Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences

Thåström, A.; Lowary, Peggy T.; Widlund, Hans R.; Cao, Hui; Kubista, Mikael; Widom, Jonathan

doi:10.1006/jmbi.1999.2686

Cited by 358 publications

(374 citation statements)

References 32 publications

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“…Periodicity of this dinucleotide is documented as characteristic of selected most stable nucleosomes [Thastrom, Lowary et al 1999]. In our work the emphasis has been always on the patterns that are characteristic of bulk chromatin.…”

Section: Discussionmentioning

confidence: 96%

Gene splice sites correlate with nucleosome positions

Kogan

Trifonov

2005

Gene

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Gene sequences in the vicinity of splice sites are found to possess dinucleotide periodicities, especially RR and YY, with the period close to the pitch of nucleosome DNA. This confirms previously reported finding about preferential positioning of splice junctions within the nucleosomes. The RR and YY dinucleotides oscillate counterphase, i.e., their respective preferred positions are shifted about half-period one from another, as it was observed earlier for AA and TT dinucleotides. Species specificity of nucleosome positioning DNA pattern is indicated by predominant use of the periodical GG(CC) dinucleotides in human and mouse genes, as opposed to predominant AA(TT) dinucleotides in Arabidopsis and C.elegans.

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Section: Discussionmentioning

confidence: 96%

Gene splice sites correlate with nucleosome positions

Kogan

Trifonov

2005

Gene

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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%

“…In the present study, we report results obtained with particular dinucleotides which are known to participate to the positioning and formation of nucleosomes [26]. The 'AA', 'GG', 'TT' and 'CC' coding rules consist in coding with 1 at the considered nucleotide positions provided at least one of the nearest neighbour nucleotides be the same nucleotide and 0 at the other positions.…”

Section: Dinucleotide Coding Rulesmentioning

confidence: 97%

“…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%

“…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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