Book of Abstracts: Albany 2009
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 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.The length of the matrix was set to be 116 nucleotides on the basis of crystallographical data, 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. 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
1Dept of Computer Science