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

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What this work says

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

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Stably maintained microdomain of localized unrestrained supercoiling at a Drosophila heat shock gene locus.

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Chromatin transitions during activation and repression of galactose‐regulated genes in yeast.

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Varying levels of positive and negative supercoiling differently affect the efficiency with which topoisomerase II catenates and decatenates DNA11Edited by J. Karn

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Long-range silencing and position effects at telomeres and centromeres: parallels and differences

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Electron microscopic visualization of the folded chromosome of Escherichia coli

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Structure of in-vivo transcribing chromatin as studied in simian virus 40 minichromosomes

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Conformational and thermodynamic properties of supercoiled DNA

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DNA structural alterations in the SV40 enhancer region are retained in vivo

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[18] Analysis of DNA structure in vivo using psoralen photobinding: Measurement of supercoiling, topological domains, and DNA-protein interactions

inferredcites →https://doi.org/10.1016/0092-8674(77)90080-0openalex-snapshot

Cross-linking of DNA with trimethylpsoralen is a probe for chromatin structure

inferredcites →https://doi.org/10.1016/0092-8674(80)90440-7openalex-snapshot

Torsional tension in the DNA double helix measured with trimethylpsoralen in living E. coli cells: Analogous measurements in insect and human cells

inferredcites →https://doi.org/10.1016/0092-8674(88)90140-7openalex-snapshot

Supercoiling of intracellular DNA can occur in eukaryotic cells

inferredcites →https://doi.org/10.1016/0092-8674(89)90574-6openalex-snapshot

DNA supercoiling and prokaryotic transcription

inferredcites →https://doi.org/10.1016/0092-8674(89)90790-3openalex-snapshot

Two different chromatin structures coexist in ribosomal RNA genes throughout the cell cycle

inferredcites →https://doi.org/10.1016/j.cell.2004.05.023openalex-snapshot

Mapping Global Histone Acetylation Patterns to Gene Expression

inferredcites →https://doi.org/10.1016/j.cell.2005.06.026openalex-snapshot

Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast

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Histone Variant H2A.Z Marks the 5′ Ends of Both Active and Inactive Genes in Euchromatin

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Chromatin state maps: new technologies, new insights

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Genomic Run-On Evaluates Transcription Rates for All Yeast Genes and Identifies Gene Regulatory Mechanisms

inferredcites →https://doi.org/10.1016/j.molcel.2006.05.014openalex-snapshot

Chromosomal Association of the Smc5/6 Complex Reveals that It Functions in Differently Regulated Pathways

inferredcites →https://doi.org/10.1016/j.molcel.2006.10.023openalex-snapshot

Genome-Wide Distribution of Yeast RNA Polymerase II and Its Control by Sen1 Helicase

inferredcites →https://doi.org/10.1016/j.sbi.2005.03.006openalex-snapshot

Nucleosome and chromatin fiber dynamics

inferredcites →https://doi.org/10.1016/s0006-3495(96)79826-0openalex-snapshot

Effect of supercoiling on the juxtaposition and relative orientation of DNA sites

inferredcites →https://doi.org/10.1016/s0092-8674(00)81958-3openalex-snapshot

Twenty-Five Years of the Nucleosome, Fundamental Particle of the Eukaryote Chromosome

inferredcites →https://doi.org/10.1021/bi00008a029openalex-snapshot

Specialized chromatin structure domain boundary elements flanking a Drosophila heat shock gene locus are under torsional strain in vivo

inferredcites →https://doi.org/10.1021/bi00321a002openalex-snapshot

Interstrand psoralen crosslinks do not introduce appreciable bends in DNA

inferredcites →https://doi.org/10.1021/bi962396qopenalex-snapshot

Measurement of Unrestrained Negative Supercoiling and Topological Domain Size in Living Human Cells

inferredcites →https://doi.org/10.1038/emboj.2009.391openalex-snapshot

Positional dependence of transcriptional inhibition by DNA torsional stress in yeast chromosomes

inferredcites →https://doi.org/10.1038/nrg1921openalex-snapshot

From artificial evolution to computational evolution: a research agenda

inferredcites →https://doi.org/10.1038/nrg1925openalex-snapshot

Insulators: exploiting transcriptional and epigenetic mechanisms

inferredcites →https://doi.org/10.1038/nrg2270openalex-snapshot

Genome-wide approaches to studying chromatin modifications

inferredcites →https://doi.org/10.1038/sj.emboj.7601142openalex-snapshot

Topoisomerase II, not topoisomerase I, is the proficient relaxase of nucleosomal DNA

inferredcites →https://doi.org/10.1073/pnas.0806337105openalex-snapshot

The Saccharomyces cerevisiae linker histone Hho1p is essential for chromatin compaction in stationary phase and is displaced by transcription

inferredcites →https://doi.org/10.1073/pnas.78.1.224openalex-snapshot

Chromosomes in living Escherichia coli cells are segregated into domains of supercoiling.

