Transcription–replication interactions reveal bacterial genome regulation

No abstract is available for this paper.

• Publication year

  2024

• Venue

  Nature

• Publication date

  2024-01-24

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1038/s41586-023-06974-wPMID 38267581PMCID PMC10923101
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Droplet-based high-throughput single microbe RNA sequencing by smRandom-seq

  2023cited by this paper
• Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular states.

  2023cited by this paper
• Improved Bacterial Single-Cell RNA-Seq through Automated MATQ-Seq and Cas9-Based Removal of rRNA Reads

  2022cited by this paper
• Ushering in a new era of single-cell transcriptomics in bacteria

  2022cited by this paper
• Single-Cell RNA Sequencing Elucidates the Structure and Organization of Microbial Communities

  2021cited by this paper
• The EcoCyc Database in 2021

  2021cited by this paper
• RNA velocity—current challenges and future perspectives

  2021cited by this paper
• The two-Cys-type TetR repressor GbaA confers resistance under disulfide and electrophile stress in Staphylococcus aureus

  2021cited by this paper
• Quantitative analysis of asynchronous transcription-translation and transcription processivity in Bacillus subtilis under various growth conditions

  2021cited by this paper
• Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria

  2021cited by this paper
• Staphylococcus aureus glucose-induced biofilm accessory protein A (GbaA) is a monothiol-dependent electrophile sensor.

  2020cited by this paper
• Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria

  2020cited by this paper
• Cell cycle-associated expression patterns predict gene function in mycobacteria

  2020cited by this paper
• Current best practices in single‐cell RNA‐seq analysis: a tutorial

  2019cited by this paper
• Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology

  2019cited by this paper
• Disruption of transcription–translation coordination in Escherichia coli leads to premature transcriptional termination

  2019cited by this paper
• Measuring Transcription at a Single Gene Copy Reveals Hidden Drivers of Bacterial Individuality

  2019influential reference
• The BioCyc collection of microbial genomes and metabolic pathways

  2019cited by this paper
• Revisiting Replication‐Induced Transcription in Escherichia coli

  2019cited by this paper
• Microbial single-cell RNA sequencing by split-pool barcoding

  2019cited by this paper
• The synchronization manifesto: a critique of whole‐culture synchronization

  2019cited by this paper
• Prokaryotic Single-Cell RNA Sequencing by In Situ Combinatorial Indexing

  2019influential reference
• SciPy 1.0: fundamental algorithms for scientific computing in Python

  2019cited by this paper
• Origins Left, Right, and Centre: Increasing the Number of Initiation Sites in the Escherichia coli Chromosome

  2018cited by this paper
• Homeostasis of protein and mRNA concentrations in growing cells

  2018cited by this paper
• RNA velocity of single cells

  2018cited by this paper
• Deep Generative Modeling for Single-cell Transcriptomics

  2018cited by this paper
• SCANPY: large-scale single-cell gene expression data analysis

  2018cited by this paper
• AureoWiki ̵ The repository of the Staphylococcus aureus research and annotation community.

  2017cited by this paper
• Fundamental principles in bacterial physiology—history, recent progress, and the future with focus on cell size control: a review

  2017cited by this paper
• Developmental constraints shape the evolution of the nematode mid-developmental transition

  2017cited by this paper
• Hard-Wired Control of Bacterial Processes by Chromosomal Gene Location

  2016cited by this paper
• PHASTER: a better, faster version of the PHAST phage search tool

  2016cited by this paper
• The mid-developmental transition and the evolution of animal body plans

  2016cited by this paper
• Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

  2015cited by this paper
• The Global Regulatory Architecture of Transcription during the Caulobacter Cell Cycle

  2015cited by this paper
• Shaping the landscape of the Escherichia coli chromosome: replication-transcription encounters in cells with an ectopic replication origin

  2015cited by this paper
• Effects of DNA replication on mRNA noise

  2015cited by this paper
• Chromosomal Arrangement of Phosphorelay Genes Couples Sporulation and DNA Replication.

