Journal
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
Volume 26, Issue 3, Pages 273-281Publisher
TAYLOR & FRANCIS INC
DOI: 10.1080/07391102.2008.10531241
Keywords
Nucleosome; Chromatin; 10-base periodicity; Nucleosome positioning; Distance analysis; Dinucleotides; RR/YY nucleosome pattern; Aa/TT nucleosome pattern; Nucleosome sequence probe; DNA bendability; Bendability matrix
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By measuring prevailing distances between YY, YR, RR, and RY dinucleotides in the large database of the nucleosome DNA fragments from C. elegans, the consensus sequence structure of the nucleosome DNA repeat of C. elegans was reconstructed: (YYYYYRRRRR)(n). An actual period was estimated to be 10.4 bases. The pattern is fully consistent with the nucleosome DNA patterns of other eukaryotes, as established earlier, and, thus, the YYYYYRRRRR repeat can be considered as consensus nucleosome DNA sequence repeat across eukaryotic species. Similar distance analysis for [A.T] dinucleotides suggested the related pattern (TTTYTARAAA)(n) where the TT and AA dinucleotides display rather out of phase behavior, contary to the AA or TT in-phase periodicity, considered in some publications. A weak 5-base periodicity in the distribution of TA dinucleotides was detected.
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