ArticleNucleic acids research2012
Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 112 papers.
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Who cites it
112 citing papers in PubMed, 183 citations in OpenAlex.
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- 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
- Nucleoid-associated protein HU constrains transcription elongation to influence cellular functions, virulence, and drug tolerance in Mycobacterium tuberculosis.Nucleic acids research · 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
- Decoding the role of DNA sequence on protein-DNA co-condensation.PLoS computational biology · 2025Article
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- Metagenomic approaches for studying ubiquitous yet diverse nucleoid associated proteins in microbial communities: challenges and advances.World journal of microbiology & biotechnology · 2025Review
- Identification of Hot and Cold Regions for Mutagenesis in the Escherichia coli tdk Gene: A Catalog of Mutational Sites.Environmental and molecular mutagenesis · 2025Article
- Complex interplay between gene deletions and the environment uncovers cellular roles for genes of unknown function inmSystems · 2025Article
- HU promotes higher order chromosome organization and influences DNA replication rates in Streptococcus pneumoniae.Nucleic acids research · 2025Article
- Identification, characterization and classification of prokaryotic nucleoid-associated proteins.Molecular microbiology · 2025Review
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- A novel mode of histone-like protein HupB regulatingCurrent research in microbial sciences · 2025Review
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- The role of two major nucleoid-associated proteins in Streptomyces, HupA and HupS, in stress survival and gene expression regulation.Microbial cell factories · 2024Article
- Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending.Nucleic acids research · 2024Article
52 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 5 institutions in 3 countries.
Funding
Abstract
IHF and HU are two heterodimeric nucleoid-associated proteins (NAP) that belong to the same protein family but interact differently with the DNA. IHF is a sequence-specific DNA-binding protein that bends the DNA by over 160°. HU is the most conserved NAP, which binds non-specifically to duplex DNA with a particular preference for targeting nicked and bent DNA. Despite their importance, the in vivo interactions of the two proteins to the DNA remain to be described at a high resolution and on a genome-wide scale. Further, the effects of these proteins on gene expression on a global scale remain contentious. Finally, the contrast between the functions of the homo- and heterodimeric forms of proteins deserves the attention of further study. Here we present a genome-scale study of HU- and IHF binding to the Escherichia coli K12 chromosome using ChIP-seq. We also perform microarray analysis of gene expression in single- and double-deletion mutants of each protein to identify their regulons. The sequence-specific binding profile of IHF encompasses ∼30% of all operons, though the expression of <10% of these is affected by its deletion suggesting combinatorial control or a molecular backup. The binding profile for HU is reflective of relatively non-specific binding to the chromosome, however, with a preference for A/T-rich DNA. The HU regulon comprises highly conserved genes including those that are essential and possibly supercoiling sensitive. Finally, by performing ChIP-seq experiments, where possible, of each subunit of IHF and HU in the absence of the other subunit, we define genome-wide maps of DNA binding of the proteins in their hetero- and homodimeric forms.
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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.