  2015cited by this paper
• Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

  2014cited by this paper
• Single-copy vectors for integration at the SaPI1 attachment site for Staphylococcus aureus.

  2014cited by this paper
• Global analysis of cell cycle gene expression of the legume symbiont Sinorhizobium meliloti

  2014cited by this paper
• Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution

  2013cited by this paper
• Tutorial

  2013cited by this paper
• A single‐molecule approach to DNA replication in Escherichia coli cells demonstrated that DNA polymerase III is a major determinant of fork speed

  2013cited by this paper
• Measuring mRNA copy number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization

  2013cited by this paper
• Ultrasensitivity of the Bacillus subtilis sporulation decision

  2012cited by this paper
• Staphylococcus aureus regulates the expression and production of the staphylococcal superantigen‐like secreted proteins in a Rot‐dependent manner

  2011cited by this paper
• Replication and segregation of an Escherichia coli chromosome with two replication origins

  2011cited by this paper
• Cooperation Between Translating Ribosomes and RNA Polymerase in Transcription Elongation

  2010cited by this paper
• Modulation of Chemical Composition and Other Parameters of the Cell at Different Exponential Growth Rates

  2008cited by this paper
• The replisome uses mRNA as a primer after colliding with RNA polymerase

  2008cited by this paper
• Optimal gene partition into operons correlates with gene functional order

  2006cited by this paper
• Modeling network dynamics

  2003cited by this paper
• Precise determinations of C and D periods by flow cytometry in Escherichia coli K-12 and B/r.

  2003cited by this paper
• Negative autoregulation speeds the response times of transcription networks.

  2002cited by this paper
• Transcription of the Escherichia coli dcw cluster: evidence for distal upstream transcripts being involved in the expression of the downstream ftsZ gene.

  2001cited by this paper
• Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays.

  2000influential reference
• Global analysis of the genetic network controlling a bacterial cell cycle.

  2000cited by this paper
• Bacillus subtilis Cell Cycle as Studied by Fluorescence Microscopy: Constancy of Cell Length at Initiation of DNA Replication and Evidence for Active Nucleoid Partitioning

  1998cited by this paper
• Cell division genes ftsQAZ in Escherichia coli require distant cis‐acting signals upstream of ddlB for full expression

  1998cited by this paper
• Does replication-induced transcription regulate synthesis of the myriad low copy number proteins of Escherichia coli?

  1995cited by this paper
• Relationship between ftsZ gene expression and chromosome replication in Escherichia coli

  1994cited by this paper
• Transcription of ftsZ oscillates during the cell cycle of Escherichia coli.

  1993cited by this paper
• Correlation of gene transcription with the time of initiation of chromosome replication in Escherichia coli

  1993cited by this paper
• E. coli oriC and the dnaA gene promoter are sequestered from dam methyltransferase following the passage of the chromosomal replication fork.

  1990cited by this paper
• The Escherichia coli cell cycle.

  1990cited by this paper
• Organization of genes in the ftsA-envA region of the Escherichia coli genetic map and identification of a new fts locus (ftsZ)

  1980cited by this paper
• Chromosome Replication and the Division Cycle of Escherichia coli B/r

  1971cited by this paper
• Chromosome replication and the division cycle of Escherichia coli B/r.

  1968cited by this paper
• Synthesis of Deoxyribonucleic Acid during the Division Cycle of Bacteria

  1959cited by this paper
• The transition between different physiological states during balanced growth of Salmonella typhimurium.

  1958cited by this paper

• Unveiling hidden variables in stressed bacteria.

  2026cites this paper
• Single-phage profiling illuminates viral individuality during cell fate determination

  2026cites this paper
• Resolving spatiotemporal dynamics in bacterial multicellular populations: approaches and challenges

  2025cites this paper
• 60 Years of Studies into the Initiation of Chromosome Replication in Bacteria

  2025cites this paper
• Mechanistic basis for non-exponential bacterial growth

  2025cites this paper
• Most bacterial gene families are biased toward specific chromosomal positions.

