Enhancement of the nucleosomal pattern in sequences of lower complexity

Alex Bolshoy; Kevin Shapiro; Edward N. Trifonov; Ilya Ioshikhes

doi:10.1093/nar/25.16.3248

Enhancement of the nucleosomal pattern in sequences of lower complexity

Alex Bolshoy, Kevin Shapiro, Edward N. Trifonov, Ilya Ioshikhes

Research output: Contribution to journal › Article › peer-review

Abstract

Intuitively, the complexity of a given DNA sequence is related to the number of various superimposed biological messages it contains. Here we assess the expectation that in nucleosome DNA sequences of lower linguistic complexity, the nucleosome DNA positioning pattern would be more pronounced than in those of higher linguistic complexity. The nucleosome DNA positioning pattern is one of the weakest (highly degenerate) sequence patterns. It has been extracted recently by specially designed multiple alignment procedures. We applied the most sensitive of these procedures to nearly equal subsets of a nucleosome database separated according to linguistic complexity. The pattern extracted from the subset of the simpler nucleosome sequences not only possesses all major attributes of the known nucleosomal pattern, but is substantially stronger with respect to amplitude in comparison with the total database. This result constitutes the first demonstration that a weak pattern can be significantly enhanced by selective treatment of a lower complexity subset of the sequence ensemble under consideration.

Original language	English
Pages (from-to)	3248-3254
Number of pages	7
Journal	Nucleic Acids Research
Volume	25
Issue number	16
DOIs	https://doi.org/10.1093/nar/25.16.3248
State	Published - 1997
Externally published	Yes

Bibliographical note

Funding Information:
The authors are thankful to E.Kolker, who kindly provided an original program for spectral analysis, and to Dr E.Shpigelman for his version of a program for the linguistic complexity calculations. The authors would also like to express their gratitude to Drs S.Brunak and H.Herzel for their invaluable suggestions during the preparation of the manuscript. A.B. was supported by the Bat Sheva de Rothschild Fund for the Advancement of Science in Israel and the National Laboratory for Bioinformatics and DNA Sequencing of the Israel Council for Higher Education and is supported by the Danish National Research Foundation. I.I. was supported by a L.Bein WIS scholarship. K.S. received the Clarice D.Kaufmann Scholarship to the 28th Dr Bessie F.Lawrence International Summer Science Institute.

ASJC Scopus subject areas

Genetics

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title = "Enhancement of the nucleosomal pattern in sequences of lower complexity",

abstract = "Intuitively, the complexity of a given DNA sequence is related to the number of various superimposed biological messages it contains. Here we assess the expectation that in nucleosome DNA sequences of lower linguistic complexity, the nucleosome DNA positioning pattern would be more pronounced than in those of higher linguistic complexity. The nucleosome DNA positioning pattern is one of the weakest (highly degenerate) sequence patterns. It has been extracted recently by specially designed multiple alignment procedures. We applied the most sensitive of these procedures to nearly equal subsets of a nucleosome database separated according to linguistic complexity. The pattern extracted from the subset of the simpler nucleosome sequences not only possesses all major attributes of the known nucleosomal pattern, but is substantially stronger with respect to amplitude in comparison with the total database. This result constitutes the first demonstration that a weak pattern can be significantly enhanced by selective treatment of a lower complexity subset of the sequence ensemble under consideration.",

author = "Alex Bolshoy and Kevin Shapiro and Trifonov, {Edward N.} and Ilya Ioshikhes",

note = "Funding Information: The authors are thankful to E.Kolker, who kindly provided an original program for spectral analysis, and to Dr E.Shpigelman for his version of a program for the linguistic complexity calculations. The authors would also like to express their gratitude to Drs S.Brunak and H.Herzel for their invaluable suggestions during the preparation of the manuscript. A.B. was supported by the Bat Sheva de Rothschild Fund for the Advancement of Science in Israel and the National Laboratory for Bioinformatics and DNA Sequencing of the Israel Council for Higher Education and is supported by the Danish National Research Foundation. I.I. was supported by a L.Bein WIS scholarship. K.S. received the Clarice D.Kaufmann Scholarship to the 28th Dr Bessie F.Lawrence International Summer Science Institute.",

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AU - Ioshikhes, Ilya

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PY - 1997

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N2 - Intuitively, the complexity of a given DNA sequence is related to the number of various superimposed biological messages it contains. Here we assess the expectation that in nucleosome DNA sequences of lower linguistic complexity, the nucleosome DNA positioning pattern would be more pronounced than in those of higher linguistic complexity. The nucleosome DNA positioning pattern is one of the weakest (highly degenerate) sequence patterns. It has been extracted recently by specially designed multiple alignment procedures. We applied the most sensitive of these procedures to nearly equal subsets of a nucleosome database separated according to linguistic complexity. The pattern extracted from the subset of the simpler nucleosome sequences not only possesses all major attributes of the known nucleosomal pattern, but is substantially stronger with respect to amplitude in comparison with the total database. This result constitutes the first demonstration that a weak pattern can be significantly enhanced by selective treatment of a lower complexity subset of the sequence ensemble under consideration.

AB - Intuitively, the complexity of a given DNA sequence is related to the number of various superimposed biological messages it contains. Here we assess the expectation that in nucleosome DNA sequences of lower linguistic complexity, the nucleosome DNA positioning pattern would be more pronounced than in those of higher linguistic complexity. The nucleosome DNA positioning pattern is one of the weakest (highly degenerate) sequence patterns. It has been extracted recently by specially designed multiple alignment procedures. We applied the most sensitive of these procedures to nearly equal subsets of a nucleosome database separated according to linguistic complexity. The pattern extracted from the subset of the simpler nucleosome sequences not only possesses all major attributes of the known nucleosomal pattern, but is substantially stronger with respect to amplitude in comparison with the total database. This result constitutes the first demonstration that a weak pattern can be significantly enhanced by selective treatment of a lower complexity subset of the sequence ensemble under consideration.

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Enhancement of the nucleosomal pattern in sequences of lower complexity

Abstract

Bibliographical note

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