Genome Diversity Center

at the Institute of Evolution, University of Haifa

(Since August 2000)
Head: Edward N. Trifonov

How DNA if folded/unfolded in the chromosomes?

The leading principle of the spatial organization of the nucleosomes in the chromatin is the sterical exclusion rules first suggested by Noll et. al. in 1981.
The DNA in the linkers connecting the nucleosomes is assumed to be non-constrained and the linker lengths determine angular rotations of the neighbouring nucleosomes.

Relevant references:

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)

Herzel, H., Weiss, O., Trifonov, E. N.,
Sequence periodicity in complete genomes of Archaea suggests positive supercoiling.
J. Biomol. Str. Dyn. 16, 341-345 (1998)

Herzel, H., Trifonov, E. N., Weiss, O., Grosse, I., Interpreting correlations in biosequences.
Physica A 249, 449-459 (1998)

Bolshoy, A., CC dinucleotides contribute to the bending of DNA in chromatin.
Nat Struct Biol. 2,446-448 (1995).

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

Ulanovsky, L. E., Trifonov, E. N.,
A different view point on the chromatin higher order structure: steric exclusion effects.
In: "Biomolecular Stereodynamics III", (Eds. R. H. Sarma and M. H. Sarma), Adenine Press, 1986, pp. 35-44

Trifonov, E. N., Topological paradox of minichromosomes?
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. 711-720