ArticleBiophysical journal2008
Nucleosome geometry and internucleosomal interactions control the chromatin fiber conformation.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 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
59 citing papers in PubMed.
- Nucleosome spacing across cell types, diseases, and ages.Nucleic acids research · 2026Review
- Chromatin higher-order folding as influenced by preferred values of linker DNA.Current opinion in structural biology · 2025Review
- Physical models reveal indirect reader protein interactions that facilitate epigenetic crosstalk.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Connected Chromatin Amplifies Acetylation-Modulated Nucleosome Interactions.Biochemistry · 2025Article
- Heterogeneous flexibility can contribute to chromatin segregation in the cell nucleus.Physical review. E · 2024Article
- Regulation of chromatin architecture by protein binding: insights from molecular modeling.Biophysical reviews · 2024Review
- Coarse-Grained Models to Study Protein-DNA Interactions and Liquid-Liquid Phase Separation.Journal of chemical theory and computation · 2024Article
- An associative memory Hamiltonian model for DNA and nucleosomes.PLoS computational biology · 2023Article
- A Bottom-Up Coarse-Grained Model for Nucleosome-Nucleosome Interactions with Explicit Ions.Journal of chemical theory and computation · 2022Article
- DNA sequence-dependent formation of heterochromatin nanodomains.Nature communications · 2022Article
- Differences in nanoscale organization of regulatory active and inactive human chromatin.Biophysical journal · 2022Article
- Article
- A glitch in the snitch: the role of linker histone H1 in shaping the epigenome in normal and diseased cells.Open biology · 2021Review
- Multiscale modeling of genome organization with maximum entropy optimization.The Journal of chemical physics · 2021Article
- Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface.Nature communications · 2021Article
- Topological polymorphism of nucleosome fibers and folding of chromatin.Biophysical journal · 2021Review
- Elucidating the influence of linker histone variants on chromatosome dynamics and energetics.Nucleic acids research · 2020Article
- Role of nucleosome positioning in 3D chromatin organization and loop formation.Journal of biosciences · 2020Article
- Chromatin Compaction Multiscale Modeling: A Complex Synergy Between Theory, Simulation, and Experiment.Frontiers in molecular biosciences · 2020Review
- Modelling and DNA topology of compact 2-start and 1-start chromatin fibres.Nucleic acids research · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Based on model structures with atomic resolution, a coarse-grained model for the nucleosome geometry was implemented. The dependence of the chromatin fiber conformation on the spatial orientation of nucleosomes and the path and length of the linker DNA was systematically explored by Monte Carlo simulations. Two fiber types were analyzed in detail that represent nucleosome chains without and with linker histones, respectively: two-start helices with crossed-linker DNA (CL conformation) and interdigitated one-start helices (ID conformation) with different nucleosome tilt angles. The CL conformation was derived from a tetranucleosome crystal structure that was extended into a fiber. At thermal equilibrium, the fiber shape persisted but relaxed into a structure with a somewhat lower linear mass density of 3.1 +/- 0.1 nucleosomes/11 nm fiber. Stable ID fibers required local nucleosome tilt angles between 40 degrees and 60 degrees. For these configurations, much higher mass densities of up to 7.9 +/- 0.2 nucleosomes/11 nm fiber were obtained. A model is proposed, in which the transition between a CL and ID fiber is mediated by relatively small changes of the local nucleosome geometry. These were found to be in very good agreement with changes induced by linker histone H1 binding as predicted from the high resolution model structures.
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.