Acetylated nucleosome assembly on telomeric DNAs (original) (raw)
Related papers
Telomeric Nucleosomes Are Intrinsically Mobile
Journal of Molecular Biology, 2007
Nucleosomes are no longer considered only static basic units that package eukaryotic DNA but they emerge as dynamic players in all chromosomal processes. Regulatory proteins can gain access to recognition sequences hidden by the histone octamer through the action of ATP-dependent chromatin remodeling complexes that cause nucleosome sliding. In addition, it is known that nucleosomes are able to spontaneously reposition along the DNA due to intrinsic dynamic properties, but it is not clear yet to what extent sequence-dependent dynamic properties contribute to nucleosome repositioning. Here, we study mobility of nucleosomes formed on telomeric sequences as a function of temperature and ionic strength. We find that telomeric nucleosomes are highly intrinsically mobile under physiological conditions, whereas nucleosomes formed on an average DNA sequence mostly remain in the initial position. This indicates that DNA sequence affects not only the thermodynamic stability and the positioning of nucleosomes but also their dynamic properties. Moreover, our findings suggest that the high mobility of telomeric nucleosomes may be relevant to the dynamics of telomeric chromatin.
Biochemical and Biophysical Research Communications, 2003
To examine the factors involved with nucleosome stability, we reconstituted nonacetylated particles containing various lengths (192, 162, and 152 base pairs) of DNA onto the Lytechinus variegatus nucleosome positioning sequence in the absence of linker histone. We characterized the particles and examined their thermal stability. DNA of less than chromatosome length (168 base pairs) produces particles with altered denaturation profiles, possibly caused by histone rearrangement in those core-like particles. We also examined the effects of tetra-acetylation of histone H4 on the thermal stability of reconstituted nucleosome particles. Tetraacetylation of H4 reduces the nucleosome thermal stability by 0.8°C as compared with nonacetylated particles. This difference is close to values published comparing bulk nonacetylated nucleosomes and core particles to ones enriched for core histone acetylation, suggesting that H4 acetylation has a dominant effect on nucleosome particle energetics.
Journal of Biological Chemistry, 1996
Vertebrate telomeres contain arrays of nucleosomes with unusually short and regular repeat lengths (Makarov, V. L., Lejnine, S., Bedoyan, J., and Langmore, J. P. (1993) Cell 73, 775-787; Lejnine, S., Makarov, V., and Langmore, J. P. (1995) Proc. Natl. Acad. Sci. U. S. A. 92, 2393-2397). In order to better define the specific structural features of telomere chromatin, we examined the condensation and H1 content of telomere nucleoproteins from rat liver. Velocity sedimentation analysis shows that telomeric nucleosome arrays condense with increasing ionic strength and molecular weight in a manner comparable with that of bulk chromatin despite the very short repeat length. However, these condensed structures do not exhibit the ϳ100-base pair deoxyribonuclease II repeat characteristic of condensed bulk chromatin. Frictional coefficient calculations suggest that telomere-specific higher order structure is more compact than bulk chromatin. Nucleoprotein gel electrophoresis shows that telomeric dinucleosomes from soluble chromatin contain H1. Finally, direct isolation and analysis of telomere nucleoproteins from formaldehyde-cross-linked nuclei indicate the presence of core histone proteins and H1. These results are consistent with the view that a major fraction of the long telomeres of rat are organized as specialized nucleosome arrays with features similar but not identical to those of bulk chromatin.
Thermal Denaturation Studies of Acetylated Nucleosomes and Oligonucleosmes
European Journal of Biochemistry, 1982
The thermal melting behaviors of control and acetylated mononucleosomes, dinucleosomes and trinucleosomes have been studied. Along each series of oligonucleosomes, the melting profiles change in a manner consistent with the increasing number of nucleosomes. For the control mononuclecrsome, the melting profile exhibits a premelting region at about 61 -64°C and a major cooperative transition at 75-77 "C. The melting profiles of the control dinucleosomes and trinucleosomes show a premelt at 61 -62 "C (similar to that of the nucleosome core) ; an intermediate transition at 73 -74 "C for the dinucleosome and at 76 -77 "C for the trinucleosome and a major cooperative transition at 79-80 "C for the dinucleosome and at 81 -82 "C for the trinucleosome. The major cooperative transition at the hignest melting temperatures in the melting profiles of the mononucleosome, dinucleosome and trinucleosome comes from the melting of the central region of DNA in the nucleosome strongly complexed with the core histones; the premelt region is attributed to two DNA segments per nucleosome which flank this central DNA region and are free or weakly complexed with histones. The origin of the intermediate transition found for the dinucleosomes and trinucleosomes is not fully understood but probably results from the melting of DNA at the entry to and exit from the nucleosome and the linker D N A which are complexed with histones. A very similar pattern of behavior is observed for the acetylated oligonucleosomes. Direct comparison of the melting profiles of acetylated and control mononucleosomes, dinucleosomes and trinucleosoines show that the premelt region is unaffected by histone acetylation whereas the intermediate and major cooperative transitions for the acetylated oligonucleosomes are broader and occur consistently at lower temperatures than for the controls. These differences support proposals that the N-terminal regions of core histones interact within the nucleosome and on linker DNA. Now that we have an outline understanding of the structure of the nucleosome at low resolution [I -31 and of the packing of nucleosomes in extended and supercoiled chromatin [4 -91, attention is directed to the role of histone acetylation on the structure and function of transcriptionally active or competent chromatin. Allfrey et al. [lo] first correlated one of the requirements of transcriptional activity with histone acetylation and this correlation has been found to hold for enhanced transcriptional activity induced by hormones or drugs (see [I I]). Cell cycle studies of histone H4 acetylation show a strong correlation between the behavior of tetraacetylated H4 and transcriptional activity [I 21. Yeast chromatin, which has a very high overall level of transcriptional activity, has been found to contain 63% of diacetylated, triacetylated and tetraacetylated histone H4 .