  2025cites this paper
• Extrusion-modulated DnaA activity oscillations coordinate DNA replication with biomass growth

  2025cites this paper
• The type IV secretion system of Patescibacteria is homologous to the bacterial monoderm conjugation machinery

  2025cites this paper
• Genome-Driven Functional Validation of Bacillus amyloliquefaciens Strain MEPW12: A Multifunctional Endophyte for Sustainable Sweet Potato Cultivation

  2025cites this paper
• Nanozyme-based synergistic therapy: FeCo-NC for effective bacterial eradication and wound tissue regeneration.

  2025cites this paper
• Scalable single-cell metagenomic analysis with Bascet and Zorn

  2025cites this paper
• Nonequilibrium polysome dynamics promote chromosome segregation and its coupling to cell growth in Escherichia coli

  2025cites this paper
• Gene expression cycles drive non-exponential bacterial growth.

  2025cites this paper
• An exciting future for microbial molecular biology and physiology

  2025cites this paper
• Transcriptional landscape of the cell cycle in a model thermoacidophilic archaeon reveals similarities to eukaryotes

  2025cites this paper
• ExcludonFinder: mapping transcriptional overlaps between neighboring genes

  2025cites this paper
• Dissecting microbial communities with single-cell transcriptome analysis.

  2025cites this paper
• Bacterial Systematic Genetics and Integrated Multi-Omics: Beyond Static Genomics Toward Predictive Models

  2025cites this paper
• Microbial function in food fermentations: Current research and future directions

  2025cites this paper
• Prokaryotic homeostasis – a solution to thrive and survive

  2025cites this paper
• Microbial single-cell omics in situ

  2025cites this paper
• Nonequilibrium polysome dynamics promote chromosome segregation and its coupling to cell growth in Escherichia coli

  2025cites this paper
• Highly multiplexed spatial transcriptomics in bacteria.

  2025cites this paper
• Emerging tools for uncovering genetic and transcriptomic heterogeneities in bacteria

  2024cites this paper
• Highly Multiplexed Spatial Transcriptomics in Bacteria

  2024cites this paper
• Bacterial single-cell RNA sequencing captures biofilm transcriptional heterogeneity and differential responses to immune pressure

  2024cites this paper
• Transcriptional and molecular simulation analysis of the response mechanism of anammox bacteria to 3,4-dimethylpyrazole phosphate stress.

  2024cites this paper
• A TRIP to understand gene regulation

  2024cites this paper
• Direct single-cell observation of a key Escherichia coli cell-cycle oscillator

  2024cites this paper
• Genetic properties underlying transcriptional variability across different perturbations

  2024cites this paper
• 2024: A “nucleoid space” odyssey featuring H‐NS

  2024cites this paper
• Bioinspired peptide/polyamino acid assemblies as quorum sensing inhibitors for the treatment of bacterial infections.

  2024cites this paper
• The impact of antibiotic induction on virulence and antibiotic resistance in Klebsiella pneumoniae: a comparative study of CSKP and CRKP strains

  2024cites this paper
• A new selective force driving metabolic gene clustering

  2024cites this paper
• DNA as a Double-Coding Device for Information Conversion and Organization of a Self-Referential Unity

  2024cites this paper
• Bacterial single-cell RNA sequencing captures biofilm transcriptional heterogeneity and differential responses to immune pressure

  2024cites this paper
• Clues to transcription/replication collision‐induced DNA damage: it was RNAP, in the chromosome, with the fork

  2024cites this paper
• mSphere of Influence: How the single cell contributes to the collective

  2024cites this paper
• Dynamics of chromosome organization in a minimal bacterial cell

  2023cites this paper
• Gene expression in growing cells: A biophysical primer

  2023cites this paper