4.6 Article

Elucidating the Influence of Chromosomal Architecture on Transcriptional Regulation in Prokaryotes - Observing Strong Local Effects of Nucleoid Structure on Gene Regulation

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

High-Resolution Mapping of the Escherichia coli Chromosome Reveals Positions of High and Low Transcription

Scott A. Scholz et al.

CELL SYSTEMS (2019)

Article Biochemistry & Molecular Biology

RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12

Alberto Santos-Zavaleta et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

E. coli gene regulatory networks are inconsistent with gene expression data

Simon J. Larsen et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

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

Virginia S. Lioy et al.

Review Microbiology

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

Thoger J. Krogh et al.

FRONTIERS IN MICROBIOLOGY (2018)

Article Astronomy & Astrophysics

Understanding the Lomb-Scargle Periodogram

Jacob T. VanderPlas

ASTROPHYSICAL JOURNAL SUPPLEMENT SERIES (2018)

Article Biotechnology & Applied Microbiology

Selection-driven cost-efficiency optimization of transcripts modulates gene evolutionary rate in bacteria

Emily A. Seward et al.

GENOME BIOLOGY (2018)

Article Biochemistry & Molecular Biology

Universal and idiosyncratic characteristic lengths in bacterial genomes

Ivan Junier et al.

PHYSICAL BIOLOGY (2018)

Article Biochemistry & Molecular Biology

Pervasive coexpression of spatially proximal genes is buffered at the protein level

Georg Kustatscher et al.

MOLECULAR SYSTEMS BIOLOGY (2017)

Article Biochemistry & Molecular Biology

Transcription-coupled DNA supercoiling dictates the chromosomal arrangement of bacterial genes

Patrick Sobetzko

NUCLEIC ACIDS RESEARCH (2016)

Article Multidisciplinary Sciences

Genome scale patterns of supercoiling in a bacterial chromosome

Avantika Lal et al.

NATURE COMMUNICATIONS (2016)

Article Multidisciplinary Sciences

Functional modules of sigma factor regulons guarantee adaptability and evolvability

Sebastian C. Binder et al.

SCIENTIFIC REPORTS (2016)

Article Biochemical Research Methods

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

Christopher Sauer et al.

ACS SYNTHETIC BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Insights into the Mechanisms of Basal Coordination of Transcription Using a Genome-Reduced Bacterium

Ivan Junier et al.

CELL SYSTEMS (2016)

Article Biotechnology & Applied Microbiology

Transcriptomic Analysis of the Adaptation of Listeria monocytogenes to Growth on Vacuum-Packed Cold Smoked Salmon

Silin Tang et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2015)

Review Microbiology

Taking the pseudo out of pseudogenes

Ian Goodhead et al.

CURRENT OPINION IN MICROBIOLOGY (2015)

Review Microbiology

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

Somenath Bakshi et al.

FRONTIERS IN MICROBIOLOGY (2015)

Review Chemistry, Multidisciplinary

DNA Dynamics and Single-Molecule Biology

Daniel Duzdevich et al.

CHEMICAL REVIEWS (2014)

Article Biochemistry & Molecular Biology

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

Jack A. Bryant et al.

NUCLEIC ACIDS RESEARCH (2014)

Review Genetics & Heredity

Spatial organization of transcription in bacterial cells

Xiaoli Weng et al.

TRENDS IN GENETICS (2014)

Article Biochemistry & Molecular Biology

The benefit of DNA supercoiling during replication

Jorge B. Schvartzman et al.

BIOCHEMICAL SOCIETY TRANSACTIONS (2013)

Article Biochemistry & Molecular Biology

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

Feng Wang et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2013)

Editorial Material Biochemistry & Molecular Biology

Looking for a promoter in 3D

Vladimir Svetlov et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2013)

Article Biochemistry & Molecular Biology

EcoCyc: fusing model organism databases with systems biology

Ingrid M. Keseler et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Biochemistry & Molecular Biology

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

Cedric Cagliero et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Physics, Multidisciplinary

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

Otto Pulkkinen et al.

PHYSICAL REVIEW LETTERS (2013)

Article Multidisciplinary Sciences

Transcription Under Torsion

Jie Ma et al.

SCIENCE (2013)

Article Evolutionary Biology

High Expression Hampers Horizontal Gene Transfer

Chungoo Park et al.

