Sequence periodicities in chicken nucleosome core DNA

Satchwell, Sandra C.; Drew, Horace R.; Travers, Andrew

doi:10.1016/0022-2836(86)90452-3

Cited by 907 publications

(969 citation statements)

References 47 publications

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“…There exists another rather well identified periodicity of 10.2-10.4 bp that is unique to the eukaryotic genomes. This periodicity is likely to be the consequence of the wrapping of DNA around the histone octamer [20,23,25,26,37,38,43,44,45,46,47,48], since a slight but significant decrease of the helical repeat has been observed experimentally in the nucleosome where the weight average of 8 independent measurements yields a periodicity of 10.39 ± 0.02 bp/turn (see Table II in [49]). This positive supercoiling is mainly seen in the distribution of some dinucleotides such as AA(= TT), GC, and GG(= CC) to some lower extent.…”

Section: Introductionmentioning

confidence: 91%

“…The perfectly well established structure of nucleosomes dictates that the DNA sequence provides a proper rotational orientation of the double helix around the core histone. It is admitted that among the sequences that favour the formation of nucleosomes, those which contribute significantly to their positioning display a characteristic periodicity of about 10.2 bp, like for example the dinucleotides AA (=TT) and GG (=CC) which are known to play a major role in the intrinsic bending and flexibility properties of the DNA double helix [20,23,25,26,37,43,44,45,46,47,48]. Actually, it has been estimated that only a small fraction of about 5% of the genome presents this periodic sequence-directed nucleosome positioning properties, that are larger than in the bulk genomic sequences.…”

Section: What Mechanisms Underly Lrc In Genome Sequences?mentioning

confidence: 99%

“…As previously emphasized, these tables are likely to provide pertinent codings of the local bending and flexibility properties of the DNA double helix. The former is deduced from experimentally determined nucleosome positioning [43]. The later is based on sensitivity of DNA fragments to the enzyme DNase I [52,154].…”

Section: Trinucleotide Coding Rulesmentioning

confidence: 99%

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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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Section: Introductionmentioning

confidence: 91%

Section: What Mechanisms Underly Lrc In Genome Sequences?mentioning

confidence: 99%

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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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“…Recognition of binding sites by DNA binding proteins such as 434 repressor, Cro, CAP, and other protein-DNA complexes has been proposed to be achieved by the sequence specific deformability of DNA (Drew & Travers, 1985;Crothers et al, 1988;Koudelka et al, 1988;Satchwell et al, 1986;Schultz et al, 1991). The bend in the DNA under consideration must be interpreted with respect to the location, magnitude, and direction of the bend introduced by the UvrB-DNA complex.…”

Section: Design Considerntions Jhr the Synthesis Of Spin-lnheludmentioning

confidence: 99%

Spin-Labeled Psoralen Probes for the Study of DNA Dynamics

Hp¹,

Dy²,

Ng³

et al. 1995

Biochemistry

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Six nitroxide spin-labeled psoralen derivatives have been synthesized and evaluated as probes for structural and dynamic studies. Sequence specific photoaddition of these derivatives to DNA oligonucleotides resulted in site-specifically cross-linked and spin-labeled oligomers. Comparison of the general line shape features of the observed electron paramagnetic resonance (EPR) spectra of several duplexes ranging in size from 8 to 46 base pairs with simulated EPR spectra indicate that the nitroxide spin-label probe reports the global tumbling motion of the oligomers. While there is no apparent large amplitude motion of the psoralen other than the overall tumbling of the DNA on the time scales investigated, there are indications of bending and other residual motions. The (A)BC excinuclease DNA repair system detects structural or dynamic features of the DNA that distinguish between damaged and undamaged DNA and are independent of the intrinsic structure of the lesion. NMR studies have shown that psoralencross-linked DNA has altered backbone dynamics and conformational populations in the immediate vicinity Psoralen-damaged DNA serves as an excellent substrate for the study of structural and dynamic motifs that DNA repair enzyme systems may recognize. Psoralens are photoreagents which form a well-characterized set of covalent nucleic acid adducts through photochemical addition ( Figure 1) (Straub et al., 1981; Kanne et al., 1982a,b). The primary reaction is cyclobutane ring formation between the 5,6 double bond of thymidine in DNA and either the 4',5' or 3,4 double bonds of the psoralen. Reaction at the 4'3' double bond creates a furanside monoadduct (MAf),' which can react further at a site with opposed and adjacent pyrimidines to create an interstrand cross-link (XL). The XL is a rigid unit formed by the psoralen and the opposite and adjacent pyrimidine bases, linking the two strands together. Reaction at the 3,4 double bond of the psoralen first creates a pyroneside monoadduct (MAP), which cannot form an interstrand cross-link.Psoralen-DNA monoadducts and cross-links are recognized and removed by the excision repair system in both

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“…A translational signal is a DNA feature that determines the position of the histone octamer along the DNA sequence. Sequences that accommodate the DNA structural shifts seen near the dyad axis of the nucleosome may serve as a translational signal [Satchwell et al, 1986;Travers and Klug, 19871. Alternatively, a translational signal may be provided by sequences in the linker region or on the edge of the nucleosome core. A rotational setting (signal), reflecting the curvature of the DNA, defines the side which faces the histone octamer.…”

Section: Parameters To Describe Nucleosome Positionsmentioning

confidence: 99%

Nucleosome positioning and gene regulation

Wallrath

Elgin

1994

J of Cellular Biochemistry

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Recent genetic and biochemical studies have revealed critical information concerning the role of nucleosomes in eukaryotic gene regulation. Nucleosomes package DNA into a dynamic chromatin structure, and by assuming defined positions in chromatin, influence gene regulation. Nucleosomes can serve as repressors, presumably by blocking access to regulatory elements; consequently, the positions of nucleosomes relative to the location of cis-acting elements are critical. Some genes have a chromatin structure that is "preset," ready for activation, while others require "remodeling" for activation. Nucleosome positioning may be determined by multiple factors, including histone-DNA interactions, boundaries defined by DNA structure or protein binding, and higher-order chromatin Structure.

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Sequence periodicities in chicken nucleosome core DNA

Cited by 907 publications

References 47 publications

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

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

Spin-Labeled Psoralen Probes for the Study of DNA Dynamics

Nucleosome positioning and gene regulation

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