inferredcites →https://doi.org/10.1073/pnas.89.13.6055openalex-snapshot

Localized torsional tension in the DNA of human cells.

inferredcites →https://doi.org/10.1093/nar/10.6.2043openalex-snapshot

New procedure using a psoralen derivative for analysis of nucleosome associated DNA sequences in chromatin of living cells

inferredcites →https://doi.org/10.1093/nar/20.17.4671openalex-snapshot

A hit-and-run system for targeted genetic manipulations in yeast

inferredcites →https://doi.org/10.1093/nar/23.10.1782openalex-snapshot

Presence of negative torsional tension in the promoter region of the transcriptionally poised dihydrofolate reductase gene in vivo

inferredcites →https://doi.org/10.1093/nar/26.6.1544openalex-snapshot

In vivo mapping of nucleosomes using psoralen-DNA crosslinking and primer extension

inferredcites →https://doi.org/10.1093/nar/gnh107openalex-snapshot

Transcriptionally competent chromatin assembled with exogenous histones in a yeast whole cell extract

inferredcites →https://doi.org/10.1101/gad.1207504openalex-snapshot

Topological domain structure of the Escherichia coli chromosome

inferredcites →https://doi.org/10.1101/gad.432107openalex-snapshot

Top1- and Top2-mediated topological transitions at replication forks ensure fork progression and stability and prevent DNA damage checkpoint activation

inferredcites →https://doi.org/10.1101/gad.6.7.1332openalex-snapshot

Topoisomerases and yeast rRNA transcription: negative supercoiling stimulates initiation and topoisomerase activity is required for elongation.

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/10.1126/science.1112178openalex-snapshot

Genome-Scale Identification of Nucleosome Positions in S. cerevisiae

inferredcites →https://doi.org/10.1126/science.1140748openalex-snapshot

Divergence of Transcription Factor Binding Sites Across Related Yeast Species

inferredcites →https://doi.org/10.1128/mcb.17.5.2825openalex-snapshot

Template Topology and Transcription: Chromatin Templates Relaxed by Localized Linearization Are Transcriptionally Active in Yeast

inferredcites →https://doi.org/10.1139/o05-141openalex-snapshot

Psoralen photocrosslinking, a tool to study the chromatin structure of RNA polymerase I - transcribed ribosomal genes

inferredcites →https://doi.org/10.1146/annurev.bb.23.060194.003141openalex-snapshot

Conformational and Thermodynamic Properties of Supercoiled DNA

inferredcites →https://doi.org/10.1146/annurev.bi.54.070185.005443openalex-snapshot

PSORALENS AS PHOTOACTIVE PROBES OF NUCLEIC ACID STRUCTURE AND FUNCTION: ORGANIC CHEMISTRY, PHOTOCHEMISTRY, AND BIOCHEMISTRY

inferredcites →https://doi.org/10.1146/annurev.biochem.70.1.369openalex-snapshot

DNA Topoisomerases: Structure, Function, and Mechanism

inferredcites →https://doi.org/10.1146/annurev.biophys.23.1.609openalex-snapshot

Conformational and Thermodynamic Properties of Supercoiled DNA

inferredcites →https://doi.org/10.1146/annurev.ge.19.120185.002413openalex-snapshot

SELECTED TOPICS IN CHROMATIN STRUCTURE

inferredcites →https://doi.org/10.1146/annurev.genet.39.073003.113546openalex-snapshot

Chromatin Insulators

inferredcites →https://doi.org/10.1186/gb-2009-10-10-r109openalex-snapshot

A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genomes

inferredcites →https://doi.org/10.1242/jcs.01225openalex-snapshot

Visualization of unconstrained negative supercoils of DNA on polytene chromosomes ofDrosophila

