ArticlePLoS computational biology2017
Binding of DNA-bending non-histone proteins destabilizes regular 30-nm chromatin structure.
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 15 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
15 citing papers in PubMed.
- Compaction of chromatin domains regulates target search times of proteins.PLoS computational biology · 2026Article
- The shifting paradigm of chromatin structure: from the 30-nm chromatin fiber to liquid-like organization.Proceedings of the Japan Academy. Series B, Physical and biological sciences · 2025Review
- Regulation of chromatin architecture by protein binding: insights from molecular modeling.Biophysical reviews · 2024Review
- Article
- Regulation of Chromatin Architecture by Transcription Factor Binding.bioRxiv : the preprint server for biology · 2023Article
- Article
- Predicting scale-dependent chromatin polymer properties from systematic coarse-graining.Nature communications · 2023Article
- An associative memory Hamiltonian model for DNA and nucleosomes.PLoS computational biology · 2023Article
- Live imaging of chromatin distribution reveals novel principles of nuclear architecture and chromatin compartmentalization.Science advances · 2021Article
- Nucleosome plasticity is a critical element of chromatin liquid-liquid phase separation and multivalent nucleosome interactions.Nature communications · 2021Article
- Physical Nature of Chromatin in the Nucleus.Cold Spring Harbor perspectives in biology · 2021Review
- Irregular Chromatin: Packing Density, Fiber Width, and Occurrence of Heterogeneous Clusters.Biophysical journal · 2020Article
- Role of nucleosome positioning in 3D chromatin organization and loop formation.Journal of biosciences · 2020Article
- Chromatin Higher-Order Folding: A Perspective with Linker DNA Angles.Biophysical journal · 2018Review
- Regulation of chromatin folding by conformational variations of nucleosome linker DNA.Nucleic acids research · 2017Article
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
Why most of the in vivo experiments do not find the 30-nm chromatin fiber, well studied in vitro, is a puzzle. Two basic physical inputs that are crucial for understanding the structure of the 30-nm fiber are the stiffness of the linker DNA and the relative orientations of the DNA entering/exiting nucleosomes. Based on these inputs we simulate chromatin structure and show that the presence of non-histone proteins, which bind and locally bend linker DNA, destroys any regular higher order structures (e.g., zig-zag). Accounting for the bending geometry of proteins like nhp6 and HMG-B, our theory predicts phase-diagram for the chromatin structure as a function of DNA-bending non-histone protein density and mean linker DNA length. For a wide range of linker lengths, we show that as we vary one parameter, that is, the fraction of bent linker region due to non-histone proteins, the steady-state structure will show a transition from zig-zag to an irregular structure-a structure that is reminiscent of what is observed in experiments recently. Our theory can explain the recent in vivo observation of irregular chromatin having co-existence of finite fraction of the next-neighbor (i + 2) and neighbor (i + 1) nucleosome interactions.
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.