Nucleosome DNA sequence structure of isochores

Frenkel, Zakharia M.; Bettecken, Thomas; Trifonov, Edward N.

doi:10.1186/1471-2164-12-203

Cited by 22 publications

(23 citation statements)

References 25 publications

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“…The Poincaré recurrences P (t) are statistically very stable and show a clear difference between various species. The statistical analysis of human and mammalian DNA sequences is now an active research field with links to genome evolution (see, e.g., [24][25][26]) and the approach based on Poincaré recurrences should bring here new useful insights.…”

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confidence: 99%

Poincaré recurrences of DNA sequences

Frahm

Shepelyansky

2012

Phys. Rev. E

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We analyze the statistical properties of Poincaré recurrences of Homo sapiens, mammalian, and other DNA sequences taken from the Ensembl Genome data base with up to 15 billion base pairs. We show that the probability of Poincaré recurrences decays in an algebraic way with the Poincaré exponent β≈4 even if the oscillatory dependence is well pronounced. The correlations between recurrences decay with an exponent ν≈0.6 that leads to an anomalous superdiffusive walk. However, for Homo sapiens sequences, with the largest available statistics, the diffusion coefficient converges to a finite value on distances larger than one million base pairs. We argue that the approach based on Poncaré recurrences determines new proximity features between different species and sheds a new light on their evolution history.

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confidence: 99%

Poincaré recurrences of DNA sequences

Frahm

Shepelyansky

2012

Phys. Rev. E

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“…34,35 It was shown that Shannon's fusing can generate motifs like TTTTCGAAAA and TTTTTGAAAA 34,35 with a periodic structure on both sides of central motif, representing a nucleosome positioning patterns. Although a string similar to central motif starting with Shannon construction of trinucleotide frequencies alpha satellite HORs is found here, they do not exhibit any periodic structure to sides of the central motif (Supplementary figure 2).…”

Section: Resultsmentioning

confidence: 99%

Start/stop Codon-like Trinucleotides (CLTs) and Extended Clusters as New Language of DNA

Rosandić¹,

Glunčić²,

Paar³

2011

Croat. Chem. Acta

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Abstract. DNA nucleotide sequences carry genetic information of different kinds, not just coding instructions for protein synthesis. They can play a role, for example, in alternative conformations and gene regulators. The present paper introduces the extended start/stop codon-like trinucleotides (CLTs) for noncoding DNA sequences, based on trinucleotide cluster extension generated by specific single-nucleotide multiplications. Extended cluster analysis gives rise to rich information potential as a "new language" of DNA ("CLT-language"). The analysis of start/stop-CLTs extended clusters provides qualitative and quantitative differentiation and characterization of alpha satellites, as well as of other repetitive and non-repetitive noncoding sequences. As a measure of CLT extension of DNA sequences the extension factor r is introduced. Start/stop CLTs enable a distinction of three segments within alpha satellite, the first and the second as wrapping sequences and the third as a linker. Within a linker there are no start/stop CLTs. On the basis of start/stop-CLTs, it is hypothesized that these noncoding sequences may be involved in the networks of gene regulators. (doi: 10.5562/cca1948)

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“…The consensuses derived from the LW sequences, perhaps, are as close to the final solution(s) as they can be at the current state of the chromatin studies, considering their strong YR(TA) periodicity and the nearly perfect fit of the consensuses to the alternating runs of purines and pyrimidines, found earlier by several different approaches (Rapoport et al, 2011;Frenkel et al, 2011;Salih et al, 2015). Still, more efforts are needed, both computational and experimental ones, to establish with full certainty the final structure(s) of the ideal nucleosome DNA sequence.…”

Section: Towards Ultimate Ideal Nucleosome Positioning Motif(s)mentioning

confidence: 97%

“…The nucleosome DNA, thus, consists of mixture of repeats TAN 8 and TAN 9 or, more generally, YRN 8 (10-mer) and YRN 9 (11-mer), elementary segments of nucleosome DNA structure. Recent analysis of the TA-periodic LW sequences revealed (ibid) that the TA decamers have the sequence structure TAGAGGCCTCta which corresponds to one period of the repeat (AGAGGCCTCT) n , or (RRRRRYYYYY) n , a universal consensus of nucleosome DNA motif, derived from a representative spectrum of eukaryotic genome sequences (Rapoport et al, 2011;Frenkel et al, 2011;ibid).…”

Section: Introductionmentioning

confidence: 98%

Sequence structure of Lowary/Widom clones forming strong nucleosomes

Trifonov

2015

Journal of Biomolecular Structure and Dynamics

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Lowary and Widom selected from random sequences those which form exceptionally stable nucleosomes, including clone 601, the current champion of strong nucleosome (SN) sequences. This unique sequence database (LW sequences) carries sequence elements which confer stability on the nucleosomes formed on the sequences, and, thus, may serve as source of information on the structure of "ideal" or close to ideal nucleosome DNA sequence. An important clue is also provided by crystallographic study of Vasudevan and coauthors on clone 601 nucleosomes. It demonstrated that YR·YR dinucleotide stacks (primarily TA·TA) follow one another at distances 10 or 11 bases or multiples thereof, such that they all are located on the interface between DNA and histone octamer. Combining this important information with alignment of the YR-containing 10-mers and 11-mers from LW sequences, the bendability matrices of the stable nucleosome DNA are derived. The matrices suggest that the periodically repeated TA (YR), RR, and YY dinucleotides are the main sequence features of the SNs. This consensus coincides with the one for recently discovered SNs with visibly periodic DNA sequences. Thus, the experimentally observed stable LW nucleosomes and SNs derived computationally appear to represent the same entity - exceptionally stable SNs.

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Nucleosome DNA sequence structure of isochores

Cited by 22 publications

References 25 publications

Poincaré recurrences of DNA sequences

Poincaré recurrences of DNA sequences

Start/stop Codon-like Trinucleotides (CLTs) and Extended Clusters as New Language of DNA

Sequence structure of Lowary/Widom clones forming strong nucleosomes

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