title: Universal full-length nucleosome mapping sequence probe.
abstract: For the computational sequence-directed mapping of the nucleosomes, the knowledge of the nucleosome positioning motifs - 10-11 base long sequences - and respective matrices of bendability, is not sufficient, since there is no justified way to fuse these motifs in one continuous nucleosome DNA sequence. Discovery of the strong nucleosome (SN) DNA sequences, with visible sequence periodicity allows derivation of the full-length nucleosome DNA bendability pattern as matrix or consensus sequence. The SN sequences of three species (A. thaliana, C. elegans, and H. sapiens) are aligned (512 sequences for each species), and long (115 dinucleotides) matrices of bendability derived for the species. The matrices have strong common property - alternation of runs of purine-purine (RR) and pyrimidine-pyrimidine (YY) dinucleotides, with average period 10.4 bases. On this basis the universal [R,Y] consensus of the nucleosome DNA sequence is derived, with exactly defined positions of respective penta- and hexamers RRRRR, RRRRRR, YYYYY, and YYYYYY.
authors.affiliation: a Genome Diversity Center, Institute of Evolution, University of Haifa , Mount Carmel, Haifa 31905 , Israel.
authors.forename: Vijay
authors.initials: V
authors.lastname: Tripathi
authors.forename: Bilal
authors.initials: B
authors.lastname: Salih
authors.forename: Edward N
authors.initials: EN
authors.lastname: Trifonov
mesh_terms: D000818:Animals; D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D016384:Consensus Sequence; D015342:DNA Probes; D018509:DNA, Helminth / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D008969:Molecular Sequence Data; D009707:Nucleosomes / Q000235:genetics*
chemical_list: D015342:DNA Probes; D018509:DNA, Helminth; D018744:DNA, Plant; D009707:Nucleosomes
keywords: RR/YY probe; matrix of bendability; nucleosome positioning; nucleosome probe; strong nucleosome