxiv : the preprint server for biology · 2026Article
- Selective targeting of a histone-like silencer Sfx to the R6K conjugal transfer operon.Nucleic acids research · 2026Article
- Analysis of Mutagenesis in the Escherichia coli tdk Gene: The Nucleoid Protein HNS Is Required for a Dramatic Cisplatin-Induced Hotspot.Environmental and molecular mutagenesis · 2026Article
- Fis suppresses late-stage virulence gene expression in Yersinia pseudotuberculosis at environmental temperatures.PLoS pathogens · 2026Article
- Selective targeting of a histone-like silencer Sfx to the R6K conjugal transfer operon.bioRxiv : the preprint server for biology · 2026Article
- NapR, a novel nucleoid-associated protein, regulates antioxidant defense in mycobacteria.mSphere · 2025Article
- Structural Studies on the M. tuberculosis Nucleoid-associated-Protein, NapA, Indicates DNA Bridging Mechanism.Journal of molecular biology · 2025Article
- Metagenomic approaches for studying ubiquitous yet diverse nucleoid associated proteins in microbial communities: challenges and advances.World journal of microbiology & biotechnology · 2025Review
- Article
- Identification of Hot and Cold Regions for Mutagenesis in the Escherichia coli tdk Gene: A Catalog of Mutational Sites.Environmental and molecular mutagenesis · 2025Article
- Future Directions of the Prokaryotic Chromosome Field.Molecular microbiology · 2025Article
- ShapeME: A tool and web front-end for de novo discovery of structural motifs underpinning protein-DNA interactions.bioRxiv : the preprint server for biology · 2025Article
- ChIP-mini: a low-input ChIP-exo protocol for elucidating DNA-binding protein dynamics in intracellular pathogens.Nucleic acids research · 2025Article
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- Spatio-temporal organization of theEcoSal Plus · 2024Review
121 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors at 5 institutions in 4 countries.
Funding
Abstract
Nucleoid-associated proteins (NAPs) are global regulators of gene expression in Escherichia coli, which affect DNA conformation by bending, wrapping and bridging the DNA. Two of these--H-NS and Fis--bind to specific DNA sequences and structures. Because of their importance to global gene expression, the binding of these NAPs to the DNA was previously investigated on a genome-wide scale using ChIP-chip. However, variation in their binding profiles across the growth phase and the genome-scale nature of their impact on gene expression remain poorly understood. Here, we present a genome-scale investigation of H-NS and Fis binding to the E. coli chromosome using chromatin immunoprecipitation combined with high-throughput sequencing (ChIP-seq). By performing our experiments under multiple time-points during growth in rich media, we show that the binding regions of the two proteins are mutually exclusive under our experimental conditions. H-NS binds to significantly longer tracts of DNA than Fis, consistent with the linear spread of H-NS binding from high- to surrounding lower-affinity sites; the length of binding regions is associated with the degree of transcriptional repression imposed by H-NS. For Fis, a majority of binding events do not lead to differential expression of the proximal gene; however, it has a significant indirect effect on gene expression partly through its effects on the expression of other transcription factors. We propose that direct transcriptional regulation by Fis is associated with the interaction of tandem arrays of Fis molecules to the DNA and possible DNA bending, particularly at operon-upstream regions. Our study serves as a proof-of-principle for the use of ChIP-seq for global DNA-binding proteins in bacteria, which should become significantly more economical and feasible with the development of multiplexing techniques.
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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.