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DNA thermodynamics shape chromosome organization and topology

https://doi.org/10.1042/bst20120334

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/j.1460-2075.1985.tb03734.xopenalex-snapshot

Negative supercoiling induces spontaneous unwinding of a bacterial promoter.

inferredcites →https://doi.org/10.1007/978-3-642-29627-7_16openalex-snapshot

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

inferredcites →https://doi.org/10.1007/s10955-011-0214-yopenalex-snapshot

Statistical Mechanics of Nucleosomes Constrained by Higher-Order Chromatin Structure

inferredcites →https://doi.org/10.1016/0092-8674(94)90343-3openalex-snapshot

A histone octamer can step around a transcribing polymerase without leaving the template

inferredcites →https://doi.org/10.1016/j.jmb.2009.02.050openalex-snapshot

A Systematic In Vitro Study of Nucleoprotein Complexes Formed by Bacterial Nucleoid-Associated Proteins Revealing Novel Types of DNA Organization

inferredcites →https://doi.org/10.1016/j.mib.2010.09.013openalex-snapshot

Effects of nucleoid-associated proteins on bacterial chromosome structure and gene expression

inferredcites →https://doi.org/10.1016/j.mib.2011.01.003openalex-snapshot

Pervasive regulation of nucleoid structure and function by nucleoid-associated proteins

inferredcites →https://doi.org/10.1016/j.molcel.2011.09.010openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.molcel.2012.07.003openalex-snapshot

A Functional Evolutionary Approach to Identify Determinants of Nucleosome Positioning: A Unifying Model for Establishing the Genome-wide Pattern

inferredcites →https://doi.org/10.1016/j.physrep.2010.10.001openalex-snapshot

Multi-scale coding of genomic information: From DNA sequence to genome structure and function

inferredcites →https://doi.org/10.1016/j.sbi.2003.12.003openalex-snapshot

IHF and HU: flexible architects of bent DNA

inferredcites →https://doi.org/10.1016/j.sbi.2009.01.004openalex-snapshot

Poly(dA:dT) tracts: major determinants of nucleosome organization

inferredcites →https://doi.org/10.1016/s0022-2836(02)00142-0openalex-snapshot

FIS Modulates the Kinetics of Successive Interactions of RNA Polymerase with the Core and Upstream Regions of the tyrT Promoter

inferredcites →https://doi.org/10.1016/s0022-2836(03)00727-7openalex-snapshot

Mechanism of Transcriptional Activation by FIS: Role of Core Promoter Structure and DNA Topology

inferredcites →https://doi.org/10.1016/s0022-2836(86)80010-9openalex-snapshot

Metaphase chromosome structure

inferredcites →https://doi.org/10.1038/304555a0openalex-snapshot

Association of an S1 nuclease-sensitive structure with short direct repeats 5′ of Drosophila heat shock genes

inferredcites →https://doi.org/10.1038/embor.2009.232openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nature11142openalex-snapshot

A map of nucleosome positions in yeast at base-pair resolution

inferredcites →https://doi.org/10.1038/newbio243161a0openalex-snapshot

Effect of DNA Conformation on Ribosomal RNA Synthesis in vitro

inferredcites →https://doi.org/10.1038/nrmicro1088openalex-snapshot

DNA supercoiling — a global transcriptional regulator for enterobacterial growth?

inferredcites →https://doi.org/10.1038/nrmicro2261openalex-snapshot

Bacterial nucleoid-associated proteins, nucleoid structure and gene expression

inferredcites →https://doi.org/10.1038/nsmb.1372openalex-snapshot

The functional response of upstream DNA to dynamic supercoiling in vivo

inferredcites →https://doi.org/10.1038/nsmb1111openalex-snapshot

Antagonistic forces that position nucleosomes in vivo

inferredcites →https://doi.org/10.1038/nsmb1233openalex-snapshot

H-NS cooperative binding to high-affinity sites in a regulatory element results in transcriptional silencing

inferredcites →https://doi.org/10.1038/sj.emboj.7601261openalex-snapshot

RNA polymerase and an activator form discrete subcomplexes in a transcription initiation complex

inferredcites →https://doi.org/10.1038/sj.embor.7400729openalex-snapshot

Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome

inferredcites →https://doi.org/10.1039/b905848fopenalex-snapshot

Stable G-quadruplexes are found outside nucleosome-bound regions

inferredcites →https://doi.org/10.1039/b909192kopenalex-snapshot

General organisational principles of the transcriptional regulation system: a tree or a circle?

inferredcites →https://doi.org/10.1042/bst20110757openalex-snapshot

DNA structure, nucleosome placement and chromatin remodelling: a perspective

inferredcites →https://doi.org/10.1046/j.1365-2958.2003.03461.xopenalex-snapshot

DNA supercoiling contributes to disconnect σS accumulation from σS‐dependent transcription in Escherichia coli

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.1104978108openalex-snapshot

The centromeric nucleosome of budding yeast is perfectly positioned and covers the entire centromere

inferredcites →https://doi.org/10.1073/pnas.1108229109openalex-snapshot

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

inferredcites →https://doi.org/10.1073/pnas.1205659109openalex-snapshot

Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy

inferredcites →https://doi.org/10.1073/pnas.84.20.7024openalex-snapshot

Supercoiling of the DNA template during transcription.

