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Mapping the Multiscale Organisation of Escherichia Coli Chromosome in a Hi-C-integrated Model

https://doi.org/10.1101/2020.06.29.178194
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Architectural organization in E. coli nucleoid
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Entropy-Based Mechanism of Ribosome-Nucleoid Segregation in E. coli Cells
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A Polymer Model for the Quantitative Reconstruction of Chromosome Architecture from HiC and GAM Data
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The MatP/matS Site-Specific System Organizes the Terminus Region of the E. coli Chromosome into a Macrodomain
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Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins
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High-Resolution Mapping of the Escherichia coli Chromosome Reveals Positions of High and Low Transcription
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Intracellular Positioning Systems Limit the Entropic Eviction of Secondary Replicons Toward the Nucleoid Edges in Bacterial Cells
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Effects of nucleoid-associated proteins on bacterial chromosome structure and gene expression
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The bacterial nucleoid: nature, dynamics and sister segregation
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The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation
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Molecular Basis for a Protein-Mediated DNA-Bridging Mechanism that Functions in Condensation of the E. coli Chromosome
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GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
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Lattice Models of Bacterial Nucleoids
inferredcites →https://doi.org/10.1038/nature12593openalex-snapshot
Single-cell Hi-C reveals cell-to-cell variability in chromosome structure
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Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae
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3D genome reconstruction from chromosomal contacts
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Double-slit photoelectron interference in strong-field ionization of the neon dimer
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SciPy 1.0: fundamental algorithms for scientific computing in Python
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Macrodomain organization of the Escherichia coli chromosome
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Two types of localization of the DNA‐binding proteins within the Escherichia coli nucleoid
inferredcites →https://doi.org/10.1051/jphys:0198800490120209500openalex-snapshot
The role of topological constraints in the kinetics of collapse of macromolecules
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Macroscopic modeling and simulations of supercoiled DNA with bound proteins
inferredcites →https://doi.org/10.1073/pnas.0611686104openalex-snapshot
Spiral structure of Escherichia coli HUαβ provides foundation for DNA supercoiling
inferredcites →https://doi.org/10.1073/pnas.0912062107openalex-snapshot
Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament
inferredcites →https://doi.org/10.1073/pnas.1302950110openalex-snapshot
Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization
inferredcites →https://doi.org/10.1073/pnas.1507592112openalex-snapshot
Live-cell superresolution microscopy reveals the organization of RNA polymerase in the bacterial nucleoid
inferredcites →https://doi.org/10.1073/pnas.1613607113openalex-snapshot
Transferable model for chromosome architecture
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Timing the start of division in E. coli : a single-cell study
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Topological Invariants of Knots and Links
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A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation
inferredcites →https://doi.org/10.1093/nar/gkt480openalex-snapshot
Modelling of crowded polymers elucidate effects of double-strand breaks in topological domains of bacterial chromosomes
inferredcites →https://doi.org/10.1093/nar/gkx541openalex-snapshot
Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome
inferredcites →https://doi.org/10.1093/nar/gky141openalex-snapshot
High-resolution 3D models of Caulobacter crescentus chromosome reveal genome structural variability and organization
inferredcites →https://doi.org/10.1101/cshperspect.a000349openalex-snapshot
Bacterial Chromosome Organization and Segregation
inferredcites →https://doi.org/10.1101/gad.1207504openalex-snapshot
Topological domain structure of the Escherichia coli chromosome
inferredcites →https://doi.org/10.1101/gad.14.2.212openalex-snapshot
Dynamic organization of chromosomal DNA in Escherichia coli
inferredcites →https://doi.org/10.1101/gad.290312.116openalex-snapshot
Colocalization of distant chromosomal loci in space in E. coli: a bacterial nucleolus
inferredcites →https://doi.org/10.1101/gad.388406openalex-snapshot
The twoEscherichia colichromosome arms locate to separate cell halves
inferredcites →https://doi.org/10.1101/gr.070276.107openalex-snapshot
Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts
inferredcites →https://doi.org/10.1111/j.1365-2958.2005.04799.xopenalex-snapshot
A genetic selection for supercoiling mutants of Escherichia coli reveals proteins implicated in chromosome structure
inferredcites →https://doi.org/10.1111/j.1365-2958.2008.06239.xopenalex-snapshot
DNA dynamics vary according to macrodomain topography in the E. coli chromosome
inferredcites →https://doi.org/10.1111/j.1365-2958.2012.08081.xopenalex-snapshot
Superresolution imaging of ribosomes and RNA polymerase in live Escherichia coli cells
inferredcites →https://doi.org/10.1111/mmi.12071openalex-snapshot
Variation of the folding and dynamics of the E scherichia coli chromosome with growth conditions
inferredcites →https://doi.org/10.1126/science.1067799openalex-snapshot
Capturing Chromosome Conformation
inferredcites →https://doi.org/10.1126/science.1181369openalex-snapshot
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
inferredcites →https://doi.org/10.1126/science.1242059openalex-snapshot
High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome
inferredcites →https://doi.org/10.1128/jb.01893-05openalex-snapshot
Active Transcription of rRNA Operons Is a Driving Force for the Distribution of RNA Polymerase in Bacteria: Effect of Extrachromosomal Copies of rrnB on the In Vivo Localization of RNA Polymerase
inferredcites →https://doi.org/10.1128/jb.181.20.6361-6370.1999openalex-snapshot
Growth Phase-Dependent Variation in Protein Composition of the Escherichia coli Nucleoid
inferredcites →https://doi.org/10.1128/mcb.00208-07openalex-snapshot
The Three-Dimensional Structure of Human Interphase Chromosomes Is Related to the Transcriptome Map
inferredcites →https://doi.org/10.1186/1471-2164-13-436openalex-snapshot
Normalization of a chromosomal contact map
inferredcites →https://doi.org/10.1186/s12864-019-6096-0openalex-snapshot
EVR: reconstruction of bacterial chromosome 3D structure models using error-vector resultant algorithm
inferredcites →https://doi.org/10.1371/journal.pcbi.1000986openalex-snapshot
Chromosome Driven Spatial Patterning of Proteins in Bacteria
inferredcites →https://doi.org/10.1371/journal.pgen.1008456openalex-snapshot
Architecture of the Escherichia coli nucleoid
inferredcites →https://doi.org/10.1371/journal.pone.0023126openalex-snapshot
Condition-Dependent Cell Volume and Concentration of Escherichia coli to Facilitate Data Conversion for Systems Biology Modeling
inferredcites →https://doi.org/10.15488/5174openalex-snapshot
Double-slit photoelectron interference in strong-field ionization of the neon dimer
inferredcites →https://doi.org/10.17863/cam.64134openalex-snapshot
SciPy 1.0: fundamental algorithms for scientific computing in Python
inferredcites →https://doi.org/10.3389/fmicb.2018.02019openalex-snapshot
Impact of Chromosomal Architecture on the Function and Evolution of Bacterial Genomes

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1101/2020.11.05.369934openalex-snapshot
Nucleoid associated proteins and their effect on E. coli chromosome
inferred← citeshttps://doi.org/10.15252/embj.2021108708openalex-snapshot
Distinct heterochromatin‐like domains promote transcriptional memory and silence parasitic genetic elements in bacteria
inferred← citeshttps://doi.org/10.48550/arxiv.2110.04769openalex-snapshot
DNA-polymer architecture orchestrates the segregation and spatio-temporal organization of E. coli chromosomes during replication in slow growth
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