Genome Diversity Center

at the Institute of Evolution, University of Haifa

(Since August 2000)
Head: Edward N. Trifonov




How nucleosomes know where to sit?


DNA molecule possesses sequence-dependent deformational anisotropy.
That allows the histone octamers to select those DNA pieces that are better wrapped around the histones.
respective sequence patterns, essentially, are periodical repetitions of certain dinucleotides.
the latest development is species specificity of the nucleosome DNA sequence patterns.

Relevant references:

Salih, F., Salih, B., Kogan, S., Trifonov, E. N.
Epigenetic nucleosomes: Alu sequences and CG as nucleosome positioning element.
J Biomolec Str Dyn 26, 9-16 (2008)

Salih, F., Salih, B., Trifonov, E. N.
Sequence-directed mapping of nucleosome positions.
J Biomolec Str Dyn 24, 489-493 (2007)

Trifonov, E. N., Kogan, S., Cohanim, A. B.
Latest on the nucleosome positioning sequence patterns.
In "DNA Structure, Chromatin and Gene Expression" (Eds. R. Kiyama, M. Shimizu),
Transworld Research Network, Trivandrum (India), pp 43-54 (2006)

Kogan, S. B., Kato, M., Kiyama, R., Trifonov, E. N.,
Sequence structure of human nucleosome DNA.
J Biomol Str Dyn 24, 43-48 (2006)

Cohanim, A. B., Kashi, Y., Trifonov, E. N.,
Three sequence rules for chromatin,
J Biomol Str Dyn 23, 559-566 (2006)

Cohanim, A. B., Kashi, Y., Trifonov, E. N.,
Yeast nucleosome DNA pattern: deconvolution from genome sequences of S. cerevisiae.
J Biomol Str Dyn 22, 687-694 (2005)

Kato, M., Onishi, Y.,Wada-Kiyama, Y., Abe, T., Ikemura, T., Kogan, S., Bolshoy, A., Trifonov, E. N., Kiyama R.,
Dinucleosome DNA of human K562 cells: experimental and computational characterizations. J. Molec. Biol. 332, 111-125 (2003)

Kiyama, R., Trifonov, E. N., What positiones nucleosomes? - A model,
FEBS Let. 523, 7-11 (2002)

Fajkus, J., Trifonov, E. N., Columnar packing of telomeric nucleosomes.
Bioch. Bioph. Res. Com. 280, 961-963 (2001)

Herzel, H., Weiss, O., Trifonov, E. N.,
10-11 bp periodicities in complete genomes reflect protein structure and DNA folding.
Bioinformatics 15, 187-193 (1999)

Ioshikhes, I., Trifonov, E. N., Zhang, M. Q.,
Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure.
Proc. Natl. Acad. Sci. USA 96, 2891-2895 (1999)

Wada-Kiyama, Y., Kuwabara, K., Sakuma, Y., Onishi, Y., Trifonov, E. N., Kiyama, R.,
Localization of curved DNA and its association with nucleosome phasing
in the promoter region of the human estrogen receptor gene.
FEBS Letters 444, 117-124 (1999)

Bolshoy, A., Shapiro, K., Trifonov, E. N., Ioshikhes, I.,
Enhancement of the nucleosomal pattern in sequences of lower complexity.
Nucl. Acids Res. 25, 3248-3254 (1997)

Bolshoy, A., Ioshikhes, I., Trifonov, E. N.,
Applicability of the multiple alignment algorithm for detection of weak patterns:
Periodically distributed DNA pattern as a study case. CABIOS 12, 383-389 (1996)

Ioshikhes, I., Bolshoy, A., Derenshteyn, K., Borodovsky, M., Trifonov, E. N.,
Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences.
J. Molec. Biol. 262, 129-139 (1996)

Ioshikhes, I., Trifonov, E. N., Nucleosomal DNA sequence database.
Nucl. Acids Res. 21, 4857-4859 (1993)

Ioshikhes, I., Bolshoy, A., Trifonov, E. N.,
Preferred positions of AA and TT dinucleotides in aligned nucleosomal DNA sequences.
J. Biomolec. Str. and Dynamics 9, 1111-1117 (1992)

