ArticlePLoS computational biology2017
Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 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
45 citing papers in PubMed.
- DNA Sequence and Histone Variant H2A.Z Jointly Govern Nucleosome Unwrapping Pathways.bioRxiv : the preprint server for biology · 2026Article
- Determinants of centromeric nucleosome conformation.bioRxiv : the preprint server for biology · 2026Article
- SMC complex unidirectionally translocates DNA by coupling segment capture with an asymmetric kleisin path.eLife · 2026Article
- Linker histone H1 represses H3 tail acetylation induced by H4 tail acetylation and alters its dynamics.Communications biology · 2026Article
- Time-Resolved Single-Molecule FRET Reveals Length-Dependent Nucleosome Decompaction by Poly(ADP-ribose).bioRxiv : the preprint server for biology · 2026Article
- DNA actively regulates the "safety-belt" dynamics of condensin during loop extrusion.Nature communications · 2026Article
- Mechanistic models of asymmetric hand-over-hand translocation and nucleosome navigation by CMG helicase.Nature communications · 2025Article
- Mechanistic basis for the opposing effects of H2A and H2B ubiquitination on nucleosome stability and dynamics.Epigenetics & chromatin · 2025Article
- Deciphering the molecular mechanisms of BPTF interactions with nucleosomes via molecular simulations.Biophysical journal · 2025Article
- Deciphering the Molecular Mechanisms of BPTF Interactions with Nucleosomes via Molecular Simulations.bioRxiv : the preprint server for biology · 2025Article
- Heterogeneous condensates of transcription factors in embryonic stem cells: Molecular simulations.Biophysical journal · 2025Article
- In silico nanoscope to study the interplay of genome organization and transcription regulation.Nucleic acids research · 2025Article
- Protein target search diffusion-association/dissociation free energy landscape around DNA binding site with flanking sequences.Biophysical journal · 2025Article
- Unveiling nucleosome dynamics: A comparative study using all-atom and coarse-grained simulations enhanced by principal component analysis.The Journal of chemical physics · 2025Article
- Integrative Modeling of 3D Genome Organization by Bayesian Molecular Dynamics Simulations with Hi-C Metainference.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Unveiling Nucleosome Dynamics: A Comparative Study Using All-Atom and Coarse-Grained Simulations Enhanced by Principal Component Analysis.bioRxiv : the preprint server for biology · 2024Article
- Molecular mechanism of parental H3/H4 recycling at a replication fork.Nature communications · 2024Article
- Nucleosomal DNA unwinding pathway through canonical and non-canonical histone disassembly.Communications biology · 2024Article
- GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models.The journal of physical chemistry. B · 2024Article
- Sequence Dependence in Nucleosome Dynamics.The journal of physical chemistry. B · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
While nucleosome positioning on eukaryotic genome play important roles for genetic regulation, molecular mechanisms of nucleosome positioning and sliding along DNA are not well understood. Here we investigated thermally-activated spontaneous nucleosome sliding mechanisms developing and applying a coarse-grained molecular simulation method that incorporates both long-range electrostatic and short-range hydrogen-bond interactions between histone octamer and DNA. The simulations revealed two distinct sliding modes depending on the nucleosomal DNA sequence. A uniform DNA sequence showed frequent sliding with one base pair step in a rotation-coupled manner, akin to screw-like motions. On the contrary, a strong positioning sequence, the so-called 601 sequence, exhibits rare, abrupt transitions of five and ten base pair steps without rotation. Moreover, we evaluated the importance of hydrogen bond interactions on the sliding mode, finding that strong and weak bonds favor respectively the rotation-coupled and -uncoupled sliding movements.
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.