What points at this work

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

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inferred← citeshttps://doi.org/10.1002/marc.202000017openalex-snapshot

Effects of Psoralen on Histone‐DNA Interactions Studied by Using Atomic Force Microscopy

inferred← citeshttps://doi.org/10.1002/pro.4171openalex-snapshot

The regulation of DNA supercoiling across evolution

inferred← citeshttps://doi.org/10.1007/978-1-0716-3930-6_8openalex-snapshot

In Vivo Genomic Supercoiling Mapping Using Psora-seq

inferred← citeshttps://doi.org/10.1007/978-1-4939-7459-7_7openalex-snapshot

The Use of Psoralen Photobinding to Study Transcription-Induced Supercoiling

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Centromere Structure and Function

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Coordinating Replication with Transcription

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The torsional state of DNA within the chromosome

inferred← citeshttps://doi.org/10.1007/s12551-016-0210-1openalex-snapshot

Effects of DNA supercoiling on chromatin architecture

inferred← citeshttps://doi.org/10.1007/s12551-016-0215-9openalex-snapshot

DNA supercoiling during transcription

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Controlling gene expression by DNA mechanics: emerging insights and challenges

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Effects of DNA supercoiling on chromatin architecture

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Controlling gene expression by DNA mechanics: emerging insights and challenges

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The importance of being supercoiled: How DNA mechanics regulate dynamic processes

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Topoisomerase IIα represses transcription by enforcing promoter-proximal pausing

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HNF1β bookmarking involves Topoisomerase 1 activation and DNA topology relaxation in mitotic chromatin

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Profiling DNA supercoiling domains in vivo

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Supercoiling in DNA and chromatin

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Pack, unpack, bend, twist, pull, push: the physical side of gene expression

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Identification of new scavengers for hydroxyl radicals and superoxide dismutase by utilising ultraviolet A photoreaction of 8-methoxypsoralen and a variety of mutants of Escherichia coli: Implications on certain diseases of DNA repair deficiency

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Transcription-mediated supercoiling regulates genome folding and loop formation

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Topoisomerase 1 activity during mitotic transcription favors the transition from mitosis to G1

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DNA Intercalated Psoralen Undergoes Efficient Photoinduced Electron Transfer

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Understanding the Molecular Mechanisms of the CRISPR Toolbox Using Single Molecule Approaches

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Centromeric DNA replication reconstitution reveals DNA loops and ATR checkpoint suppression

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Genome scale patterns of supercoiling in a bacterial chromosome

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High-resolution digital profiling of the epigenome

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Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

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Transcription-dependent dynamic supercoiling is a short-range genomic force

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The helix turns at 60: writhing free in chromosomes

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Transcription-generated torsional stress destabilizes nucleosomes

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Supercoiling and looping promote DNA base accessibility and coordination among distant sites

inferred← citeshttps://doi.org/10.1038/s41467-025-65567-5openalex-snapshot

Torsion is a dynamic regulator of DNA replication stalling and reactivation

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

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Negative supercoil at gene boundaries modulates gene topology

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Topoisomerase-modulated genome-wide DNA supercoiling domains colocalize with nuclear compartments and regulate human gene expression

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The nucleolar shell provides anchoring sites for DNA untwisting

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Ufd2p promotes efficient crossover formation by destabilizing Top2p during meiosis

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Replication, checkpoint suppression and structure of centromeric DNA

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Mechanical determinants of chromatin topology and gene expression

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Investigating DNA supercoiling in eukaryotic genomes

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Influence of DNA topology on the photoreactions of various psoralen derivatives with duplex DNAs

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Weak interactions in higher-order chromatin organization

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A rapid method to visualize human mitochondrial DNA replication through rotary shadowing and transmission electron microscopy

inferred← citeshttps://doi.org/10.1093/nar/gkac244openalex-snapshot

Psoralen mapping reveals a bacterial genome supercoiling landscape dominated by transcription

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Negative supercoils regulate meiotic crossover patterns in budding yeast

inferred← citeshttps://doi.org/10.1093/nar/gkad1055openalex-snapshot

Supercoiling-dependent DNA binding: quantitative modeling and applications to bulk and single-molecule experiments

inferred← citeshttps://doi.org/10.1093/nar/gkae320openalex-snapshot

Controlling genome topology with sequences that trigger post-replication gap formation during replisome passage: the E. coli RRS elements

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Coordinated control of genome–nuclear lamina interactions by topoisomerase 2B and lamin B receptor

inferred← citeshttps://doi.org/10.1093/nar/gkag553openalex-snapshot

RNAPII and DNA supercoiling regulate cohesin engagement in neurons

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Transcription-induced supercoiling as the driving force of chromatin loop extrusion during formation of TADs in interphase chromosomes

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Transcription-induced supercoiling explains formation of self-interacting chromatin domains in S. pombe

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Are TADs supercoiled?