Beckmann, J. S., Trifonov, E. N., Splice junctions follow a 205-base ladder.
Proc. Natl. Acad. Sci. USA 88, 2380-2383 (1991)

Trifonov, E. N., DNA as chromatin organizer.
In: "Theoretical Biochemistry and Molecular Biophysics, v. 1: DNA" (Eds. D. L. Beveridge and R. Lavery),
Adenine. Press, New York, 1991, pp. 377-388

Trifonov, E. N., Mengeritsky, G., Bent DNA in chromatin versus free curved DNA.
In: "Structure and Expression. Volume 3: DNA Bending and Curvature",
(Eds. W. K. Olson, M. H. Sarma, R. H. Sarma and M. Sundaralingam), Adenine Press, 1988, pp 159-167

Trifonov, E. N., Mengeritsky, G., Simian virus 40 replication pause sites map with the nucleosomes.
J. Virol., 52, 1011-1012 (1984)

Wartenfeld, R., Mengeritsky, G., Trifonov, E. N.,
Periodicity in nucleosomal DNA sequences. CODATA Bull., 56, 14-16 (1984).
Also reprinted in:
"The Role of Data in Scientific Progress", (Ed. P. S. Glaeser), North Holland, Amsterdam, 1985, pp. 111-113

Mengeritsky, G., Trifonov, E. N., Nucleotide sequence-directed mapping of the nucleosomes of SV40 chromatin.
Cell Biophysics 6, 1-9 (1984)

Ulanovsky, L. E., Trifonov, E. N., Superhelicity of nucleosomal DNA changes its double-helical repeat.
Cell Biophysics 5, 281-283 (1983)

Mengeritsky, G., Trifonov, E. N., Nucleotide sequence-directed mapping of the nucleosomes.
Nucl. Acids Res. 11, 3833-3851 (1983)

Trifonov, E. N., Nucleosomal DNA structure.
In: "Nucleic Acids: the vectors of life" (Eds. B. Pullman and J. Jortner),
D. Reidel Publ. Company, Dordrecht-Boston-Lancaster, 1983, pp. 373-385

Trifonov, E. N., Sequence-dependent variations of B-DNA structure and protein-DNA recognition.
Cold Spring Harbor Symp. Quant. Biol. 47, 271-278 (1983)

Trifonov, E. N., Structure of DNA in chromatin.
In: "International Cell Biology 1980-1981" (Ed. H. Schweiger), Springer-Verlag, Berlin, 1981, pp. 128-138

Trifonov, E. N., Deformational anisotropy of DNA molecule.
In: "Structural Aspects of Recognition and Assembly in Biological Macromolecules",
(Eds. M. Balaban, J. Sussman, W. Traub and A. Yonath), Balaban ISS, Rehovot-Philadelphia, 1981, pp. 525-536

Trifonov, E. N., Sequence-dependent deformational anisotropy of chromatin DNA.
Nucl. Acids Res. 8, 4041-4053 (1980)

Trifonov, E. N., Sussman, J. L., The pitch of chromatin DNA is reflected in its nucleotide sequence.
Proc. Natl. Acad. Sci. USA 77, 3816-3820 (1980)

Trifonov, E. N., Bettecken, T., On the orientational nature of sensitivity of nucleosomal DNA to nuclease digestion.
In: "Molecular Mechanisms of Biological Recognition" (Ed. M. Balaban),
Elsevier/North Holland Biomed. Press, 1979, pp. 233-234

Trifonov, E. N., Sussman, J. L., Smooth bending of DNA in chromatin.
In: "Molecular Mechanisms of Biological Recognition" (Ed. M. Balaban),
Elsevier/North Holland Biomed. Press, 1979, pp. 227-232

Trifonov, E. N., Bettecken, T., Noninteger pitch and nuclease sensitivity of chromatin DNA.
Biochemistry 18, 454-456 (1979)

Trifonov, E. N., The helical model of the nucleosome core.
Nucl. Acids Res. 5, 1371-1380 (1978)

Sussman, J. L., Trifonov, E. N., Possibility of non-kinked packing of DNA in chromatin.
Proc. Natl. Acad. Sci. USA 75, 103-107 (1978)