ArticleNucleic acids research2012
The mechanics behind DNA sequence-dependent properties of the nucleosome.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 110 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
110 citing papers in PubMed, 202 citations in OpenAlex.
- Mechanism of NanR transcriptional activation of sialic acid metabolism in Streptococcus pneumoniae.Nucleic acids research · 2026Article
- Article
- Linker histones consolidate heterogenous nucleosome fiber contacts by linking together multiple nucleosomes.Nature communications · 2026Article
- IMPACTS OF DNA METHYLATION ON H2A.Z DEPOSITION AND NUCLEOSOME STABILITY.bioRxiv : the preprint server for biology · 2025Article
- H2B.W2, a spermatocyte-specific histone variant, disrupts nucleosome stability, and reduces chromatin compaction.Nucleic acids research · 2025Article
- Predicting rare DNA conformations via dynamical graphical models: a case study of the B→A transition.Nucleic acids research · 2025Article
- Initiation of base excision repair is modulated by nucleosome occupancy modifying sequences.DNA repair · 2025Article
- Revealing long-range heterogeneous organization of nucleoproteins with 6mA footprinting by ipdTrimming.Genome biology · 2025Article
- Article
- Structural and functional insights into the nuclear role of Parkinson's disease-associated α-synuclein as a histone chaperone.Communications biology · 2025Article
- Cryo-EM Structures of Native Chromatin Units From Human Cells.Genes to cells : devoted to molecular & cellular mechanisms · 2025Article
- FRET analysis of the unwrapping of nucleosomal DNA containing a sequence characteristic of the + 1 nucleosome.Scientific reports · 2025Article
- High-Resolution Cryo-EM Analyses of Nucleosomes.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Probing mechanical selection in diverse eukaryotic genomes through accurate prediction of 3D DNA mechanics.bioRxiv : the preprint server for biology · 2024Article
- High Nucleotide Skew Palindromic DNA Sequences Function as Potential Replication Origins due to their Unzipping Propensity.Journal of molecular evolution · 2024Article
- Article
- Nucleosomal DNA unwinding pathway through canonical and non-canonical histone disassembly.Communications biology · 2024Article
- Structural dynamics in chromatin unraveling by pioneer transcription factors.Biophysical reviews · 2024Review
- Energy-driven genome regulation by ATP-dependent chromatin remodellers.Nature reviews. Molecular cell biology · 2024Review
- Predictions of DNA mechanical properties at a genomic scale reveal potentially new functional roles of DNA flexibility.NAR genomics and bioinformatics · 2023Article
50 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chromatin organization and composition impart sophisticated regulatory features critical to eukaryotic genomic function. Although DNA sequence-dependent histone octamer binding is important for nucleosome activity, many aspects of this phenomenon have remained elusive. We studied nucleosome structure and stability with diverse DNA sequences, including Widom 601 derivatives with the highest known octamer affinities, to establish a simple model behind the mechanics of sequence dependency. This uncovers the unique but unexpected role of TA dinucleotides and a propensity for G|C-rich sequence elements to conform energetically favourably at most locations around the histone octamer, which rationalizes G|C% as the most predictive factor for nucleosome occupancy in vivo. In addition, our findings reveal dominant constraints on double helix conformation by H3-H4 relative to H2A-H2B binding and DNA sequence context-dependency underlying nucleosome structure, positioning and stability. This provides a basis for improved prediction of nucleosomal properties and the design of tailored DNA constructs for chromatin investigations.
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.