Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
Biochemistry
2011 Nov 22;5046:9973-81. doi: 10.1021/bi201377x.
Show Gene links
Show Anatomy links
The divalent cations Ca2+ and Mg2+ play specific roles in stabilizing histone-DNA interactions within nucleosomes that are partially redundant with the core histone tail domains.
Yang Z
,
Hayes JJ
.
???displayArticle.abstract???
We previously reported that reconstituted nucleosomes undergo sequence-dependent translational repositioning upon removal of the core histone tail domains under physiological conditions, indicating that the tails influence the choice of position. We report here that removal of the core histone tail domains increases the exposure of the DNA backbone in nucleosomes to hydroxyl radicals, a nonbiased chemical cleavage reagent, indicative of an increase in the motility of the DNA on the histone surface. Moreover, we demonstrate that the divalent cations Mg(2+) and Ca(2+) can replace the role of the tail domains with regard to stabilization of histone-DNA interactions within the nucleosome core and restrict repositioning of nucleosomes upon tail removal. However, when nucleosomes were incubated with Mg(2+) after tail removal, the original distribution of translational positions was not re-established, indicating that divalent cations increase the energy barrier between translational positions rather than altering the free energy differences between positions. Interestingly, other divalent cations such as Zn(2+), Fe(2+), Co(2+), and Mn(2+) had little or no effect on the stability of histone-DNA interactions within tailless nucleosomes. These results support the idea that specific binding sites for Mg(2+) and Ca(2+) ions exist within the nucleosome and play a critical role in nucleosome stability that is partially redundant with the core histone tail domains.
Allahverdi,
The effects of histone H4 tail acetylations on cation-induced chromatin folding and self-association.
2011, Pubmed
Allahverdi,
The effects of histone H4 tail acetylations on cation-induced chromatin folding and self-association.
2011,
Pubmed
Anderson,
Spontaneous access of proteins to buried nucleosomal DNA target sites occurs via a mechanism that is distinct from nucleosome translocation.
2002,
Pubmed
Aoyagi,
Nucleosome sliding induced by the xMi-2 complex does not occur exclusively via a simple twist-diffusion mechanism.
2003,
Pubmed
,
Xenbase
Ausio,
Use of selectively trypsinized nucleosome core particles to analyze the role of the histone "tails" in the stabilization of the nucleosome.
1989,
Pubmed
Belmont,
Visualization of G1 chromosomes: a folded, twisted, supercoiled chromonema model of interphase chromatid structure.
1994,
Pubmed
Bucceri,
Rapid accessibility of nucleosomal DNA in yeast on a second time scale.
2006,
Pubmed
Davey,
Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution.
2002,
Pubmed
,
Xenbase
Davey,
DNA-dependent divalent cation binding in the nucleosome core particle.
2002,
Pubmed
Dong,
DNA and protein determinants of nucleosome positioning on sea urchin 5S rRNA gene sequences in vitro.
1990,
Pubmed
Duguid,
Raman spectroscopy of DNA-metal complexes. I. Interactions and conformational effects of the divalent cations: Mg, Ca, Sr, Ba, Mn, Co, Ni, Cu, Pd, and Cd.
1993,
Pubmed
Duguid,
Raman spectroscopy of DNA-metal complexes. II. The thermal denaturation of DNA in the presence of Sr2+, Ba2+, Mg2+, Ca2+, Mn2+, Co2+, Ni2+, and Cd2+.
1995,
Pubmed
Garcia-Ramirez,
Role of the histone "tails" in the folding of oligonucleosomes depleted of histone H1.
1992,
Pubmed
Hamiche,
Histone tails modulate nucleosome mobility and regulate ATP-dependent nucleosome sliding by NURF.
2001,
Pubmed
Han,
Nucleosome loss activates yeast downstream promoters in vivo.
1988,
Pubmed
Hansen,
Conformational dynamics of the chromatin fiber in solution: determinants, mechanisms, and functions.
2002,
Pubmed
Hayes,
Histone contributions to the structure of DNA in the nucleosome.