The histone core exerts a dominant constraint on the structure of DNA in a nucleosome
Biochemistry, 1991
We have examined the structures of unique sequence, A/T-rich DNAs that are predicted to be relatively rigid [oligo(dA)-oligo(dT)], flexible [oligo[d(A-T)]], and curved, using the hydroxyl radical as a cleavage reagent. A 50-basapair segment containing each of these distinct DNA sequences was placed adjacent to the T7 R N A polymerase promoter, a sequence that will strongly position nucleosomes. The final length of the DNA fragments was 142 bp, enough DNA to assemble a single nucleosome. Cleavage of DNA in solution, while bound to a calcium phosphate crystal, and after incorporation into a nucleosome is examined. We find that the distinct A/T-rich DNAs have very different structural features in solution and helical periodicities when bound to calcium phosphate. In contrast, the organization of the different DNA sequences when associated with a histone octamer is very similar. We conclude that the histone core exerts a dominant constraint on the structure of DNA in a nucleosome and that inclusion of these various unique sequences has only a very small effect on overall nucleosome stability and structure.
Mechanisms of stabilizing nucleosome structure. Study of dissociation of histone octamer from DNA
Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression, 1997
The influence of ionic strength on DNA-histone and histone-histone interactions in reconstituted nucleosomes was studied by measuring the parameters of histone tyrosine fluorescence: fluorescence intensity and l position. The first max parameter is sensitive to histone-DNA interactions. The changes of the second one accrue due to hydrogen bond Ž. formationrdisruption between tyrosines in the histone H2A-H2B dimer and the H3-H4 tetramer. The simultaneous 2 measurement of these parameters permits the recording of both the dissociation of histone complexes from DNA, as well as changes in histone-histone interactions. As ionic strength is increased, the H2A-H2B histone dimer dissociated first, Ž. w Ž. followed by dissociation of the H3-H4 tetramer Yager, T.G., McMurray, C.T. and Van Holde, K.E. 1989 Biochemistry 2 x 28, 2271-2276. The H2A-H2B dimer is dissociated in two stages: first, the ionic bonds with DNA were disrupted, followed by the dissociation of the histone dimer from the tetramer. And secondly, the disruption of dimer-tetramer specific H-bonds. It was established that the energy of electrostatic interactions of the histone dimer with DNA within the nucleosome is much less than the energy of interaction of the histone dimer with the tetramer.
Journal of Molecular Biology, 1989
DNA originating from chicken erythrocyte mononucleosomes was cloned and sequenced. The properties of nucleosome reconstruction were compared for two cloned inserts, selected on account of their interesting sequence organization, length and difference in DNA bending. Cloned fragment 223 (182 base-pairs) carries alternately (A)3-4 and (T),-, runs approximately every ten base-pairs and is bent; cloned fragment 213 (182 base-pairs) contains a repeated C4-,ATAAGG consensus sequence and is apparently not bent. Our experiments indicate the preference of the bent DNA fragment 223 over fragment 213 to associate in vitro with 'an octamer of histones under stringent conditions. We provide evidence that the in vitro nucleosome formation is hampered in the case of fragment 213. whereas the reconstituted nucleosomes were equally stable once formed. For the correct determination of the positioning of the histone octamer with regard to the two nucleosomederived cloned DNA sequences, the complementary use of micrococcal nuclease, exonuclease TJI and DNase I is a prerequisite. No unique, but rotationally related, positions of the histone octamer were found on these nucleosome-derived DNA fragment,s. The sequence-dependent anisotropic flexibility, as well as intrinsic bending of the L)?u'A, resulting in a rotational setting of the DNA fragment's on the histone core, seems to be a strong determinant for the allowed octamer positions, Exonuclease III digestion indicates a different histone-DPI'A association when oligo(d(C. G),) st,retches are involved. The apparent stagger near oligo(d(A. T),) stretches generated by DNase I digestion on reconstituted nucleosome 223 was found to be inverted from the normal two-base 3' overhang to a two-base 5' overhang. Two possibilities. of the oligo(d(A. T),) minor groove location relative to the histone core are envisaged to explain this anomaly in stagger.
DNA Sequence Mediates Nucleosome Structure and Stability
Biophysical Journal, 2008
Nucleosomes form the fundamental repeating unit of eukaryotic chromatin. Subtle modifications in nucleosome structure and histone tails regulate chromatin states; hence, a comprehensive understanding of alterations in nucleosome structure is of fundamental importance in chromatin biophysics. The nature of core histone organization and nucleosome dynamics have been extensively studied using biophysical experiments, multiscale computational models, and simulations ((1,2) and references therein). However, the precise mechanisms of how DNA sequence mediates nucleosome structure and stability remains to be completely understood.
Nucleic Acids Research, 1986
Free DNA in solution exhibits an untwisting of the double helix with increasing temperature. We have shown previously that when DNA is reconstituted with histones to form nucleosome core particles, both the core DNA and the adjacent linker DNA are constrained from thermal untwisting. The origin of this constraint is unknown. Here we examine the effect of two modifications of nucleosome structure on the constraint against thermal untwisting, and also on DNA topology. In one experiment, we removed the highly positively charged histone amino and carboxy termini by trypsinization. Alternatively, we added histone H5, a histone HI variant from chick erythrocytes. Neither of these modifications had any major effect on DNA topology or twist in the nucleosome.