title: Nucleosome DNA bendability matrix (C. elegans).
abstract: 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.
authors.affiliation: Department of Computer Science, Ben Gurion University of the Negev, P.O.B 653, Be'er Sheva 84105, Israel.
authors.forename: I
authors.initials: I
authors.lastname: Gabdank
authors.forename: D
authors.initials: D
authors.lastname: Barash
authors.forename: E N
authors.initials: EN
authors.lastname: Trifonov
mesh_terms: D000818:Animals; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics*; D002875:Chromosomes / Q000235:genetics; D018509:DNA, Helminth / Q000235:genetics*; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D018509:DNA, Helminth; D009707:Nucleosomes