1991,
Pubmed
,
Xenbase
Hayes,
Site-directed cleavage of DNA by a linker histone--Fe(II) EDTA conjugate: localization of a globular domain binding site within a nucleosome.
1996,
Pubmed
,
Xenbase
Hayes,
In vitro reconstitution and analysis of mononucleosomes containing defined DNAs and proteins.
1997,
Pubmed
,
Xenbase
Kan,
The H3 tail domain participates in multiple interactions during folding and self-association of nucleosome arrays.
2007,
Pubmed
,
Xenbase
Kan,
The H4 tail domain participates in intra- and internucleosome interactions with protein and DNA during folding and oligomerization of nucleosome arrays.
2009,
Pubmed
Kaplan,
Nucleosome sequence preferences influence in vivo nucleosome organization.
2010,
Pubmed
Kassabov,
High-resolution mapping of changes in histone-DNA contacts of nucleosomes remodeled by ISW2.
2002,
Pubmed
Lee,
A positive role for histone acetylation in transcription factor access to nucleosomal DNA.
1993,
Pubmed
,
Xenbase
Liu,
Mechanism(s) of SWI/SNF-induced nucleosome mobilization.
2011,
Pubmed
Lomvardas,
Nucleosome sliding via TBP DNA binding in vivo.
2001,
Pubmed
Luger,
Crystal structure of the nucleosome core particle at 2.8 A resolution.
1997,
Pubmed
Mann,
Histone H3 N-terminal mutations allow hyperactivation of the yeast GAL1 gene in vivo.
1992,
Pubmed
Meersseman,
Mobile nucleosomes--a general behavior.
1992,
Pubmed
Panetta,
Differential nucleosome positioning on Xenopus oocyte and somatic 5 S RNA genes determines both TFIIIA and H1 binding: a mechanism for selective H1 repression.
1998,
Pubmed
,
Xenbase
Polach,
Effects of core histone tail domains on the equilibrium constants for dynamic DNA site accessibility in nucleosomes.
2000,
Pubmed
Thoma,
Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin.
1979,
Pubmed
Thåström,
Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences.
1999,
Pubmed
Tse,
Hybrid trypsinized nucleosomal arrays: identification of multiple functional roles of the H2A/H2B and H3/H4 N-termini in chromatin fiber compaction.
1997,
Pubmed
Tse,
Disruption of higher-order folding by core histone acetylation dramatically enhances transcription of nucleosomal arrays by RNA polymerase III.
1998,
Pubmed
,
Xenbase
Tullius,
Hydroxyl radical footprinting: a high-resolution method for mapping protein-DNA contacts.
1987,
Pubmed
Vettese-Dadey,
Acetylation of histone H4 plays a primary role in enhancing transcription factor binding to nucleosomal DNA in vitro.
1996,
Pubmed
Whitehouse,
Antagonistic forces that position nucleosomes in vivo.
2006,
Pubmed
Widlund,
Nucleosome structural features and intrinsic properties of the TATAAACGCC repeat sequence.
1999,
Pubmed
Yang,
The core histone N-terminal tail domains negatively regulate binding of transcription factor IIIA to a nucleosome containing a 5S RNA gene via a novel mechanism.
2005,
Pubmed
,
Xenbase
Yang,
The core histone tail domains contribute to sequence-dependent nucleosome positioning.
2007,
Pubmed
,
Xenbase
Yang,
Large scale preparation of nucleosomes containing site-specifically chemically modified histones lacking the core histone tail domains.
2004,
Pubmed
Zhang,
High-resolution genome-wide mapping of the primary structure of chromatin.
2011,
Pubmed
Zhang,
A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome.
2011,
Pubmed
Zheng,
Salt-dependent intra- and internucleosomal interactions of the H3 tail domain in a model oligonucleosomal array.
2005,
Pubmed
,
Xenbase
Zheng,
Intra- and inter-nucleosomal protein-DNA interactions of the core histone tail domains in a model system.
2003,
Pubmed
,
Xenbase