Chromosome organization in bacteria: mechanistic insights into genome structure and function

Self-organised segregation of bacterial chromosomal origins

(2019) Andreas Hofmann et al.   eLife

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

(2018) Virginia S. Lioy et al.   CELL

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

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

StpA and Hha stimulate pausing by RNA polymerase by promoting DNA–DNA bridging of H-NS filaments

(2018) Beth A Boudreau et al.   NUCLEIC ACIDS RESEARCH

Real-time imaging of DNA loop extrusion by condensin

(2018) Mahipal Ganji et al.   SCIENCE

Sub-kb Hi-C in D. melanogaster reveals conserved characteristics of TADs between insect and mammalian cells

(2018) Qi Wang et al.   Nature Communications

MukB ATPases are regulated independently by the N- and C-terminal domains of MukF kleisin

(2018) Katarzyna Zawadzka et al.   eLife

Global DNA Compaction in Stationary-Phase Bacteria Does Not Affect Transcription

(2018) Richard Janissen et al.   CELL

A Bacterial Chromosome Structuring Protein Binds Overtwisted DNA to Stimulate Type II Topoisomerases and Enable DNA Replication

(2018) Monica S. Guo et al.   CELL

How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome

(2018) Bo Duan et al.   NUCLEIC ACIDS RESEARCH

Structure and function of archaeal histones

(2018) Bram Henneman et al.   PLoS Genetics

Post-translational modification of nucleoid-associated proteins: an extra layer of functional modulation in bacteria?

(2018) Ivar W. Dilweg et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Bacterial FtsZ protein forms phase‐separated condensates with its nucleoid‐associated inhibitor SlmA

(2018) Begoña Monterroso et al.   EMBO REPORTS

SATB family chromatin organizers as master regulators of tumor progression

(2018) Rutika Naik et al.   ONCOGENE

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

(2017) M. Jordan Rowley et al.   MOLECULAR CELL

3D structures of individual mammalian genomes studied by single-cell Hi-C

(2017) Tim J. Stevens et al.   NATURE

Cell-cycle dynamics of chromosomal organization at single-cell resolution

(2017) Takashi Nagano et al.   NATURE

A novel nucleoid-associated protein coordinates chromosome replication and chromosome partition

(2017) James A. Taylor et al.   NUCLEIC ACIDS RESEARCH

Structure of histone-based chromatin in Archaea

(2017) Francesca Mattiroli et al.   SCIENCE

Bacillus subtilis SMC complexes juxtapose chromosome arms as they travel from origin to terminus

(2017) Xindan Wang et al.   SCIENCE

SMC Progressively Aligns Chromosomal Arms in Caulobacter crescentus but Is Antagonized by Convergent Transcription

(2017) Ngat T. Tran et al.   Cell Reports

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

Mechanism of environmentally driven conformational changes that modulate H-NS DNA-bridging activity

(2017) Ramon A van der Valk et al.   eLife

Horizontally acquired AT-rich genes in Escherichia coli cause toxicity by sequestering RNA polymerase

(2017) Lisa E. Lamberte et al.   Nature Microbiology

The bacterial enhancer-dependent RNA polymerase

(2016) N. Zhang et al.   BIOCHEMICAL JOURNAL

Structure and function of bacterial H-NS protein

(2016) D. C. Grainger   BIOCHEMICAL SOCIETY TRANSACTIONS

Replication fork passage drives asymmetric dynamics of a critical nucleoid‐associated protein in Caulobacter

(2016) Rodrigo Arias‐Cartin et al.   EMBO JOURNAL

Transcription rate and transcript length drive formation of chromosomal interaction domain boundaries

(2016) Tung BK Le et al.   EMBO JOURNAL

SMC complexes: from DNA to chromosomes

(2016) Frank Uhlmann   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture

(2016) Caelin Cubeñas-Potts et al.   NUCLEIC ACIDS RESEARCH

DNA Sequence Determinants Controlling Affinity, Stability and Shape of DNA Complexes Bound by the Nucleoid Protein Fis

(2016) Stephen P. Hancock et al.   PLoS One

Cell cycle progression inCaulobacterrequires a nucleoid-associated protein with high AT sequence recognition

(2016) Dante P. Ricci et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MatP regulates the coordinated action of topoisomerase IV and MukBEF in chromosome segregation

(2016) Sophie Nolivos et al.   Nature Communications

Genome scale patterns of supercoiling in a bacterial chromosome

(2016) Avantika Lal et al.   Nature Communications

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

The MaoP/maoS Site-Specific System Organizes the Ori Region of the E. coli Chromosome into a Macrodomain

(2016) Michèle Valens et al.   PLoS Genetics

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

(2015) Tsung-Han S. Hsieh et al.   CELL

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

(2015) Sergey V. Ulianov et al.   GENOME RESEARCH

The DNA-Binding Protein from Starved Cells (Dps) Utilizes Dual Functions To Defend Cells against Multiple Stresses

