ArticleNucleic acids research2010
A method for genome-wide analysis of DNA helical tension by means of psoralen-DNA photobinding.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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65 citing papers in PubMed, 92 citations in OpenAlex.
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- The Roles of Topoisomerases in Transcriptional Regulation.International journal of molecular sciences · 2026Review
- Dynamic Supercoiling Sponsors Transcription Amplification by MYC.bioRxiv : the preprint server for biology · 2026Article
- Real-time imaging of rotation during synthesis by the replisome.Science advances · 2026Article
- TOP2B modulates DNA supercoiling and chromatin contacts during transcriptional induction.Science advances · 2025Article
- Torsion is a dynamic regulator of DNA replication stalling and reactivation.Nature communications · 2025Article
- Coordinated control of genome-nuclear lamina interactions by topoisomerase 2B and lamin B receptor.Nucleic acids research · 2025Article
- The plusses and minuses of DNA torsion.eLife · 2025Article
- High-Resolution Genome-Wide Maps Reveal Widespread Presence of Torsional Insulation.bioRxiv : the preprint server for biology · 2025Article
- Topoisomerase-modulated genome-wide DNA supercoiling domains colocalize with nuclear compartments and regulate human gene expression.Nature structural & molecular biology · 2025Article
- Spatio-temporal organization of theEcoSal Plus · 2024Review
- Controlling genome topology with sequences that trigger post-replication gap formation during replisome passage: the E. coli RRS elements.Nucleic acids research · 2024Article
- Controlling Genome Topology with Sequences that Trigger Post-replication Gap Formation During Replisome Passage: ThebioRxiv : the preprint server for biology · 2024Article
- The nucleolar shell provides anchoring sites for DNA untwisting.Communications biology · 2024Article
- Supercoiling-dependent DNA binding: quantitative modeling and applications to bulk and single-molecule experiments.Nucleic acids research · 2024Article
- In Vivo Genomic Supercoiling Mapping Using Psora-seq.Methods in molecular biology (Clifton, N.J.) · 2024Article
- How Do Thermophiles Organize Their Genomes?Microbes and environments · 2024Review
- Aclarubicin stimulates RNA polymerase II elongation at closely spaced divergent promoters.Science advances · 2023Article
- Mechanical determinants of chromatin topology and gene expression.Nucleus (Austin, Tex.) · 2022Review
5 more citing papers are in PubMed but not listed here.
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4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The helical tension of chromosomal DNA is one of the epigenetic landmarks most difficult to examine experimentally. The occurrence of DNA crosslinks mediated by psoralen photobinding (PB) stands as the only suitable probe for assessing this problem. PB is affected by chromatin structure when is done to saturation; but it is mainly determined by DNA helical tension when it is done to very low hit conditions. Hence, we developed a method for genome-wide analysis of DNA helical tension based on PB. We adjusted in vitro PB conditions that discern DNA helical tension and applied them to Saccharomyces cerevisiae cells. We selected the in vivo cross-linked DNA sequences and identified them on DNA arrays. The entire procedure was robust. Comparison of PB obtained in vivo with that obtained in vitro with naked DNA revealed that numerous chromosomal regions had deviated PB values. Similar analyses in yeast topoisomerase mutants uncovered further PB alterations across specific chromosomal domains. These results suggest that distinct chromosome compartments might confine different levels of DNA helical tension in yeast. Genome-wide analysis of psoralen-DNA PB can be, therefore, a useful approach to uncover a trait of the chromosome architecture not amenable to other techniques.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.