DNA sequence encodes information for nucleosome array formation 1 1Edited by T. Richmond

Key, Liu; Stein, Arnold

doi:10.1006/jmbi.1997.1136

Cited by 23 publications

(20 citation statements)

References 57 publications

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“…The periodic positioning of these dinucleotides with a rather definite phase shift between them (e.g., about 5 bases between AA and TT as well as in between AA and GC) contributes in a coherent manner to a global curvature of DNA which is likely to amplify the affinity for the histone octamer and therefore to favour the wrapping of DNA on the histone surface [6,18]. Larger periodicities are further observed that may also be related to the hierarchical organization of DNA via successive foldings of higher order structured nucleoprotein complexes [24]. Actually, the 200-and 400-base periodicities identified in eukaryotic sequences might correspond to the characteristic sizes of a nucleosome or of a dinucleosome [38].…”

Section: Introductionmentioning

confidence: 94%

“…Indeed, one cannot exclude the possibility that the rather well positioned nucleosomes be concentrated in vast regions leading to the formation of somehow distinct chromatin structures which may facilitate DNA function in a chromatin context, i.e. the functioning of particular genes or loci [24]. Since a large proportion (about 95%) of genomic DNA has a free energy for nucleosome formation that little differs from that of random DNA, one may be tempted to conclude that the DNA sequence has no appreciable influence on nucleosome formation for the vast majority of them.…”

Section: What Mechanisms Underly Lrc In Genome Sequences?mentioning

confidence: 99%

“…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]. The actual challenge is thus to find a way to extract these structural informations from an appropriate reading of the DNA text.…”

Section: Introductionmentioning

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: 94%

Section: What Mechanisms Underly Lrc In Genome Sequences?mentioning

confidence: 99%

Section: Introductionmentioning

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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“…The cause of apparent variability in chromatin structure and its relationship with the function is not clear. It is plausible that nucleosome arrays displaying different nucleosome arrangements form stretches of chromatin having distinct higher-order structures (6,7) or different modes of flexibility (8) due to variations in the rotational orientation between adjacent nucleosomes (2). Knowledge of the mechanisms by which distinctive higher-order chromatin structures intrinsically form should provide new insights into how histone modification and the presence of non-histone chromosomal proteins can remodel chromatin structure in a functional way (9).…”

Section: Introductionmentioning

confidence: 99%

Long-range oscillation in a periodic DNA sequence motif may influence nucleosome array formation

Dalal

Fleury

Cioffi

et al. 2005

Nucleic Acids Research

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We have experimentally examined the characteristics of nucleosome array formation in different regions of mouse liver chromatin, and have computationally analyzed the corresponding genomic DNA sequences. We have shown that the mouse adenosine deaminase (MADA) gene locus is packaged into an exceptionally regular nucleosome array with a shortened repeat, consistent with our computational prediction based on the DNA sequence. A survey of the mouse genome indicates that <10% of 70 kb windows possess a nucleosome-ordering signal, consisting of regular long-range oscillations in the period-10 triplet motif non-T, A/T, G (VWG), which is as strong as the signal in the MADA locus. A strong signal in the center of this locus, confirmed by in vitro chromatin assembly experiments, appears to cooperate with weaker, in-phase signals throughout the locus. In contrast, the mouse odorant receptor (MOR) locus, which lacks locus-wide signals, was representative of ∼40% of the mouse genomic DNA surveyed. Within this locus, nucleosome arrays were similar to those of bulk chromatin. Genomic DNA sequences which were computationally similar to MADA or MOR resulted in MADA- or MOR-like nucleosome ladders experimentally. Overall, we provide evidence that computationally predictable information in the DNA sequence may affect nucleosome array formation in animal tissue.

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“…Since it has recently been shown, using randomly selected chicken genomic DNA sequences, that both the regularity of nucleosomal arrays and the value of the nucleosome repeat length are highly DNA sequence-dependent (63) and since the different plasmid regions tested might have different affinities for core histones, we wished to exclude the possibility that these phenomena were responsible for the MNase pattern obtained in the regions proximal to the heterochromatic insert, which indicate a higher nucleosome density in these regions compared with the more distant ones. A control was thus performed to confirm the effect of satellite DNA on the process of nucleosome formation in the flanking regions.…”

Section: Fig 2 In Vitro Chromatin Assemblymentioning

confidence: 99%

In Vitro Reconstitution of Artemia Satellite Chromatin

Motta¹,

Landsberger

Merli

et al. 1998

Journal of Biological Chemistry

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We report the characterization of an in vitro chromatin assembly system derived from Artemia embryos and its application to the study of AluI-113 satellite DNA organization in nucleosomes. The system efficiently reconstitutes chromatin templates by associating DNA, core histones, and H1. The polynucleosomal complexes show physiological spacing of repeat length 190 ؎ 5 base pairs, and the internucleosomal distances are modulated by energy-using activities that contribute to the dynamics of chromatin conformation. The assembly extract was used to reconstitute tandemly repeated AluI-113 sequences. The establishment of preferred histone octamer/satellite DNA interactions was observed. In vitro, AluI-113 elements dictated the same nucleosome translational localizations as found in vivo. Specific rotational constraints seem to be the central structural requirement for nucleosome association. Satellite dinucleosomes showed decreased translational mobility compared with mononucleosomes. This could be the consequence of interactions between rotationally positioned nucleosomes separated by linker DNA of uniform length. AluI-113 DNA led to weak cooperativity of nucleosome association in the proximal flanking regions, which decreased with distance. Moreover, the structural properties of satellite chromatin can spread, thus leading to a specific organization of adjacent nucleosomes.Most higher eukaryotic DNA is folded into a dynamic nucleoprotein structure, which is subject to progressive and reversible modifications of its condensation state during transitions between interphasic and metaphasic chromatin. However, there are chromosomal regions that maintain cytological properties comparable with those of the metaphase chromosome throughout the cell cycle (1). Termed heterochromatin, these highly condensed regions consist of simple DNA sequences repeated in long tandem arrays and are typically localized around centromeres and telomeres (reviewed in Refs. 2 and 3). Heterochromatic regions are replicated late during S phase (4, 5); they do not participate in meiotic recombination and are generally associated with the transcriptionally repressed state (reviewed in Ref. 6). These regions can influence the expression of juxtaposed genes in a manner dependent on their distance from the point of juxtaposition, a phenomenon called "position effect variegation" (7-9). Position effect variegation is thought to take place either by compartmentalization within transcriptionally inactive nuclear regions or by virtue of the spread of the heterochromatic structure (reviewed in Refs. 10 and 11).Heterochromatin is generally defined as highly organized chromatin structures stabilized by multiprotein complexes and is functionally correlated with diffusible transcription repressing properties (11). Genetic and molecular studies have shown that the process of heterochromatinization involves the spread of particular chromatin structures in the cases of pericentric insertions of euchromatic genes in Drosophila (12), centromeric insertion of the ur...

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DNA sequence encodes information for nucleosome array formation 1 1Edited by T. Richmond

Cited by 23 publications

References 57 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

Long-range oscillation in a periodic DNA sequence motif may influence nucleosome array formation

In Vitro Reconstitution of Artemia Satellite Chromatin

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