ArticlePLoS computational biology2006
Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization.
Article in PLoS computational biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 56 citations in OpenAlex.
- The Bitome: digitized genomic features reveal fundamental genome organization.Nucleic acids research · 2020Article
- Correlated chromosomal periodicities according to the growth rate and gene expression.Scientific reports · 2020Article
- Spatial Patterns of Gene Expression in Bacterial Genomes.Journal of molecular evolution · 2020Article
- The highly conserved chromosomal periodicity of transcriptomes and the correlation of its amplitude with the growth rate in Escherichia coli.DNA research : an international journal for rapid publication of reports on genes and genomes · 2020Article
- The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function.Nucleic acids research · 2019Article
- Periodic Variation of Mutation Rates in Bacterial Genomes Associated with Replication Timing.mBio · 2018Article
- WoPPER: Web server for Position Related data analysis of gene Expression in Prokaryotes.Nucleic acids research · 2017Article
- GREAT: a web portal for Genome Regulatory Architecture Tools.Nucleic acids research · 2016Article
- Comparative genomics reveals conserved positioning of essential genomic clusters in highly rearranged Thermococcales chromosomes.Biochimie · 2015Article
- Perturbed states of the bacterial chromosome: a thymineless death case study.Frontiers in microbiology · 2015Review
- Sequencing of bacterial genomes: principles and insights into pathogenesis and development of antibiotics.Genes · 2013Article
- On the mutational topology of the bacterial genome.G3 (Bethesda, Md.) · 2013Article
- Article
- Regulatory consequences of gene translocation in bacteria.Nucleic acids research · 2012Article
- Genomic arrangement of regulons in bacterial genomes.PloS one · 2012Article
- Article
- CAGO: a software tool for dynamic visual comparison and correlation measurement of genome organization.PloS one · 2011Article
- Replication-biased genome organisation in the crenarchaeon Sulfolobus.BMC genomics · 2010Article
- Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Article
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Authors and funding
4 authors at 1 institution in 1 country.
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Abstract
Genome organization can be studied through analysis of chromosome position-dependent patterns in sequence-derived parameters. A comprehensive analysis of such patterns in prokaryotic sequences and genome-scale functional data has yet to be performed. We detected spatial patterns in sequence-derived parameters for 163 chromosomes occurring in 135 bacterial and 16 archaeal organisms using wavelet analysis. Pattern strength was found to correlate with organism-specific features such as genome size, overall GC content, and the occurrence of known motility and chromosomal binding proteins. Given additional functional data for Escherichia coli, we found significant correlations among chromosome position dependent patterns in numerous properties, some of which are consistent with previously experimentally identified chromosome macrodomains. These results demonstrate that the large-scale organization of most sequenced genomes is significantly nonrandom, and, moreover, that this organization is likely linked to genome size, nucleotide composition, and information transfer processes. Constraints on genome evolution and design are thus not solely dependent upon information content, but also upon an intricate multi-parameter, multi-length-scale organization of the chromosome.
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Registered trials
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