ArticleScientific reports2019
DNA accessibility of chromatosomes quantified by automated image analysis of AFM data.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
11 citing papers in PubMed, 23 citations in OpenAlex.
- Poly(ADP-Ribose) polymerase1 Has Potential to Facilitate the Nucleosome Disassembly.International journal of molecular sciences · 2026Article
- A modular framework for automated segmentation and analysis of AFM imaging of chromatin organization.Nucleic acids research · 2026Article
- Nanoscale Characterization of Interaction of Nucleosomes with H1 Linker Histone.International journal of molecular sciences · 2024Article
- Real-Time Multistep Asymmetrical Disassembly of Nucleosomes and Chromatosomes Visualized by High-Speed Atomic Force Microscopy.ACS central science · 2024Article
- PARP3 Affects Nucleosome Compaction Regulation.International journal of molecular sciences · 2023Article
- Quantifying epigenetic modulation of nucleosome breathing by high-throughput AFM imaging.Biophysical journal · 2022Article
- A High-throughput Pipeline to Determine DNA and Nucleosome Conformations by AFM Imaging.Bio-protocol · 2021Article
- DNA sequence-dependent positioning of the linker histone in a nucleosome: A single-pair FRET study.Biophysical journal · 2021Article
- Atomic force microscopy-A tool for structural and translational DNA research.APL bioengineering · 2021Review
- Automated AFM analysis of DNA bending reveals initial lesion sensing strategies of DNA glycosylases.Scientific reports · 2020Article
- Dynamics of the nucleosomal histone H3 N-terminal tail revealed by high precision single-molecule FRET.Nucleic acids research · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA compaction and accessibility in eukaryotes are governed by nucleosomes and orchestrated through interactions between DNA and DNA-binding proteins. Using QuantAFM, a method for automated image analysis of atomic force microscopy (AFM) data, we performed a detailed statistical analysis of structural properties of mono-nucleosomes. QuantAFM allows fast analysis of AFM images, including image preprocessing, object segmentation, and quantification of different structural parameters to assess DNA accessibility of nucleosomes. A comparison of nucleosomes reconstituted with and without linker histone H1 quantified H1's already described ability of compacting the nucleosome. We further employed nucleosomes bearing two charge-modifying mutations at position R81 and R88 in histone H2A (H2A R81E/R88E) to characterize DNA accessibility under destabilizing conditions. Upon H2A mutation, even in presence of H1, the DNA opening angle at the entry/exit site was increased and the DNA wrapping length around the histone core was reduced. Interestingly, a distinct opening of the less bendable DNA side was observed upon H2A mutation, indicating an enhancement of the intrinsic asymmetry of the Widom-601 nucleosomes. This study validates AFM as a technique to investigate structural parameters of nucleosomes and highlights how the DNA sequence, together with nucleosome modifications, can influence the DNA accessibility.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.