Impact of Chromosomal Architecture on the Function and Evolution of Bacterial Genomes

Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins

(2018) Virginia S. Lioy et al.   CELL

Dimerization site 2 of the bacterial DNA-binding protein H-NS is required for gene silencing and stiffened nucleoprotein filament formation

(2018) Yuki Yamanaka et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Waking the neighbours: disruption of H-NS repression by overlapping transcription

(2018) Joseph T. Wade et al.   MOLECULAR MICROBIOLOGY

Biochemical mechanisms determine the functional compatibility of heterologous genes

(2018) Andreas Porse et al.   Nature Communications

Spatial organization of DNA sequences directs the assembly of bacterial chromatin by a nucleoid-associated protein

(2017) Aleksandre Japaridze et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Entropic elasticity and dynamics of the bacterial chromosome: A simulation study

(2017) M. C. F. Pereira et al.   JOURNAL OF CHEMICAL PHYSICS

How best to identify chromosomal interactions: a comparison of approaches

(2017) James O J Davies et al.   NATURE METHODS

The chromosomal organization of horizontal gene transfer in bacteria

(2017) Pedro H. Oliveira et al.   Nature Communications

Long range chromosome organization in Escherichia coli: The position of the replication origin defines the non-structured regions and the Right and Left macrodomains

(2017) Stéphane Duigou et al.   PLoS Genetics

Model-based genome-wide determination of RNA chain elongation rates in Escherichia coli

(2017) Peter Großmann et al.   Scientific Reports

Colocalization of distant chromosomal loci in space in E. coli : a bacterial nucleolus

(2016) Tamas Gaal et al.   GENES & DEVELOPMENT

Lack of the H-NS Protein Results in Extended and Aberrantly Positioned DNA during Chromosome Replication and Segregation in Escherichia coli

(2016) Emily Helgesen et al.   JOURNAL OF BACTERIOLOGY

Transitions of Double-Stranded DNA Between the A- and B-Forms

(2016) James T. Waters et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The nature of mutations induced by replication–transcription collisions

(2016) T. Sabari Sankar et al.   NATURE

Genome scale patterns of supercoiling in a bacterial chromosome

(2016) Avantika Lal et al.   Nature Communications

Effect of Genome Position on Heterologous Gene Expression in Bacillus subtilis: An Unbiased Analysis

(2016) Christopher Sauer et al.   ACS Synthetic Biology

DNA Replication Control Is Linked to Genomic Positioning of Control Regions in Escherichia coli

(2016) Jakob Frimodt-Møller et al.   PLoS Genetics

H-NS Facilitates Sequence Diversification of Horizontally Transferred DNAs during Their Integration in Host Chromosomes

(2016) Koichi Higashi et al.   PLoS Genetics

The Causes and Consequences of Topological Stress during DNA Replication

(2016) Andrea Keszthelyi et al.   Genes

Genes on a Wire: The Nucleoid-Associated Protein HU Insulates Transcription Units in Escherichia coli

(2016) Michael Berger et al.   Scientific Reports

Bacterial Chromosome Organization and Segregation

(2015) Anjana Badrinarayanan et al.   Annual Review of Cell and Developmental Biology

H-NS Regulates Gene Expression and Compacts the Nucleoid: Insights from Single-Molecule Experiments

(2015) Ricksen S. Winardhi et al.   BIOPHYSICAL JOURNAL

Taking the pseudo out of pseudogenes

(2015) Ian Goodhead et al.   CURRENT OPINION IN MICROBIOLOGY

DNA structure and function

(2015) Andrew Travers et al.   FEBS Journal

A virus that infects a hyperthermophile encapsidates A-form DNA

(2015) F. DiMaio et al.   SCIENCE

Growth phase dependent changes in the structure and protein composition of nucleoid in Escherichia coli

(2015) AliAzam Talukder et al.   Science China-Life Sciences

Building bridges within the bacterial chromosome

(2015) Dan Song et al.   TRENDS IN GENETICS

Characterization of the Escherichia coli σS core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis

