ArticleNucleic acids research2006
Involvement of DNA curvature in intergenic regions of prokaryotes.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 64 citations in OpenAlex.
- Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction.Briefings in bioinformatics · 2022Article
- Genomic and Phenotypic Biology of Novel Strains ofFrontiers in plant science · 2021Article
- Genome-Wide Analyses Revealed Remarkable Heterogeneity in Pathogenicity Determinants, Antimicrobial Compounds, and CRISPR-Cas Systems of Complex Phytopathogenic GenusPathogens (Basel, Switzerland) · 2019Article
- Genomic Signatures Among Acanthamoeba polyphaga Entoorganisms Unveil Evidence of Coevolution.Journal of molecular evolution · 2019Article
- Regulation of Expression and Evolution of Genes in Plastids of Rhodophytic Branch.Life (Basel, Switzerland) · 2016Article
- The structural code of cyanobacterial genomes.Nucleic acids research · 2014Article
- Assessing diversity of DNA structure-related sequence features in prokaryotic genomes.DNA research : an international journal for rapid publication of reports on genes and genomes · 2014Article
- Investigating the interplay between nucleoid-associated proteins, DNA curvature, and CRISPR elements using comparative genomics.PloS one · 2014Article
- Differences in DNA curvature-related sequence periodicity between prokaryotic chromosomes and phages, and relationship to chromosomal prophage content.BMC genomics · 2012Article
- PerPlot & PerScan: tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences.Microbial informatics and experimentation · 2011Article
- Genome-scale computational analysis of DNA curvature and repeats in Arabidopsis and rice uncovers plant-specific genomic properties.BMC genomics · 2011Article
- Promoter prediction in E. coli based on SIDD profiles and Artificial Neural Networks.BMC bioinformatics · 2010Article
- Comparative analysis of sequence periodicity among prokaryotic genomes points to differences in nucleoid structure and a relationship to gene expression.Journal of bacteriology · 2010Article
- Article
- Investigations of oligonucleotide usage variance within and between prokaryotes.PLoS computational biology · 2008Article
- A survey of genomic properties for the detection of regulatory polymorphisms.PLoS computational biology · 2007Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It is known that DNA curvature plays a certain role in gene regulation. The distribution of curved DNA in promoter regions is evolutionarily preserved, and it is mainly determined by temperature of habitat. However, very little is known on the distribution of DNA curvature in termination sites. Our main objective was to comprehensively analyze distribution of curved sequences upstream and downstream to the coding genes in prokaryotic genomes. We applied CURVATURE software to 170 complete prokaryotic genomes in a search for possible typical distribution of DNA curvature around starts and ends of genes. Performing cluster analyses and other statistical tests, we obtained novel results regarding various factors influencing curvature distribution in intergenic regions, such as growth temperature, A+T composition and genome size. We also analyzed intergenic regions between converging genes in 15 selected genomes. The results show that six genomes presented peaks of curvature excess larger than 3 SDs. Insufficient statistics did not allow us to draw further conclusion. Our hypothesis is that DNA curvature could affect transcription termination in many prokaryotes either directly, through contacts with RNA polymerase, or indirectly, via contacts with some regulatory proteins.
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