Issue June 2005

category image Volume 22
No. 6 (p 615-878)
June 2005
ISSN 0739-110

Yeast Nucleosome DNA Pattern: Deconvolution from Genome Sequences of S. cerevisiae (p. 687-694)

Positional correlation analysis for the complete genome of Saccharomyces cerevisiae is performed with the aim to reveal possible chromatin-related sequence features. A strong periodicity with the period 10.4 bases is detected in the distance histograms for the dinucleotides AA and TT, with the characteristic decay distance of approximately 50 base pairs. The oscillations are observed as well in the distributions of other dinucleotides. However, the respective amplitudes are small, consistent with secondary effects, due to dominant periodicity of AA and TT. The observations are in accord with earlier data on the chromatin sequence periodicities and nucleosome DNA sequence patterns. The autocorrelations of AA and TT dinucleotides in yeast include also a counter-phase component. A tentative DNA sequence pattern for the yeast nucleosomes is suggested and verified by comparison of its autocorrelation plots with the respective natural autocorrelations. The nucleosome mapping guided by the pattern is in accord with experimental data on the linker length distribution in yeast.

Amir B. Cohanim1
Yechezkel Kashi1
Edward N. Trifonov2,*

1Department of Biotechnology and Food Engineering
Technion, Haifa 32000, Israel
2Genome Diversity Center
Institute of Evolution
University of Haifa
Haifa 31905, Israel
*Email: trifonov@research.haifa.ac.il

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