(2015) Clelia Peano et al.   Scientific Reports

Gene Regulation by H-NS as a Function of Growth Conditions Depends on Chromosomal Position in Escherichia coli

(2015) Elisa Brambilla et al.   G3-Genes Genomes Genetics

Control regions for chromosome replication are conserved with respect to sequence and location among Escherichia coli strains

(2015) Jakob Frimodt-Møller et al.   Frontiers in Microbiology

The spatial biology of transcription and translation in rapidly growing Escherichia coli

(2015) Somenath Bakshi et al.   Frontiers in Microbiology

oriC-encoded instructions for the initiation of bacterial chromosome replication

(2015) Marcin WolaÅ„ski et al.   Frontiers in Microbiology

Function of Nucleoid-Associated Proteins in Chromosome Structuring and Transcriptional Regulation

(2015) Charles J. Dorman   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

Insights into structural variations and genome rearrangements in prokaryotic genomes

(2014) Vinita Periwal et al.   BIOINFORMATICS

DNA Dynamics and Single-Molecule Biology

(2014) Daniel Duzdevich et al.   CHEMICAL REVIEWS

The bacterial nucleoid: nature, dynamics and sister segregation

(2014) Nancy Kleckner et al.   CURRENT OPINION IN MICROBIOLOGY

Spatial organization of bacterial chromosomes

(2014) Xindan Wang et al.   CURRENT OPINION IN MICROBIOLOGY

Chromosome position effects on gene expression in Escherichia coli K-12

(2014) Jack A. Bryant et al.   NUCLEIC ACIDS RESEARCH

Torsion-Mediated Interaction between Adjacent Genes

(2014) Sam Meyer et al.   PLoS Computational Biology

The benefit of DNA supercoiling during replication

(2013) Jorge B. Schvartzman et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Co-operative roles for DNA supercoiling and nucleoid-associated proteins in the regulation of bacterial transcription

(2013) Charles J. Dorman   BIOCHEMICAL SOCIETY TRANSACTIONS

Supercoiling in DNA and chromatin

(2013) Nick Gilbert et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A novel role for antibiotic resistance plasmids in facilitatingSalmonellaadaptation to non-host environments

(2013) Sonia Paytubi et al.   ENVIRONMENTAL MICROBIOLOGY

DNA thermodynamic stability and supercoil dynamics determine the gene expression program during the bacterial growth cycle

(2013) Patrick Sobetzko et al.   Molecular BioSystems

Organization and segregation of bacterial chromosomes

(2013) Xindan Wang et al.   NATURE REVIEWS GENETICS

Genome architecture and global gene regulation in bacteria: making progress towards a unified model?

(2013) Charles J. Dorman   NATURE REVIEWS MICROBIOLOGY

Looking for a promoter in 3D

(2013) Vladimir Svetlov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription

(2013) Cedric Cagliero et al.   NUCLEIC ACIDS RESEARCH

Distance Matters: The Impact of Gene Proximity in Bacterial Gene Regulation

(2013) Otto Pulkkinen et al.   PHYSICAL REVIEW LETTERS

Transcription Under Torsion

(2013) J. Ma et al.   SCIENCE

Exploring the costs of horizontal gene transfer

(2013) David A. Baltrus   TRENDS IN ECOLOGY & EVOLUTION

Size-controlled silver nanoparticles synthesized over the range 5–100 nm using the same protocol and their antibacterial efficacy

(2013) Shekhar Agnihotri et al.   RSC Advances

Regulation of Sister Chromosome Cohesion by the Replication Fork Tracking Protein SeqA

(2013) Mohan C. Joshi et al.   PLoS Genetics

Global Genomic Arrangement of Bacterial Genes Is Closely Tied with the Total Transcriptional Efficiency

(2013) Qin Ma et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Architectural organization in E. coli nucleoid

