ArticleGenome research2004
Stress-induced DNA duplex destabilization (SIDD) in the E. coli genome: SIDD sites are closely associated with promoters.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- TORCphysics: a physical model of DNA-topology-controlled gene expression.Nucleic acids research · 2026Article
- DNA superhelicity.Nucleic acids research · 2024Article
- Conserved microRNAs and Flipons Shape Gene Expression during Development by Altering Promoter Conformations.International journal of molecular sciences · 2023Article
- DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling.Frontiers in microbiology · 2023Review
- Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA.Nucleic acids research · 2020Article
- Article
- Intensive targeting of regulatory competence genes by transposable elements in streptococci.Molecular genetics and genomics : MGG · 2019Article
- Human MettL3-MettL14 complex is a sequence-specific DNA adenine methyltransferase active on single-strand and unpaired DNA in vitro.Cell discovery · 2019Article
- Environment-directed activation of the Escherichia coliflhDC operon by transposons.Microbiology (Reading, England) · 2017Article
- Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome.Cell systems · 2017Article
- Hopping into a hot seat: Role of DNA structural features on IS5-mediated gene activation and inactivation under stress.PloS one · 2017Article
- Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation.Nucleic acids research · 2016Article
- Distinguishing between productive and abortive promoters using a random forest classifier in Mycoplasma pneumoniae.Nucleic acids research · 2015Article
- Characterization of chromosomal translocation breakpoint sequences in solid tumours: "an in silico analysis".The open medical informatics journal · 2015Article
- Potential non-B DNA regions in the human genome are associated with higher rates of nucleotide mutation and expression variation.Nucleic acids research · 2014Article
- Torsion-mediated interaction between adjacent genes.PLoS computational biology · 2014Article
- The genome-wide distribution of non-B DNA motifs is shaped by operon structure and suggests the transcriptional importance of non-B DNA structures in Escherichia coli.Nucleic acids research · 2013Article
- Transmission of an oxygen availability signal at the Salmonella enterica serovar Typhimurium fis promoter.PloS one · 2013Article
- A fundamental regulatory mechanism operating through OmpR and DNA topology controls expression of Salmonella pathogenicity islands SPI-1 and SPI-2.PLoS genetics · 2012Article
- Theoretical analysis of competing conformational transitions in superhelical DNA.PLoS computational biology · 2012Article
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3 authors.
Funding
Abstract
We present the first analysis of stress-induced DNA duplex destabilization (SIDD) in a complete chromosome, the Escherichia coli K12 genome. We used a newly developed method to calculate the locations and extents of stress-induced destabilization to single-base resolution at superhelix density sigma = -0.06. We find that SIDD sites in this genome show a statistically highly significant tendency to avoid coding regions. And among intergenic regions, those that either contain documented promoters or occur between divergently transcribing coding regions, and hence may be inferred to contain promoters, are associated with strong SIDD sites in a statistically highly significant manner. Intergenic regions located between convergently transcribing genes, which are inferred not to contain promoters, are not significantly enriched for destabilized sites. Statistical analysis shows that a strongly destabilized intergenic region has an 80% chance of containing a promoter, whereas an intergenic region that does not contain a strong SIDD site has only a 24% chance. We describe how these observations may illuminate specific mechanisms of regulation, and assist in the computational identification of promoter locations in prokaryotes.
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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.