Yeast Nucleosome DNA Pattern: Deconvolution from Genome Sequences of S. cerevisiae

• Published in: Journal of biomolecular structure & dynamics Vol. 22; no. 6; pp. 687 - 693
• Main Authors: Cohanim, Amir B., Kashi, Yechezkel, Trifonov, Edward N.
• Format: Journal Article
• Language: English
• Published: England Taylor & Francis Group 01.06.2005
• Subjects: Algorithms; Base Composition; Base Sequence; DNA, Fungal - chemistry; Genome; Models, Chemical; Nucleosomes - chemistry; Nucleotides - chemistry; Saccharomyces cerevisiae - genetics; Sequence Analysis, DNA; Sequence Homology, Nucleic Acid
• ISSN: 0739-1102; 1538-0254
• DOI: 10.1080/07391102.2005.10507035

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.