Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)

Complete Nucleosome DNA Bendability Matrix and Sequence-Directed Nucleosome Mapping (C. elegans)

Signal regeneration procedure described in our previous work[1] was used to derive the complete nucleosome DNA bendability matrix of C. elegans, by using a database of nucleosome core DNA sequences from C. elegans[2].The length of the matrix was set to be 116 nucleotides on the basis of crystallographical data[3], according to which there are 12 contact sites between DNA minor grooves and arginine residues of the histones in nucleosome core particle. The matrix 8x115 displays periodical variation of eight major dinucleotides (CG, AT, CC, GG, AA, TT, GA and TC) along the nucleosome DNA. It consists, essentially, of 11 repeats of the previously established 8x10 matrix of bendability[1]. Symmetrical modulation of the amplitudes is observed along the nucleosome DNA. The derived DNA bendability matrix can be used for the sequence-directed mapping of nucleosome positions in the genome of C. elegans and, as a reasonable approximation, - in other species.

I.G. is partially supported by the Lynn and William Frankel Center for Computer Sciences at Ben-Gurion University.

References and Footnotes
  1. Gabdank et al. Journal of Biomolecular Structure and Dynamics 26(4), 403-412, 2009.
  2. S. M. Johnson et al. Genome Research 16, 1505-1516, 2006.
  3. G. Arents, E. N. Moudrianakis. Proc. Natl Acad. Sci. USA 90, 10489-10493, 1993.

I. Gabdank1
D. Barash1
E. N. Trifonov2,3*

1Dept of Computer Science
Ben Gurion Univ. of the Negev
P.O.B 653
Be?er Sheva 84105
2Genome Diversity Center
Institute of Evolution
University of Haifa
Mount Carmel
Haifa 31905
3Division of Functional Genomics and Proteomics
Faculty of Science
Masaryk University
Kamenice 5
Brno CZ-62500
Czech Republic

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