inferredcites →https://doi.org/10.1074/jbc.271.4.1998openalex-snapshot

Promoter Selectivity of Escherichia coli RNA Polymerase Eσ70 and Eσ38 Holoenzymes

inferredcites →https://doi.org/10.1074/jbc.274.8.5227openalex-snapshot

In Vitro Evolution of Preferred Topoisomerase II DNA Cleavage Sites

inferredcites →https://doi.org/10.1074/jbc.275.11.8103openalex-snapshot

Roles of Topoisomerases in Maintaining Steady-state DNA Supercoiling in Escherichia coli

inferredcites →https://doi.org/10.1088/1478-3975/8/3/035011openalex-snapshot

DNA stress and strain,in silico,in vitroandin vivo

inferredcites →https://doi.org/10.1093/nar/29.24.5107openalex-snapshot

An architectural role of the Escherichia coli chromatin protein FIS in organising DNA

inferredcites →https://doi.org/10.1093/nar/gkm712openalex-snapshot

High-affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomes

inferredcites →https://doi.org/10.1098/rsta.2011.0231openalex-snapshot

DNA information: from digital code to analogue structure

inferredcites →https://doi.org/10.1101/087969348.20.139openalex-snapshot

4 Primer on the Topology and Geometry of DNA Supercoiling

inferredcites →https://doi.org/10.1101/gr.078261.108openalex-snapshot

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

inferredcites →https://doi.org/10.1111/j.1365-2958.1996.tb02622.xopenalex-snapshot

DNA supercoiling depends on the phosphorylation potential in Escherichia coli

inferredcites →https://doi.org/10.1126/science.1128794openalex-snapshot

Selective Silencing of Foreign DNA with Low GC Content by the H-NS Protein in Salmonella

inferredcites →https://doi.org/10.1128/jb.174.24.8043-8056.1992openalex-snapshot

Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli

inferredcites →https://doi.org/10.1128/mcb.06365-11openalex-snapshot

Remodelers Organize Cellular Chromatin by Counteracting Intrinsic Histone-DNA Sequence Preferences in a Class-Specific Manner

inferredcites →https://doi.org/10.5860/choice.28-3289openalex-snapshot

DNA topology and its biological effects

What points at this work

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

inferred← citeshttps://doi.org/10.2139/ssrn.3748592openalex-extracted

inferred← citeshttps://doi.org/10.1007/978-3-319-17425-9_4openalex-snapshot

Organization of the Genetic System: Proteins as Vehicles of Distinction

inferred← citeshttps://doi.org/10.1007/s00018-013-1394-1openalex-snapshot

Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information

inferred← citeshttps://doi.org/10.1007/s12551-016-0211-0openalex-snapshot

Supercoiling biases the formation of loops involved in gene regulation

inferred← citeshttps://doi.org/10.1016/j.bpj.2013.10.011openalex-snapshot

Dynamic DNA Underpins Chromosome Dynamics

inferred← citeshttps://doi.org/10.1016/j.isci.2021.102408openalex-snapshot

DNA Sequence-Directed Cooperation between Nucleoid-Associated Proteins

inferred← citeshttps://doi.org/10.1016/j.jtbi.2017.05.033openalex-snapshot

Large-scale chromosome folding versus genomic DNA sequences: A discrete double Fourier transform technique

inferred← citeshttps://doi.org/10.1038/srep31512openalex-snapshot

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

inferred← citeshttps://doi.org/10.1039/c3mb25515hopenalex-snapshot

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

inferred← citeshttps://doi.org/10.1042/bst20130006openalex-snapshot

Topological Aspects of DNA Function and Protein Folding

inferred← citeshttps://doi.org/10.1074/jbc.m117.780239openalex-snapshot

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

inferred← citeshttps://doi.org/10.1093/femsre/fuac049openalex-snapshot

The roles of nucleoid-associated proteins and topoisomerases in chromosome structure, strand segregation, and the generation of phenotypic heterogeneity in bacteria

inferred← citeshttps://doi.org/10.1109/globalsip.2014.7032341openalex-snapshot

Relating digital information, thermodynamic stability, and classes of functional genes in E. coli

inferred← citeshttps://doi.org/10.1111/febs.13307openalex-snapshot

DNA structure and function

inferred← citeshttps://doi.org/10.1128/ecosalplus.esp-0016-2019openalex-snapshot

Chromosomal Organization and Regulation of Genetic Function in Escherichia coli Integrates the DNA Analog and Digital Information

inferred← citeshttps://doi.org/10.1128/mbio.00353-15openalex-snapshot

Chromosomal “Stress-Response” Domains Govern the Spatiotemporal Expression of the Bacterial Virulence Program

inferred← citeshttps://doi.org/10.1159/000368852openalex-snapshot

Order from the Order: How a Spatiotemporal Genetic Program Is Encoded in a 2-D Genetic Map of the Bacterial Chromosome

inferred← citeshttps://doi.org/10.1186/s13637-016-0037-xopenalex-snapshot

Relationship between digital information and thermodynamic stability in bacterial genomes

inferred← citeshttps://doi.org/10.3390/biom11070924openalex-snapshot

Composition of Transcription Machinery and Its Crosstalk with Nucleoid-Associated Proteins and Global Transcription Factors

inferred← citeshttps://doi.org/10.3390/biom12060831openalex-snapshot

Spatiotemporal Coupling of DNA Supercoiling and Genomic Sequence Organization—A Timing Chain for the Bacterial Growth Cycle?

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