ArticleNucleic acids research2012
A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 82 citations in OpenAlex.
- Spatio-temporal organization of theEcoSal Plus · 2024Review
- Interpretation of organizational role of proteins on E. coli nucleoid via Hi-C integrated model.Biophysical journal · 2023Article
- Relationship between the Chromosome Structural Dynamics and Gene Expression-A Chicken and Egg Dilemma?Microorganisms · 2022Review
- The economy of chromosomal distances in bacterial gene regulation.NPJ systems biology and applications · 2021Article
- Nonrandom segregation of sister chromosomes byProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Composition of Transcription Machinery and Its Crosstalk with Nucleoid-Associated Proteins and Global Transcription Factors.Biomolecules · 2021Review
- A Hi-C data-integrated model elucidates E. coli chromosome's multiscale organization at various replication stages.Nucleic acids research · 2021Article
- Genome Complexity Browser: Visualization and quantification of genome variability.PLoS computational biology · 2020Article
- Chromosomal Organization and Regulation of Genetic Function inEcoSal Plus · 2020Article
- Coherent Domains of Transcription Coordinate Gene Expression During Bacterial Growth and Adaptation.Microorganisms · 2019Review
- Heterogeneous Loop Model to Infer 3D Chromosome Structures from Hi-C.Biophysical journal · 2019Article
- Direct imaging of the circular chromosome in a live bacterium.Nature communications · 2019Article
- The E. coli transcriptional regulatory network and its spatial embedding.The European physical journal. E, Soft matter · 2019Article
- Chromosomal organization of transcription: in a nutshell.Current genetics · 2018Review
- Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome.Nucleic acids research · 2017Article
- Supra-operonic clusters of functionally related genes (SOCs) are a source of horizontal gene co-transfers.Scientific reports · 2017Article
- Coevolution of the Organization and Structure of Prokaryotic Genomes.Cold Spring Harbor perspectives in biology · 2016Review
- Segregation of chromosome arms in growing and non-growing Escherichia coli cells.Frontiers in microbiology · 2015Article
- Polymer modeling of the E. coli genome reveals the involvement of locus positioning and macrodomain structuring for the control of chromosome conformation and segregation.Nucleic acids research · 2014Article
- Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information.Cellular and molecular life sciences : CMLS · 2013Review
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
What physical mechanism leads to organization of a highly condensed and confined circular chromosome? Computational modeling shows that confinement-induced organization is able to overcome the chromosome's propensity to mix by the formation of topological domains. The experimentally observed high precision of separate subcellular positioning of loci (located on different chromosomal domains) in Escherichia coli naturally emerges as a result of entropic demixing of such chromosomal loops. We propose one possible mechanism for organizing these domains: regulatory control defined by the underlying E. coli gene regulatory network requires the colocalization of transcription factor genes and target genes. Investigating this assumption, we find the DNA chain to self-organize into several topologically distinguishable domains where the interplay between the entropic repulsion of chromosomal loops and their compression due to the confining geometry induces an effective nucleoid filament-type of structure. Thus, we propose that the physical structure of the chromosome is a direct result of regulatory interactions. To reproduce the observed precise ordering of the chromosome, we estimate that the domain sizes are distributed between 10 and 700 kb, in agreement with the size of topological domains identified in the context of DNA supercoiling.
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