Sequence Structure of Human Nucleosome DNA

Abstract 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.

[1]  Edward N Trifonov,et al.  Gene splice sites correlate with nucleosome positions. , 2004, Gene.

[2]  Ryoiti Kiyama,et al.  Dinucleosome DNA of human K562 cells: experimental and computational characterizations. , 2003, Journal of molecular biology.

[3]  J. Widom,et al.  Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites. , 2000, Journal of molecular biology.

[4]  E. Trifonov,et al.  The pitch of chromatin DNA is reflected in its nucleotide sequence. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[5]  E. Trifonov,et al.  Nucleotide sequence-directed mapping of the nucleosomes. , 1983, Nucleic acids research.

[6]  Masaru Tomita,et al.  ApA Dinucleotide Periodicity in Prokaryote, Eukaryote, and Organelle Genomes , 1999, Journal of Molecular Evolution.

[7]  M. Bina,et al.  Periodicity of dinucleotides in nucleosomes derived from simian virus 40 chromatin. , 1994, Journal of molecular biology.

[8]  Megumi Kato,et al.  Biochemical screening of stable dinucleosomes using DNA fragments from a dinucleosome DNA library. , 2005, Journal of molecular biology.

[9]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[10]  Joshua Jortner,et al.  Modelling of Biomolecular Structures and Mechanisms , 1995 .

[11]  R. Simpson.  Structure of the chromatosome, a chromatin particle containing 160 base pairs of DNA and all the histones. , 1978, Biochemistry.

[12]  Hanspeter Herzel,et al.  10-11 bp periodicities in complete genomes reflect protein structure and DNA folding , 1999, Bioinform..

[13]  J. Widom,et al.  Nucleosomal locations of dominant DNA sequence motifs for histone-DNA interactions and nucleosome positioning. , 2004, Journal of molecular biology.

[14]  Lani F. Wu,et al.  Genome-Scale Identification of Nucleosome Positions in S. cerevisiae , 2005, Science.

[15]  D M Crothers,et al.  Artificial nucleosome positioning sequences. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Yechezkel Kashi,et al.  Yeast Nucleosome DNA Pattern: Deconvolution from Genome Sequences of S. cerevisiae , 2005, Journal of biomolecular structure & dynamics.

[17]  Alexander Bolshoy,et al.  CC dinucleotides contribute to the bending of DNA in chromatin , 1995, Nature Structural Biology.

[18]  V. Zhurkin,et al.  Anisotropic flexibility of DNA and the nucleosomal structure. , 1979, Nucleic acids research.

[19]  A. Ehrenhofer-Murray,et al.  Chromatin dynamics at DNA replication, transcription and repair. , 2004, European journal of biochemistry.

[20]  M. Borodovsky,et al.  Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences. , 1996, Journal of molecular biology.

[21]  J. Widom,et al.  Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences. , 1999, Journal of molecular biology.