ArticleNucleic acids research2009
Distinctive sequence patterns in metazoan and yeast nucleosomes: implications for linker histone binding to AT-rich and methylated DNA.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 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
31 citing papers in PubMed, 67 citations in OpenAlex.
- Interpretable deep residual network uncovers nucleosome positioning and associated features.Nucleic acids research · 2024Article
- DNA sequence-dependent positioning of the linker histone in a nucleosome: A single-pair FRET study.Biophysical journal · 2021Article
- A critical role for linker DNA in higher-order folding of chromatin fibers.Nucleic acids research · 2021Article
- Minimal Cylinder Analysis Reveals the Mechanical Properties of Oncogenic Nucleosomes.Biophysical journal · 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
- The nucleosome position-encoding WW/SS sequence pattern is depleted in mammalian genes relative to other eukaryotes.Nucleic acids research · 2019Article
- Sensitive effect of linker histone binding mode and subtype on chromatin condensation.Nucleic acids research · 2019Article
- Emerging roles of linker histones in regulating chromatin structure and function.Nature reviews. Molecular cell biology · 2018Review
- Regulation of chromatin folding by conformational variations of nucleosome linker DNA.Nucleic acids research · 2017Article
- Feature-based classification of human transcription factors into hypothetical sub-classes related to regulatory function.BMC bioinformatics · 2016Article
- A Small Number of Residues Can Determine if Linker Histones Are Bound On or Off Dyad in the Chromatosome.Journal of molecular biology · 2016Article
- Cell cycle progression in Caulobacter requires a nucleoid-associated protein with high AT sequence recognition.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome.Nucleic acids research · 2016Article
- Novel nucleosomal particles containing core histones and linker DNA but no histone H1.Nucleic acids research · 2016Article
- Article
- HistoneDB 2.0: a histone database with variants--an integrated resource to explore histones and their variants.Database : the journal of biological databases and curation · 2016Article
- Structural Mechanisms of Nucleosome Recognition by Linker Histones.Molecular cell · 2015Article
- Crop epigenetics and the molecular hardware of genotype × environment interactions.Frontiers in plant science · 2015Review
- Prediction of nucleosome rotational positioning in yeast and human genomes based on sequence-dependent DNA anisotropy.BMC bioinformatics · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Linker histones (LHs) bind to the DNA entry/exit points of nucleosomes and demonstrate preference for AT-rich DNA, although the recognized sequence patterns remain unknown. These patterns are expected to be more pronounced in metazoan nucleosomes with abundant LHs, compared to yeast nucleosomes with few LHs. To test this hypothesis, we compared the nucleosome core particle (NCP) sequences from chicken, Drosophila and yeast, extending them by the flanking sequences extracted from the genomes. We found that the known approximately 10-bp periodic oscillation of AT-rich elements goes beyond the ends of yeast nucleosomes, but is distorted in metazoan sequences where the 'out-of-phase' AT-peaks appear at the NCP ends. The observed difference is likely to be associated with sequence-specific LH binding. We therefore propose a new structural model for LH binding to metazoan nucleosomes, postulating that the highly conserved nonpolar 'wing' region of the LH globular domain (tetrapeptide GVGA) recognizes AT-rich fragments through hydrophobic interactions with the thymine methyl groups. These interactions lead to DNA bending at the NCP ends and formation of a 'stem-like' structure. The same mechanism accounts for the high affinity of LH to methylated DNA-a feature critical for stabilization of the higher-order structure of chromatin and for repression of transcription.
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.