ArticleMolecular systems biology2010
Chromosomal periodicity and positional networks of genes in Escherichia coli.
Article in Molecular systems biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 34 citations in OpenAlex.
- Article
- Bacterial nucleoid is a riddle wrapped in a mystery inside an enigma.Journal of bacteriology · 2024Review
- Growth rate-associated transcriptome reorganization in response to genomic, environmental, and evolutionary interruptions.Frontiers in microbiology · 2023Article
- Elucidating the Influence of Chromosomal Architecture on Transcriptional Regulation in Prokaryotes - Observing Strong Local Effects of Nucleoid Structure on Gene Regulation.Frontiers in microbiology · 2020Article
- Chromosomal organization of transcription: in a nutshell.Current genetics · 2018Review
- Selection, periodicity and potential function for Highly Iterative Palindrome-1 (HIP1) in cyanobacterial genomes.Nucleic acids research · 2018Article
- Broad-scale redistribution of mRNA abundance and transcriptional machinery in response to growth rate inMicrobial genomics · 2017Article
- The genome-scale interplay amongst xenogene silencing, stress response and chromosome architecture in Escherichia coli.Nucleic acids research · 2015Article
- Genome architecture and global gene regulation in bacteria: making progress towards a unified model?Nature reviews. Microbiology · 2013Review
- Article
- Global genomic arrangement of bacterial genes is closely tied with the total transcriptional efficiency.Genomics, proteomics & bioinformatics · 2013Article
- Multilevel comparative analysis of the contributions of genome reduction and heat shock to the Escherichia coli transcriptome.BMC genomics · 2013Article
- DNA movies and panspermia.Life (Basel, Switzerland) · 2011Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The structure of dynamic folds in microbial chromosomes is largely unknown. Here, we find that genes with a highly biased codon composition and characterizing a functional core in Escherichia coli K12 show to be periodically distributed along the arcs, suggesting an encoded three-dimensional genomic organization helping functional activities among which are translation and, possibly, transcription. This extends to functional classes of genes that are shown to systematically organize into two independent positional gene networks, one driven by metabolic genes and the other by genes involved in cellular processing and signaling. We conclude that functional reasons justify periodic gene organization. This finding generates new questions on evolutionary pressures imposed on the chromosome. Our methodological approach is based on single genome analysis. Given either core genes or genes organized in functional classes, we analyze the detailed distribution of distances between pairs of genes through a parameterized model based on signal processing and find that these groups of genes tend to be separated by a regular integral distance. The methodology can be applied to any set of genes and can be taken as a footprint for large-scale bacterial and archaeal analysis.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.