Issue August 2006

category image Volume 24
No. 1 (p 1-90)
August 2006
ISSN 0739-110

Sequence Structure of Human Nucleosome DNA (p. 43-48)

Positional distributions of various dinucleotides in experimentally derived human nucleosome DNA sequences are analyzed. Nucleosome positioning in this species is found to depend largely on GG and CC dinucleotides periodically distributed along the nucleosome DNA sequence, with the period of 10.4 bases. The GG and CC dinucleotides oscillate counterphase, i.e., their respective preferred positions are shifted about a half-period from one another, as it was observed earlier for AA and TT dinucleotides. Other purine-purine and pyrimidine-pyrimidine dinucleotides (RR and YY) display the same periodical and counterphase pattern. The dominance of oscillating GG and CC dinucleotides in human nucleosomes and the contribution of AG(CT), GA(TC), and AA(TT) suggest a general nucleosome DNA sequence pattern -- counterphase oscillation of RR and YY dinucleotides. AA and TT dinucleotides, commonly accepted as major players, are only weak contributors in the case of human nucleosomes.

Key words: Chromatin; Periodical pattern; GG/CC periodicity; RR/YY periodicity; Nucleosome signal.

Simon B. Kogan1
Megumi Kato2
Ryoiti Kiyama2
Edward N. Trifonov1,*

1Genome Diversity Center
Institute of Evolution
University of Haifa
Mount Carmel
Haifa 31905, Israel
2Research Institute for Biological Resources and Functions
National Institute of Advanced Industrial Science and Technology
1-1-1 Higashi Tsukuba
Ibaraki 305-8566, Japan
*trifonov@research.haifa.ac.il

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