(2015) Vlad O. Karas et al.   JOURNAL OF BACTERIOLOGY

Condensin- and Replication-Mediated Bacterial Chromosome Folding and Origin Condensation Revealed by Hi-C and Super-resolution Imaging

(2015) Martial Marbouty et al.   MOLECULAR CELL

The quantitative and condition-dependent Escherichia coli proteome

(2015) Alexander Schmidt et al.   NATURE BIOTECHNOLOGY

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Kite Proteins: a Superfamily of SMC/Kleisin Partners Conserved Across Bacteria, Archaea, and Eukaryotes

(2015) Jan J. Palecek et al.   STRUCTURE

Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

(2015) Matteo Vietri Rudan et al.   Cell Reports

The Molecular Basis for Control of ETEC Enterotoxin Expression in Response to Environment and Host

(2015) James R. J. Haycocks et al.   PLoS Pathogens

A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT

(2015) Pengfei Ding et al.   PLoS Pathogens

Bridged filaments of histone-like nucleoid structuring protein pause RNA polymerase and aid termination in bacteria

(2015) Matthew V Kotlajich et al.   eLife

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

The SMC Condensin Complex Is Required for Origin Segregation in Bacillus subtilis

(2014) Xindan Wang et al.   CURRENT BIOLOGY

Widespread suppression of intragenic transcription initiation by H-NS

(2014) S. S. Singh et al.   GENES & DEVELOPMENT

Direct regulation of topoisomerase activity by a nucleoid-associated protein

(2014) Soumitra Ghosh et al.   NUCLEIC ACIDS RESEARCH

Structural, Kinetic and Proteomic Characterization of Acetyl Phosphate-Dependent Bacterial Protein Acetylation

(2014) Misty L. Kuhn et al.   PLoS One

The SMC Complex MukBEF Recruits Topoisomerase IV to the Origin of Replication Region in Live Escherichia coli

(2014) E. Nicolas et al.   mBio

Structural Insights into the Regulation of Foreign Genes inSalmonellaby the Hha/H-NS Complex

(2013) Sabrina S. Ali et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Acetyl-Phosphate Is a Critical Determinant of Lysine Acetylation in E. coli

(2013) Brian T. Weinert et al.   MOLECULAR CELL

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

Organization and segregation of bacterial chromosomes

(2013) Xindan Wang et al.   NATURE REVIEWS GENETICS

High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome

(2013) T. B. K. Le et al.   SCIENCE

Genome-scale Analysis of Escherichia coli FNR Reveals Complex Features of Transcription Factor Binding

(2013) Kevin S. Myers et al.   PLoS Genetics

H-NS Can Facilitate Specific DNA-binding by RNA Polymerase in AT-rich Gene Regulatory Regions

(2013) Shivani S. Singh et al.   PLoS Genetics

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

A MatP-divisome interaction coordinates chromosome segregation with cell division inE. coli

(2012) Olivier Espéli et al.   EMBO JOURNAL

The Escherichia coli SMC Complex, MukBEF, Shapes Nucleoid Organization Independently of DNA Replication

(2012) A. Badrinarayanan et al.   JOURNAL OF BACTERIOLOGY

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

Gene silencing by H-NS from distal DNA site

(2012) Minsang Shin et al.   MOLECULAR MICROBIOLOGY

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Self-organization of domain structures by DNA-loop-extruding enzymes

(2012) E. Alipour et al.   NUCLEIC ACIDS RESEARCH

In Vivo Architecture and Action of Bacterial Structural Maintenance of Chromosome Proteins

(2012) A. Badrinarayanan et al.   SCIENCE

Rates of Gyrase Supercoiling and Transcription Elongation Control Supercoil Density in a Bacterial Chromosome

(2012) Nikolay Rovinskiy et al.   PLoS Genetics

Long-Range Chromosome Organization in E. coli: A Site-Specific System Isolates the Ter Macrodomain

(2012) Axel Thiel et al.   PLoS Genetics

Nucleoid-associated protein HU controls three regulons that coordinate virulence, response to stress and general physiology in Salmonella enterica serovar Typhimurium

(2011) M. W. Mangan et al.   MICROBIOLOGY-SGM

The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation

(2011) Mark A. Umbarger et al.   MOLECULAR CELL

A new family of bacterial condensins

(2011) Zoya M. Petrushenko et al.   MOLECULAR MICROBIOLOGY

SMC is recruited to oriC by ParB and promotes chromosome segregation in Streptococcus pneumoniae