(2012) Mirjana Macvanin et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

High Expression Hampers Horizontal Gene Transfer

(2012) Chungoo Park et al.   Genome Biology and Evolution

Molecular Basis for a Protein-Mediated DNA-Bridging Mechanism that Functions in Condensation of the E. coli Chromosome

(2012) Pauline Dupaigne et al.   MOLECULAR CELL

Variation of the folding and dynamics of theEscherichia colichromosome with growth conditions

(2012) Nastaran Hadizadeh Yazdi et al.   MOLECULAR MICROBIOLOGY

Gene location and DNA density determine transcription factor distributions in Escherichia coli

(2012) Thomas E Kuhlman et al.   Molecular Systems Biology

The promoter-search mechanism of Escherichia coli RNA polymerase is dominated by three-dimensional diffusion

(2012) Feng Wang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dissociation and re-association of RNA polymerase with DNA during osmotic stress response in Escherichia coli

(2012) Cedric Cagliero et al.   NUCLEIC ACIDS RESEARCH

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

A Fundamental Regulatory Mechanism Operating through OmpR and DNA Topology Controls Expression of Salmonella Pathogenicity Islands SPI-1 and SPI-2

(2012) Andrew D. S. Cameron et al.   PLoS Genetics

Trends and barriers to lateral gene transfer in prokaryotes

(2011) Ovidiu Popa et al.   CURRENT OPINION IN MICROBIOLOGY

Spatial Distribution and Diffusive Motion of RNA Polymerase in Live Escherichia coli

(2011) B. P. Bratton et al.   JOURNAL OF BACTERIOLOGY

Mechanism of Bacterial Transcription Initiation: RNA Polymerase - Promoter Binding, Isomerization to Initiation-Competent Open Complexes, and Initiation of RNA Synthesis

(2011) Ruth M. Saecker et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins

(2011) B. R. G. Gordon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle

(2011) P. Sobetzko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromosome Organization by a Nucleoid-Associated Protein in Live Bacteria

(2011) W. Wang et al.   SCIENCE

DNA condensation in bacteria: Interplay between macromolecular crowding and nucleoid proteins

(2010) Renko de Vries   BIOCHIMIE

Salmonella entericaResponse Regulator SsrB Relieves H-NS Silencing by Displacing H-NS Bound in Polymerization Mode and Directly Activates Transcription

(2010) Don Walthers et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Modeling Three-Dimensional Chromosome Structures Using Gene Expression Data

(2010) Guanghua Xiao et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

The Complexity Hypothesis Revisited: Connectivity Rather Than Function Constitutes a Barrier to Horizontal Gene Transfer

(2010) O. Cohen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bacterial nucleoid-associated proteins, nucleoid structure and gene expression

(2010) Shane C. Dillon et al.   NATURE REVIEWS MICROBIOLOGY

Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament

(2010) P. A. Wiggins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA Polymerase Active Center: The Molecular Engine of Transcription

(2009) Evgeny Nudler   Annual Review of Biochemistry

Active Transcription of rRNA Operons Condenses the Nucleoid in Escherichia coli: Examining the Effect of Transcription on Nucleoid Structure in the Absence of Transertion

(2009) J. E. Cabrera et al.   JOURNAL OF BACTERIOLOGY

The H-NS-like protein StpA represses the RpoS (σ38) regulon during exponential growth ofSalmonellaTyphimurium

(2009) Sacha Lucchini et al.   MOLECULAR MICROBIOLOGY

The transition from transcriptional initiation to elongation

(2008) Joseph T Wade et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Anti-silencing: overcoming H-NS-mediated repression of transcription in Gram-negative enteric bacteria

(2008) D. M. Stoebel et al.   MICROBIOLOGY-SGM

DNA dynamics vary according to macrodomain topography in theE. colichromosome

(2008) Olivier Espeli et al.   MOLECULAR MICROBIOLOGY

Escherichia coli and its chromosome

(2008) Rodrigo Reyes-Lamothe et al.   TRENDS IN MICROBIOLOGY