Direct detection of linker DNA bending in defined-length oligomers of chromatin.

Yao, Jiaqi; Lowary, Peggy T.; Widom, Jonathan

doi:10.1073/pnas.87.19.7603

Cited by 74 publications

(64 citation statements)

References 36 publications

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“…1. The sucrose gradients reveal that Ϸ10% of the DNA is formed into nucleosomes, as expected, and the mobility of the nucleosomes in the gradients is consistent with their being mononucleosomes, not dinucleosomes, which sediment at or near the bottom (21). Moreover, the amount of histone octamer supplied in the reaction is sufficient to turn 10% of the DNA into only mononucleosomes, not into dinucleosomes.…”

Section: Resultsmentioning

confidence: 57%

Nucleosome packaging and nucleosome positioning of genomic DNA

Lowary

Widom

1997

Proc. Natl. Acad. Sci. U.S.A.

119

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The goals of this study were to assess the extent to which bulk genomic DNA sequences contribute to their own packaging in nucleosomes and to reveal the relationship between nucleosome packaging and positioning. Using a competitive nucleosome reconstitution assay, we found that at least 95% of bulk DNA sequences have an affinity for histone octamer in nucleosomes that is similar to that of randomly synthesized DNA; they contribute little to their own packaging at the level of individual nucleosomes. An equation was developed that relates the measured free energy to the fractional occupancy of specific nucleosome positions. Evidently, the bulk of eukaryotic genomic DNA is also not evolved or constrained for significant sequence-directed nucleosome positioning at the level of individual nucleosomes. Implications for gene regulation in vivo are discussed.DNA in nucleosomes is tightly bent in comparison to its persistence length, a length scale of DNA stiffness (1). Substantial mechanical work must be done against the bending stiffness to package DNA in nucleosomes; this mechanical work is done at the expense of the favorable free energy of histone-DNA interactions and subtracts from the net thermodynamic stability of the particles. The free energies involved are surprisingly large. Taking the persistence length of DNA to be 50 nm and assuming that DNA in a nucleosome is uniformly bent in a circular trajectory at a radius of curvature of 4.4 nm leads to an estimated free energy cost (1) for bending DNA in a nucleosome of Ϸ75 kcal⅐mol Ϫ1 . Indeed, because of previous estimates such as this, it was once considered remarkable that nucleosome exist at all. Analogous problems exist for DNA twist.The discovery that certain DNA sequences are naturally bent (2) suggested that eukaryotic genomic DNA sequences might be evolved or constrained to facilitate their packaging in nucleosomes (3, 4). Moreover, one might anticipate the existence of a relationship between the free energy of nucleosomal packaging and the phenomenon of nucleosome positioning (such an equation is developed in the present study), suggesting the possibility that nucleosome positioning signals may be encoded in genomic DNA. This idea is interesting in part because of the relationship between nucleosome positioning and gene regulation (5).Results from several studies support the hypothesis that genomes are evolved to facilitate their own packaging. (i) Analyses of DNA fragments present in isolated nucleosome core particles, chromatosomes, and dinucleosomes reveal nonrandom periodic distributions of certain dinucleotides and longer sequences, with particular relative phases (see ref. 6 and references therein). The results suggest that such sequences facilitate the bending of DNA that is necessary for nucleosome formation and that the bending may be produced by an anisotropic flexibility of the AϩT-rich and GϩC-rich regions.(ii) Shrader and Crothers (7, 8) designed sequences de novo that obeyed these rules. The designed sequences were found to bind his...

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Section: Resultsmentioning

confidence: 57%

Nucleosome packaging and nucleosome positioning of genomic DNA

Lowary

Widom

1997

Proc. Natl. Acad. Sci. U.S.A.

119

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“…D, internucleosomal cross-linking data shown in A-C were quantified as described in Fig. 4C and plotted reflects the salt-dependent folding of nucleosome arrays (27)(28)(29). However we were unable to detect internucleosomal interactions of the H3 tail domain in dinucleosomes.…”

Section: Discussionmentioning

confidence: 97%

Salt-dependent Intra- and Internucleosomal Interactions of the H3 Tail Domain in a Model Oligonucleosomal Array

