ArticleNucleic acids research2009
Gains and unexpected lessons from genome-scale promoter mapping.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Posttranscriptional 3'-Terminal Modifications ofMicroorganisms · 2025Article
- The emergence and evolution of gene expression in genome regions replete with regulatory motifs.eLife · 2024Article
- Phylogeny and structural modeling of the transcription factor CsqR (YihW) from Escherichia coli.Scientific reports · 2024Article
- Sense and antisense RNA products of theFrontiers in molecular biosciences · 2023Article
- Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia.Scientific reports · 2022Article
- Divergently Transcribed ncRNAs inFrontiers in molecular biosciences · 2021Article
- Suppression ofFrontiers in molecular biosciences · 2021Article
- Excessive Promoters as Silencers of Genes Horizontally Acquired byFrontiers in molecular biosciences · 2020Article
- Spatial organization of RNA polymerase and its relationship with transcription inProceedings of the National Academy of Sciences of the United States of America · 2019Article
- Density of σ70 promoter-like sites in the intergenic regions dictates the redistribution of RNA polymerase during osmotic stress in Escherichia coli.Nucleic acids research · 2019Article
- The genes of the sulphoquinovose catabolism in Escherichia coli are also associated with a previously unknown pathway of lactose degradation.Scientific reports · 2018Article
- The nucleoid protein Dps binds genomic DNA of Escherichia coli in a non-random manner.PloS one · 2017Article
- Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC).BMC genomics · 2016Article
- Visualizing the activity of Escherichia coli divergent promoters and probing their dependence on superhelical density using dual-colour fluorescent reporter vector.Scientific reports · 2015Article
- Upstream binding of idling RNA polymerase modulates transcription initiation from a nearby promoter.The Journal of biological chemistry · 2015Article
- The whole set of constitutive promoters recognized by RNA polymerase RpoD holoenzyme of Escherichia coli.PloS one · 2014Article
- Promoters of Escherichia coli versus promoter islands: function and structure comparison.PloS one · 2013Article
- High-density transcriptional initiation signals underline genomic islands in bacteria.PloS one · 2012Article
- Redefining Escherichia coli σ(70) promoter elements: -15 motif as a complement of the -10 motif.Journal of bacteriology · 2011Article
- Identification of Rgg binding sites in the Streptococcus pyogenes chromosome.Journal of bacteriology · 2011Article
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5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Potential promoters in the genome of Escherichia coli were searched by pattern recognition software PlatProm and classified on the basis of positions relative to gene borders. Beside the expected promoters located in front of the coding sequences we found a considerable amount of intragenic promoter-like signals with a putative ability to drive either antisense or alternative transcription and revealed unusual genomic regions with extremely high density of predicted transcription start points (promoter 'islands'), some of which are located in coding sequences. PlatProm scores converted into probability of RNA polymerase binding demonstrated certain correlation with the enzyme retention registered by ChIP-on-chip technique; however, in 'dense' regions the value of correlation coefficient is lower than throughout the entire genome. Experimental verification confirmed the ability of RNA polymerase to interact and form multiple open complexes within promoter 'island' associated with appY, yet transcription efficiency was lower than might be expected. Analysis of expression data revealed the same tendency for other promoter 'islands', thus assuming functional relevance of non-productive RNA polymerase binding. Our data indicate that genomic DNA of E. coli is enriched by numerous unusual promoter-like sites with biological role yet to be understood.
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