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Transcriptional supercoiling boosts topoisomerase II-mediated knotting of intracellular DNA

inferred← citeshttps://doi.org/10.1101/2020.05.12.091058openalex-snapshot

Control of RNA Polymerase II Promoter-Proximal Pausing by DNA Supercoiling

inferred← citeshttps://doi.org/10.1101/2024.10.11.617876openalex-snapshot

High-Resolution Genome-Wide Maps Reveal Widespread Presence of Torsional Insulation

inferred← citeshttps://doi.org/10.1101/2024.10.14.618193openalex-snapshot

Spatial organization of supercoil dynamics during DNA replication

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Transcription-mediated replication hindrance: a major driver of genome instability

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The physics of epigenetics

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DNA topology in chromatin is defined by nucleosome spacing

inferred← citeshttps://doi.org/10.1126/sciadv.adg3257openalex-snapshot

Aclarubicin stimulates RNA polymerase II elongation at closely spaced divergent promoters

inferred← citeshttps://doi.org/10.1126/sciadv.adu6524openalex-snapshot

TOP2B modulates DNA supercoiling and chromatin contacts during transcriptional induction

inferred← citeshttps://doi.org/10.1126/sciadv.adx4089openalex-snapshot

Real-time imaging of rotation during synthesis by the replisome

inferred← citeshttps://doi.org/10.1126/science.adv0134openalex-snapshot

Chromatin buffers torsional stress during transcription

inferred← citeshttps://doi.org/10.1128/ecosalplus.esp-0001-2022openalex-snapshot

Spatio-temporal organization of the E. coli chromosome from base to cellular length scales

inferred← citeshttps://doi.org/10.1128/mcb.01066-10openalex-snapshot

A Simple Topological Filter in a Eukaryotic Transposon as a Mechanism To Suppress Genome Instability

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Torque Measurement at the Single-Molecule Level

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Surveying the epigenomic landscape, one base at a time

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Surveying the epigenomic landscape, one base at a time

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How Do Thermophiles Organize Their Genomes?

inferred← citeshttps://doi.org/10.15252/embj.201488091openalex-snapshot

Chromatin regulates DNA torsional energy via topoisomerase II‐mediated relaxation of positive supercoils

inferred← citeshttps://doi.org/10.3109/10409238.2011.614593openalex-snapshot

The SMC complexes, DNA and chromosome topology: right or knot?

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The Causes and Consequences of Topological Stress during DNA Replication

inferred← citeshttps://doi.org/10.3390/ijms27031552openalex-snapshot

The Roles of Topoisomerases in Transcriptional Regulation

inferred← citeshttps://doi.org/10.4137/grsb.s13756openalex-snapshot

DNA Conformational Transitions Induced by Supercoiling Control Transcription in Chromatin

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DNA torsion as a feedback mediator of transcription and chromatin dynamics

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Transcriptional inhibition by DNA torsional stress

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Dynamic Supercoiling Sponsors Transcription Amplification by MYC

inferred← citeshttps://doi.org/10.64898/2026.02.12.705511openalex-snapshot

DNA supercoiling links transcription and chromatin architecture during human stem cell differentiation

inferred← citeshttps://doi.org/10.64898/2026.08.24.746546openalex-snapshot

CpG islands act as topological sinks for transcription-induced DNA supercoiling

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In vivo study of DNA topology in hyperthermophilic archaeon Thermococcus kodakarensis

inferred← citeshttps://doi.org/10.7554/elife.105675openalex-snapshot

High-Resolution Genome-Wide Maps Reveal Widespread Presence of Torsional Insulation

inferred← citeshttps://doi.org/10.7554/elife.105675.1openalex-snapshot

High-Resolution Genome-Wide Maps Reveal Widespread Presence of Torsional Insulation

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The plusses and minuses of DNA torsion

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High-resolution, genome-wide mapping of positive supercoiling in chromosomes

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