Zheng

Hansen

et al. 2005

Journal of Biological Chemistry

113

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The core histone tail domains are known to be key regulators of chromatin structure and function. The tails are required for condensation of nucleosome arrays into secondary and tertiary chromatin structures, yet little is known regarding tail structures or sites of tail interactions in chromatin. We have developed a system to test the hypothesis that the tails participate in internucleosomal interactions during salt-dependent chromatin condensation, and here we used it to examine interactions of the H3 tail domain. We found that the H3 tail participates primarily in intranucleosome interactions when the nucleosome array exists in an extended "beads-ona-string" conformation and that tail interactions reorganize to engage in primarily internucleosome interactions as the array successively undergoes salt-dependent folding and oligomerization. These results indicated that the location and interactions of the H3 tail domain are dependent upon the degree of condensation of the nucleosomal array, suggesting a mechanism by which alterations in tail interactions may elaborate different structural and functional states of chromatin.The eukaryotic genome is assembled into vast arrays of nucleosomes, which are in turn condensed into 30-nm chromatin fibers and other secondary chromatin structures (1-3). In vitro evidence indicates that the folding of nucleosome arrays into secondary structures is strongly favored at physiological concentrations of mono-and divalent salts, as is the oligomerization of arrays into higher order, tertiary chromatin structures (2, 4, 5). The stability of secondary and tertiary chromatin structures is influenced by the incorporation of specific non-allelic variants of the core histone proteins, the binding of linker histones, and association of ancillary chromatin proteins (2, 3). It is generally believed that for genomic DNA to be accessible to various enzymatic machineries, the chromatin fiber has to undergo transient decondensation, facilitated by specific posttranslational modifications such as lysine acetylation within the histone tail domains or ATP-dependent chromatin remodeling (6, 7).The core histone tail domains are essential for compaction of oligonucleosome arrays into secondary chromatin structures and for efficient assembly of oligomeric tertiary structures (1, 2, 8 -10). However, the structures and interactions of the histone tail domains and the molecular mechanisms by which they facilitate chromatin compaction remain largely uncharacterized. Evidence indicates that these highly basic domains interact with both protein and DNA targets within chromatin (11-15), and it is generally assumed that the core histone tail domains participate in internucleosomal as well as intranucleosome interactions within condensed chromatin. Indeed, several crystal structures of nucleosome core particles indicate that the tails project away from the main body of the nucleosome to potentially mediate internucleosomal interactions (2,16,17). These interactions may occur in cis, between nucleosomes within...

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“…This hierarchical folding of the DNA molecule is likely to imply constraints on the molecule bending and flexibility properties and on the capability of interacting with and of being anchored to protein matrix and scaffold. So far, such constraints have been evidenced to favour the formation and positioning of nucleosomes [15,16,17,18,19]. These structural properties depend upon the local nucleotides composition and therefore can be seen as statistical features of the DNA primary structure [20,21,22,23,24,25,26].…”

Section: Introductionmentioning

confidence: 99%

Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

Audit

Vaillant

Arnéodo

et al. 2004

Journal of Biological Physics

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Abstract. Analyses of genomic DNA sequences have shown in previous works that base pairs are correlated at large distances with scale-invariant statistical properties. We show in the present study that these correlations between nucleotides (letters) result in fact from long-range correlations (LRC) between sequence-dependent DNA structural elements (words) involved in the packaging of DNA in chromatin. Using the wavelet transform technique, we perform a comparative analysis of the DNA text and of the corresponding bending profiles generated with curvature tables based on nucleosome positioning data. This exploration through the optics of the so-called 'wavelet transform microscope' reveals a characteristic scale of 100 − 200 bp that separates two regimes of different LRC. We focus here on the existence of LRC in the small-scale regime ( 200 bp). Analysis of genomes in the three kingdoms reveals that this regime is specifically associated to the presence of nucleosomes. Indeed, small scale LRC are observed in eukaryotic genomes and to a less extent in archaeal genomes, in contrast with their absence in eubacterial genomes. Similarly, this regime is observed in eukaryotic but not in bacterial viral DNA genomes. There is one exception for genomes of Poxviruses, the only animal DNA viruses that do not replicate in the cell nucleus and do not present small scale LRC. Furthermore, no small scale LRC are detected in the genomes of all examined RNA viruses, with one exception in the case of retroviruses. Altogether, these results strongly suggest that small-scale LRC are a signature of the nucleosomal structure. Finally, we discuss possible interpretations of these small-scale LRC in terms of the mechanisms that govern the positioning, the stability and the dynamics of the nucleosomes along the DNA chain. This paper is maily devoted to a pedagogical presentation of the theoretical concepts and physical methods which are well suited to perform a statistical analysis of genomic sequences. We review the results obtained with the so-called waveletbased multifractal analysis when investigating the DNA sequences of various organisms in the three kingdoms. Some of these results have been announced in B. Audit et al. [1,2].

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Direct detection of linker DNA bending in defined-length oligomers of chromatin.

Cited by 74 publications

References 36 publications

Nucleosome packaging and nucleosome positioning of genomic DNA

Nucleosome packaging and nucleosome positioning of genomic DNA

Salt-dependent Intra- and Internucleosomal Interactions of the H3 Tail Domain in a Model Oligonucleosomal Array

Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

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