GENOME BIOLOGY AND EVOLUTION (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Review Biotechnology & Applied Microbiology

Histone-Like Proteins of Bacteria (Review)

A. M. Anuchin et al.

APPLIED BIOCHEMISTRY AND MICROBIOLOGY (2011)

Article Biophysics

Entropy-Based Mechanism of Ribosome-Nucleoid Segregation in E. coli Cells

Jagannath Mondal et al.

BIOPHYSICAL JOURNAL (2011)

Article Biochemistry & Molecular Biology

Coordination of genomic structure and transcription by the main bacterial nucleoid-associated protein HU

Michael Berger et al.

EMBO REPORTS (2010)

Article Biochemistry & Molecular Biology

Chromosomal periodicity and positional networks of genes in Escherichia coli

Anthony Mathelier et al.

MOLECULAR SYSTEMS BIOLOGY (2010)

Review Microbiology

Bacterial nucleoid-associated proteins, nucleoid structure and gene expression

Shane C. Dillon et al.

NATURE REVIEWS MICROBIOLOGY (2010)

Article Multidisciplinary Sciences

Cryptic prophages help bacteria cope with adverse environments

Xiaoxue Wang et al.

NATURE COMMUNICATIONS (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Mathematical & Computational Biology

Dissecting the logical types of network control in gene expression profiles

Carsten Marr et al.

BMC SYSTEMS BIOLOGY (2008)

Article Biochemistry & Molecular Biology

Many Microbe Microarrays Database: Uniformly normalized affymetrix compendia with structured experimental metadata

Jeremiah J. Faith et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Multidisciplinary Sciences

Chromosomal periodicity of evolutionarily conserved gene pairs

Matthew A. Wright et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Biotechnology & Applied Microbiology

Autocorrelation analysis reveals widespread spatial biases in microarray experiments

Amnon Koren et al.

BMC GENOMICS (2007)

Article Biochemistry & Molecular Biology

Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome

Nicolas Blot et al.

EMBO REPORTS (2006)

Article Biochemistry & Molecular Biology

Measuring chromosome dynamics on different time scales using resolvases with varying half-lives

RA Stein et al.

MOLECULAR MICROBIOLOGY (2005)

Review Genetics & Heredity

The evolution of genetic regulatory systems in bacteria

HH McAdams et al.

NATURE REVIEWS GENETICS (2004)

Article Biochemistry & Molecular Biology

Fundamental structural units of the Escherichia coli nucleoid revealed by atomic force microscopy

J Kim et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Cell Biology

Topological domain structure of the Escherichia coli chromosome

L Postow et al.

GENES & DEVELOPMENT (2004)

Article Biochemistry & Molecular Biology

Nucleoid restructuring in stationary-state bacteria

D Frenkiel-Krispin et al.

MOLECULAR MICROBIOLOGY (2004)

Article Biochemistry & Molecular Biology

Macrodomain organization of the Escherichia coli chromosome

M Valens et al.

EMBO JOURNAL (2004)

Article Biotechnology & Applied Microbiology

Spatial patterns of transcriptional activity in the chromosome of Escherichia coli

KS Jeong et al.

GENOME BIOLOGY (2004)

Article Biotechnology & Applied Microbiology

Relationship between gene co-expression and probe localization on microarray slides

Y Kluger et al.

BMC GENOMICS (2003)

Article Biochemistry & Molecular Biology

The distribution of RNA polymerase in Escherichia coli is dynamic and sensitive to environmental cues

JE Cabrera et al.

MOLECULAR MICROBIOLOGY (2003)

Article Biochemistry & Molecular Biology

Global gene expression profiling in Escherichia coli K12 -: The effects of oxygen availability and FNR

K Salmon et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2003)

Article Biochemistry & Molecular Biology

Spurious spatial periodicity of co-expression in microarray data due to printing design

G Balázsi et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemistry & Molecular Biology

Congruent evolution of different classes of non-coding DNA in prokaryotic genomes

IB Rogozin et al.

NUCLEIC ACIDS RESEARCH (2002)

Article Biochemistry & Molecular Biology

Toroidal nucleoids in Escherichia coli exposed to chloramphenicol

SB Zimmerman

JOURNAL OF STRUCTURAL BIOLOGY (2002)