ArticleNucleic acids research2005
A-tract clusters may facilitate DNA packaging in bacterial nucleoid.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Single-molecule dynamic structural biology with vertically arranged DNA on a fluorescence microscope.Nature methods · 2025Article
- Bacterial nucleoid is a riddle wrapped in a mystery inside an enigma.Journal of bacteriology · 2024Review
- DNA structural properties of DNA binding sites for 21 transcription factors in the mycobacterial genome.Frontiers in cellular and infection microbiology · 2023Article
- Manipulation of topoisomerase expression inhibits cell division but not growth and reveals a distinctive promoter structure in Synechocystis.Nucleic acids research · 2022Article
- Amyloid-like Hfq interaction with single-stranded DNA: involvement in recombination and replication inQRB discovery · 2022Article
- Dissection of Structural Reorganization of Wheat 5B Chromosome Associated With Interspecies Recombination Suppression.Frontiers in plant science · 2022Article
- Human Virus Genomes Are Enriched in Conserved Adenine/Thymine/Uracil Multiple Tracts That Pause Polymerase Progression.Frontiers in microbiology · 2022Article
- Selection for ancient periodic motifs that do not impart DNA bending.PLoS genetics · 2020Article
- Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes.Nucleic acids research · 2020Article
- Crystal structure of an Escherichia coli Hfq Core (residues 2-69)-DNA complex reveals multifunctional nucleic acid binding sites.Nucleic acids research · 2020Article
- Unsupervised statistical discovery of spaced motifs in prokaryotic genomes.BMC genomics · 2017Article
- Organization of DNA in a bacterial nucleoid.BMC microbiology · 2016Article
- Simulating the entropic collapse of coarse-grained chromosomes.Biophysical journal · 2015Article
- 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
- Transposable prophage Mu is organized as a stable chromosomal domain of E. coli.PLoS genetics · 2013Article
- 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
- Analysis of phage Mu DNA transposition by whole-genome Escherichia coli tiling arrays reveals a complex relationship to distribution of target selection protein B, transcription and chromosome architectural elements.Journal of biosciences · 2011Article
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4 authors.
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Abstract
Molecular mechanisms of bacterial chromosome packaging are still unclear, as bacteria lack nucleosomes or other apparent basic elements of DNA compaction. Among the factors facilitating DNA condensation may be a propensity of the DNA molecule for folding due to its intrinsic curvature. As suggested previously, the sequence correlations in genome reflect such a propensity [Trifonov and Sussman (1980) Proc. Natl Acad. Sci. USA, 77, 3816-3820]. To further elaborate this concept, we analyzed positioning of A-tracts (the sequence motifs introducing the most pronounced DNA curvature) in the Escherichia coli genome. First, we observed that the A-tracts are over-represented and distributed 'quasi-regularly' throughout the genome, including both the coding and intergenic sequences. Second, there is a 10-12 bp periodicity in the A-tract positioning indicating that the A-tracts are phased with respect to the DNA helical repeat. Third, the phased A-tracts are organized in approximately 100 bp long clusters. The latter feature was revealed with the help of a novel approach based on the Fourier series expansion of the A-tract distance autocorrelation function. Since the A-tracts introduce local bends of the DNA duplex and these bends accumulate when properly phased, the observed clusters would facilitate DNA looping. Also, such clusters may serve as binding sites for the nucleoid-associated proteins that have affinities for curved DNA (such as HU, H-NS, Hfq and CbpA). Therefore, we suggest that the approximately 100 bp long clusters of the phased A-tracts constitute the 'structural code' for DNA compaction by providing the long-range intrinsic curvature and increasing stability of the DNA complexes with architectural proteins.
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