(2011) Anita Minnen et al.   MOLECULAR MICROBIOLOGY

An SMC ATPase mutant disrupts chromosome segregation in Caulobacter

(2011) Monica A. Schwartz et al.   MOLECULAR MICROBIOLOGY

Condensin structures chromosomal DNA through topological links

(2011) Sara Cuylen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Prokaryotic ParA–ParB–parS system links bacterial chromosome segregation with the cell cycle

(2011) Jolanta Mierzejewska et al.   PLASMID

Nucleoid occlusion factor SlmA is a DNA-activated FtsZ polymerization antagonist

(2011) Hongbaek Cho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Chromosomal Macrodomains and Associated Proteins: Implications for DNA Organization and Replication in Gram Negative Bacteria

(2011) Remus T. Dame et al.   PLoS Genetics

Molecular mechanism by which the nucleoid occlusion factor, SlmA, keeps cytokinesis in check

(2010) Nam Ky Tonthat et al.   EMBO JOURNAL

The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

(2010) S. Stella et al.   GENES & DEVELOPMENT

Contribution of SMC (Structural Maintenance of Chromosomes) and SpoIIIE to Chromosome Segregation in Staphylococci

(2010) W. Yu et al.   JOURNAL OF BACTERIOLOGY

Dimerization and DNA-dependent aggregation of the Escherichia coli nucleoid protein and chaperone CbpA

(2010) Sarah Cosgriff et al.   MOLECULAR MICROBIOLOGY

A method for genome-wide analysis of DNA helical tension by means of psoralen–DNA photobinding

(2010) Ignacio Bermúdez et al.   NUCLEIC ACIDS RESEARCH

Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli

(2010) Christina Kahramanoglou et al.   NUCLEIC ACIDS RESEARCH

H-NS forms a superhelical protein scaffold for DNA condensation

(2010) S. T. Arold et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Physical and functional interaction between the condensin MukB and the decatenase topoisomerase IV in Escherichia coli

(2010) R. Hayama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lsr2 is a nucleoid-associated protein that targets AT-rich sequences and virulence genes in Mycobacterium tuberculosis

(2010) B. R. G. Gordon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic Distribution of SeqA Protein across the Chromosome of Escherichia coli K-12

(2010) M. A. Sanchez-Romero et al.   mBio

Bacterial Chromosome Organization and Segregation

(2010) E. Toro et al.   Cold Spring Harbor Perspectives in Biology

The Transcriptional Regulator Rok Binds A+T-Rich DNA and Is Involved in Repression of a Mobile Genetic Element in Bacillus subtilis

(2010) Wiep Klaas Smits et al.   PLoS Genetics

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

(2010) Nynke L. van Berkum et al.   Jove-Journal of Visualized Experiments

Structural Studies of a Bacterial Condensin Complex Reveal ATP-Dependent Disruption of Intersubunit Interactions

(2009) Jae-Sung Woo et al.   CELL

Recruitment of Condensin to Replication Origin Regions by ParB/SpoOJ Promotes Chromosome Segregation in B. subtilis

(2009) Stephan Gruber et al.   CELL

Recruitment of SMC by ParB-parS Organizes the Origin Region and Promotes Efficient Chromosome Segregation

(2009) Nora L. Sullivan et al.   CELL

Noc protein binds to specific DNA sequences to coordinate cell division with chromosome segregation

(2009) Ling Juan Wu et al.   EMBO JOURNAL

Differential Binding Profiles of StpA in Wild-Type and hns Mutant Cells: a Comparative Analysis of Cooperative Partners by Chromatin Immunoprecipitation-Microarray Analysis

(2009) E. Uyar et al.   JOURNAL OF BACTERIOLOGY

DNA supercoiling and its role in DNA decatenation and unknotting

(2009) Guillaume Witz et al.   NUCLEIC ACIDS RESEARCH

The HU Regulon Is Composed of Genes Responding to Anaerobiosis, Acid Stress, High Osmolarity and SOS Induction

(2009) Jacques Oberto et al.   PLoS One

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

The MatP/matS Site-Specific System Organizes the Terminus Region of the E. coli Chromosome into a Macrodomain

(2008) Romain Mercier et al.   CELL

The Major Architects of Chromatin: Architectural Proteins in Bacteria, Archaea and Eukaryotes

(2008) Martijn S. Luijsterburg et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

ATP-Induced Shrinkage of DNA with MukB Protein and the MukBEF Complex of Escherichia coli

(2008) N. Chen et al.   JOURNAL OF BACTERIOLOGY

A handcuff model for the cohesin complex

(2008) Nenggang Zhang et al.   JOURNAL OF CELL BIOLOGY

DNA dynamics vary according to macrodomain topography in theE. colichromosome

(2008) Olivier Espeli et al.   MOLECULAR MICROBIOLOGY

Caulobacter requires a dedicated mechanism to initiate chromosome segregation

(2008) E. Toro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA