Correlation between the flexibility and periodic dinucleotide patterns in yeast nucleosomal DNA sequences

Qinqin Wu, Weiqiang Zhou, Jiajun Wang, Hong Yan

Research output: Contribution to journalArticle

Abstract

Nucleosome formation and positioning, which play important roles in a number of biological processes, are thought to be related to the distinctive periodic dinucleotide patterns observed in the DNA sequence wrapped around the protein octamer. Previous research shows that flexibility is a key structural property of a nucleosomal DNA sequence. However, the relationship between the flexibility and the periodic dinucleotide patterns has received little attention in research in the past. In this study, we propose the use of three different models to measure the flexibility of yeast DNA sequences. Although the three models involve different parameters, they deliver consistent results showing that yeast nucleosomal DNA sequences are more flexible than non-nucleosomal ones. In contrast to random flexibility values along non-nucleosomal DNA sequences, the flexibility of nucleosomal DNA sequences shows a clear periodicity of 10.14 base pairs, which is consistent with the periodicity of dinucleotide distributions. We also demonstrate that there is a strong relationship between the peak positions of the flexibility and the dinucleotide frequencies. Correlation between the flexibility and the dinucleotide patterns of CA/TG, CG, GC, GG/CC, AG/CT, AC/GT and GA/TC are positive with an average value of 0.5946. The highest correlation is shown by CA/TG with a value of 0.7438 and the lowest correlation is shown by AA/TT with a value of -0.7424. The source codes and data sets are available for downloading on http://www.hy8.com/bioinformatics.htm.

Original languageEnglish (US)
Pages (from-to)92-98
Number of pages7
JournalJournal of Theoretical Biology
Volume284
Issue number1
DOIs
StatePublished - Sep 7 2011
Externally publishedYes

Fingerprint

DNA sequences
Yeast
DNA Sequence
Yeasts
Flexibility
yeasts
nucleotide sequences
Periodicity
periodicity
Biological Phenomena
nucleosomes
Nucleosomes
Bioinformatics
Computational Biology
Research
bioinformatics
Base Pairing
Structural properties
Structural Properties
Positioning

Keywords

  • DNA sequence flexibility
  • Nucleosome positioning and formation
  • Nucleosomes
  • Periodic dinucleotides

ASJC Scopus subject areas

  • Statistics and Probability
  • Modeling and Simulation
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Agricultural and Biological Sciences(all)
  • Applied Mathematics

Cite this

Correlation between the flexibility and periodic dinucleotide patterns in yeast nucleosomal DNA sequences. / Wu, Qinqin; Zhou, Weiqiang; Wang, Jiajun; Yan, Hong.

In: Journal of Theoretical Biology, Vol. 284, No. 1, 07.09.2011, p. 92-98.

Research output: Contribution to journalArticle

@article{c6700d23d30b41c79850e4db4e66661a,
title = "Correlation between the flexibility and periodic dinucleotide patterns in yeast nucleosomal DNA sequences",
abstract = "Nucleosome formation and positioning, which play important roles in a number of biological processes, are thought to be related to the distinctive periodic dinucleotide patterns observed in the DNA sequence wrapped around the protein octamer. Previous research shows that flexibility is a key structural property of a nucleosomal DNA sequence. However, the relationship between the flexibility and the periodic dinucleotide patterns has received little attention in research in the past. In this study, we propose the use of three different models to measure the flexibility of yeast DNA sequences. Although the three models involve different parameters, they deliver consistent results showing that yeast nucleosomal DNA sequences are more flexible than non-nucleosomal ones. In contrast to random flexibility values along non-nucleosomal DNA sequences, the flexibility of nucleosomal DNA sequences shows a clear periodicity of 10.14 base pairs, which is consistent with the periodicity of dinucleotide distributions. We also demonstrate that there is a strong relationship between the peak positions of the flexibility and the dinucleotide frequencies. Correlation between the flexibility and the dinucleotide patterns of CA/TG, CG, GC, GG/CC, AG/CT, AC/GT and GA/TC are positive with an average value of 0.5946. The highest correlation is shown by CA/TG with a value of 0.7438 and the lowest correlation is shown by AA/TT with a value of -0.7424. The source codes and data sets are available for downloading on http://www.hy8.com/bioinformatics.htm.",
keywords = "DNA sequence flexibility, Nucleosome positioning and formation, Nucleosomes, Periodic dinucleotides",
author = "Qinqin Wu and Weiqiang Zhou and Jiajun Wang and Hong Yan",
year = "2011",
month = "9",
day = "7",
doi = "10.1016/j.jtbi.2011.06.026",
language = "English (US)",
volume = "284",
pages = "92--98",
journal = "Journal of Theoretical Biology",
issn = "0022-5193",
publisher = "Academic Press Inc.",
number = "1",

}

TY - JOUR

T1 - Correlation between the flexibility and periodic dinucleotide patterns in yeast nucleosomal DNA sequences

AU - Wu, Qinqin

AU - Zhou, Weiqiang

AU - Wang, Jiajun

AU - Yan, Hong

PY - 2011/9/7

Y1 - 2011/9/7

N2 - Nucleosome formation and positioning, which play important roles in a number of biological processes, are thought to be related to the distinctive periodic dinucleotide patterns observed in the DNA sequence wrapped around the protein octamer. Previous research shows that flexibility is a key structural property of a nucleosomal DNA sequence. However, the relationship between the flexibility and the periodic dinucleotide patterns has received little attention in research in the past. In this study, we propose the use of three different models to measure the flexibility of yeast DNA sequences. Although the three models involve different parameters, they deliver consistent results showing that yeast nucleosomal DNA sequences are more flexible than non-nucleosomal ones. In contrast to random flexibility values along non-nucleosomal DNA sequences, the flexibility of nucleosomal DNA sequences shows a clear periodicity of 10.14 base pairs, which is consistent with the periodicity of dinucleotide distributions. We also demonstrate that there is a strong relationship between the peak positions of the flexibility and the dinucleotide frequencies. Correlation between the flexibility and the dinucleotide patterns of CA/TG, CG, GC, GG/CC, AG/CT, AC/GT and GA/TC are positive with an average value of 0.5946. The highest correlation is shown by CA/TG with a value of 0.7438 and the lowest correlation is shown by AA/TT with a value of -0.7424. The source codes and data sets are available for downloading on http://www.hy8.com/bioinformatics.htm.

AB - Nucleosome formation and positioning, which play important roles in a number of biological processes, are thought to be related to the distinctive periodic dinucleotide patterns observed in the DNA sequence wrapped around the protein octamer. Previous research shows that flexibility is a key structural property of a nucleosomal DNA sequence. However, the relationship between the flexibility and the periodic dinucleotide patterns has received little attention in research in the past. In this study, we propose the use of three different models to measure the flexibility of yeast DNA sequences. Although the three models involve different parameters, they deliver consistent results showing that yeast nucleosomal DNA sequences are more flexible than non-nucleosomal ones. In contrast to random flexibility values along non-nucleosomal DNA sequences, the flexibility of nucleosomal DNA sequences shows a clear periodicity of 10.14 base pairs, which is consistent with the periodicity of dinucleotide distributions. We also demonstrate that there is a strong relationship between the peak positions of the flexibility and the dinucleotide frequencies. Correlation between the flexibility and the dinucleotide patterns of CA/TG, CG, GC, GG/CC, AG/CT, AC/GT and GA/TC are positive with an average value of 0.5946. The highest correlation is shown by CA/TG with a value of 0.7438 and the lowest correlation is shown by AA/TT with a value of -0.7424. The source codes and data sets are available for downloading on http://www.hy8.com/bioinformatics.htm.

KW - DNA sequence flexibility

KW - Nucleosome positioning and formation

KW - Nucleosomes

KW - Periodic dinucleotides

UR - http://www.scopus.com/inward/record.url?scp=79960020284&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79960020284&partnerID=8YFLogxK

U2 - 10.1016/j.jtbi.2011.06.026

DO - 10.1016/j.jtbi.2011.06.026

M3 - Article

VL - 284

SP - 92

EP - 98

JO - Journal of Theoretical Biology

JF - Journal of Theoretical Biology

SN - 0022-5193

IS - 1

ER -