ArticleScientific reports2018
A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 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
28 citing papers in PubMed, 55 citations in OpenAlex.
- Molecular dynamics guided all-atom reconstruction of cryo-ET maps reveals mechanisms of histone tail mediated chromatin compaction.Nature communications · 2026Article
- Quantifying the effect of magnesium ions on nucleosome stability in chromatin fibers.Biophysical journal · 2026Article
- Article
- Structural insights into γH2Ax containing nucleosomes.Nucleic acids research · 2025Article
- Multiscale modeling reveals the ion-mediated phase separation of nucleosome core particles.Biophysical journal · 2024Article
- The nucleosome reference frame and standard geometries for octasomes.Biophysical reviews · 2024Review
- Cryoelectron tomography reveals the multiplex anatomy of condensed native chromatin and its unfolding by histone citrullination.Molecular cell · 2023Article
- Role of the histone tails in histone octamer transfer.Nucleic acids research · 2023Article
- Genome modeling: From chromatin fibers to genes.Current opinion in structural biology · 2023Review
- Columnar structure of human telomeric chromatin.Nature · 2022Article
- Cell-Free DNA Fragmentation Patterns in a Cancer Cell Line.Diagnostics (Basel, Switzerland) · 2022Article
- A Bottom-Up Coarse-Grained Model for Nucleosome-Nucleosome Interactions with Explicit Ions.Journal of chemical theory and computation · 2022Article
- Recent Advances in Investigating Functional Dynamics of Chromatin.Frontiers in genetics · 2022Review
- Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails.Nature communications · 2021Article
- Histone H4 lysine 20 mono-methylation directly facilitates chromatin openness and promotes transcription of housekeeping genes.Nature communications · 2021Article
- Significant compaction of H4 histone tail upon charge neutralization by acetylation and its mimics, possible effects on chromatin structure.Journal of molecular biology · 2021Article
- A critical role for linker DNA in higher-order folding of chromatin fibers.Nucleic acids research · 2021Article
- Chiral Systems Made from DNA.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2021Review
- Organization of the Pluripotent Genome.Cold Spring Harbor perspectives in biology · 2021Review
- Linker histone defines structure and self-association behaviour of the 177 bp human chromatosome.Scientific reports · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chromatin condensation is driven by the energetically favourable interaction between nucleosome core particles (NCPs). The close NCP-NCP contact, stacking, is a primary structural element of all condensed states of chromatin in vitro and in vivo. However, the molecular structure of stacked nucleosomes as well as the nature of the interactions involved in its formation have not yet been systematically studied. Here we undertake an investigation of both the structural and physico-chemical features of NCP structure and the NCP-NCP stacking. We introduce an "NCP-centred" set of parameters (NCP-NCP distance, shift, rise, tilt, and others) that allows numerical characterisation of the mutual positions of the NCPs in the stacking and in any other structures formed by the NCP. NCP stacking in more than 140 published NCP crystal structures were analysed. In addition, coarse grained (CG) MD simulations modelling NCP condensation was carried out. The CG model takes into account details of the nucleosome structure and adequately describes the long range electrostatic forces as well as excluded volume effects acting in chromatin. The CG simulations showed good agreement with experimental data and revealed the importance of the H2A and H4 N-terminal tail bridging and screening as well as tail-tail correlations in the stacked nucleosomes.
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.