ArticlePloS one2015
Two arginine residues suppress the flexibility of nucleosomal DNA in the canonical nucleosome core.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Cnp1 N-terminal dynamics regulate L1 loop recognition by Mis15 to orchestrate kinetochore assembly in Schizosaccharomyces pombe.Journal of molecular cell biology · 2026Article
- Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1.Nature communications · 2024Article
- Histone 3.3-related chromatinopathy: missense variants throughout H3-3A and H3-3B cause a range of functional consequences across species.Human genetics · 2024Review
- Cryo-EM and biochemical analyses of the nucleosome containing the human histone H3 variant H3.8.Journal of biochemistry · 2023Article
- Histone divergence in trypanosomes results in unique alterations to nucleosome structure.Nucleic acids research · 2023Article
- Nucleosome Structures Built from Highly Divergent Histones: Parasites and Giant DNA Viruses.Epigenomes · 2022Review
- Unusual nucleosome formation and transcriptome influence by the histone H3mm18 variant.Nucleic acids research · 2022Article
- Molecular dynamics simulations reveal how H3K56 acetylation impacts nucleosome structure to promote DNA exposure for lesion sensing.DNA repair · 2021Article
- Torsional stress can regulate the unwrapping of two outer half superhelical turns of nucleosomal DNA.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Phase-plate cryo-EM structure of the Widom 601 CENP-A nucleosome core particle reveals differential flexibility of the DNA ends.Nucleic acids research · 2020Article
- Molecular Mechanism of Spontaneous Nucleosome Unraveling.Journal of molecular biology · 2019Article
- Free energy profile for unwrapping outer superhelical turn of CENP-A nucleosome.Biophysics and physicobiology · 2019Article
- Histone Tail Dynamics in Partially Disassembled Nucleosomes During Chromatin Remodeling.Frontiers in molecular biosciences · 2019Article
- Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA.PLoS computational biology · 2018Article
- Apolipoprotein E4 inhibits autophagy gene products through direct, specific binding to CLEAR motifs.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2018Article
- H4 Tails Potentially Produce the Diversity in the Orientation of Two Nucleosomes.Biophysical journal · 2017Article
- Structural dynamics of nucleosome mediated by acetylations at H3K56 and H3K115,122.European biophysics journal : EBJ · 2017Article
- Distinct Roles of Histone H3 and H2A Tails in Nucleosome Stability.Scientific reports · 2016Article
- H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation.PLoS computational biology · 2016Article
- Shearing of the CENP-A dimerization interface mediates plasticity in the octameric centromeric nucleosome.Scientific reports · 2015Article
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5 authors.
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Abstract
The dynamics of nucleosomes containing either canonical H3 or its centromere-specific variant CENP-A were investigated using molecular dynamics simulations. The simulations showed that the histone cores were structurally stable during simulation periods of 100 ns and 50 ns, while DNA was highly flexible at the entry and exit regions and partially dissociated from the histone core. In particular, approximately 20-25 bp of DNA at the entry and exit regions of the CENP-A nucleosome exhibited larger fluctuations than DNA at the entry and exit regions of the H3 nucleosome. Our detailed analysis clarified that this difference in dynamics was attributable to a difference in two basic amino acids in the αN helix; two arginine (Arg) residues in H3 were substituted by lysine (Lys) residues at the corresponding sites in CENP-A. The difference in the ability to form hydrogen bonds with DNA of these two residues regulated the flexibility of nucleosomal DNA at the entry and exit regions. Our exonuclease III assay consistently revealed that replacement of these two Arg residues in the H3 nucleosome by Lys enhanced endonuclease susceptibility, suggesting that the DNA ends of the CENP-A nucleosome are more flexible than those of the H3 nucleosome. This difference in the dynamics between the two types of nucleosomes may be important for forming higher order structures in different phases.
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