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J Biomol Struct Dyn. 2009 Feb;26(4):403-11.

Nucleosome DNA bendability matrix (C. elegans).

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Department of Computer Science, Ben Gurion University of the Negev, P.O.B 653, Be'er Sheva 84105, Israel.


An original signal extraction procedure is applied to database of 146 base nucleosome core DNA sequences from C. elegans (S. M. Johnson et al. Genome Research 16, 1505-1516, 2006). The positional preferences of various dinucleotides within the 10.4 base nucleosome DNA repeat are calculated, resulting in derivation of the nucleosome DNA bendability matrix of 16x10 elements. A simplified one-line presentation of the matrix ("consensus" repeat) is ...A(TTTCCGGAAA)T.... All 6 chromosomes of C. elegans conform to the bendability pattern. The strongest affinity to their respective positions is displayed by dinucleotides AT and CG, separated within the repeat by 5 bases. The derived pattern makes a basis for sequence-directed mapping of nucleosome positions in the genome of C. elegans. As the first complete matrix of bendability available the pattern may serve for iterative calculations of the species-specific matrices of bendability applicable to other genomic sequences.

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