ArticleBMC genomics2015
Spatial features for Escherichia coli genome organization.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 25 citations in OpenAlex.
- Spatial chromosome organization and adaptation of the radiation-resistant extremophile Deinococcus radiodurans.The Journal of biological chemistry · 2025Article
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- Chromosome structure modeling tools and their evaluation in bacteria.Briefings in bioinformatics · 2024Review
- High-Throughput Mapping of Chromosomal Conformations in E. coli Under Physiological Conditions Using Massively Multiplexed Mu Transposition.Methods in molecular biology (Clifton, N.J.) · 2024Article
- The Spatial Organization of Bacterial Transcriptional Regulatory Networks.Microorganisms · 2022Article
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- Transcription of Bacterial Chromatin.Journal of molecular biology · 2019Review
- Genomic identification and functional analysis of essential genes in Caenorhabditis elegans.BMC genomics · 2018Article
- Genome-wide analysis of fitness data and its application to improve metabolic models.BMC bioinformatics · 2018Article
- High-resolution 3D models of Caulobacter crescentus chromosome reveal genome structural variability and organization.Nucleic acids research · 2018Article
- Selection, periodicity and potential function for Highly Iterative Palindrome-1 (HIP1) in cyanobacterial genomes.Nucleic acids research · 2018Article
- Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome.Nucleic acids research · 2017Article
- WoPPER: Web server for Position Related data analysis of gene Expression in Prokaryotes.Nucleic acids research · 2017Article
- GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes.BMC genomics · 2017Article
- Spatial Colocalization of Human Ohnolog Pairs Acts to Maintain Dosage-Balance.Molecular biology and evolution · 2016Article
- Spatially coordinated replication and minimization of expression noise constrain three-dimensional organization of yeast genome.DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
- Gene expression homeostasis and chromosome architecture.Bioarchitecture · 2014Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn bacterial genomes, the compactly encoded genes and operons are well organized, with genes in the same biological pathway or operons in the same regulon close to each other on the genome sequence. In addition, the linearly close genes have a higher probability of co-expression and their protein products tend to form protein-protein interactions. However, the organization features of bacterial genomes in a three-dimensional space remain elusive. The DNA interaction data of Escherichia coli, measured by the genome conformation capture (GCC) technique, have recently become available, which allowed us to investigate the spatial features of bacterial genome organization.
resultsBy renormalizing the GCC data, we compared the interaction frequency of operon pairs in the same regulon with that of random operon pairs. The results showed that arrangements of operons in the E. coli genome tend to minimize the spatial distance between operons in the same regulon. A similar global organization feature exists for genes in biological pathways of E. coli. In addition, the genes close to each other spatially (even if they are far from each other on the genome sequence) tend to be co-expressed and form protein-protein interactions. These results provided new insights into the organization principles of bacterial genomes and support the notion of transcription factory.
conclusionsThis study revealed the organization features of Escherichia coli genomic functional units in the 3D space and furthered our understanding of the link between the three-dimensional structure of chromosomes and biological function.
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