Sequence Structure of Hidden 10.4-base Repeat in the Nucleosomes of C. elegans

• Published in: Journal of biomolecular structure & dynamics Vol. 26; no. 3; pp. 273 - 281
• Main Authors: Salih, F., Salih, B., Trifonov, E. N.
• Format: Journal Article
• Language: English
• Published: England Taylor & Francis Group 01-12-2008
• Subjects: 10-base periodicity; AA/TT nucleosome pattern; Animals; Base Sequence; Bendability matrix; Caenorhabditis elegans - genetics; Chromatin; Dinucleotides; Distance analysis; DNA bendability; Molecular Sequence Data; Nucleosome; Nucleosome positioning; Nucleosome sequence probe; Nucleosomes - metabolism; Repetitive Sequences, Nucleic Acid; RR/YY nucleosome pattern; Sequence Analysis, DNA
• ISSN: 0739-1102; 1538-0254
• DOI: 10.1080/07391102.2008.10531241

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)
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. 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)
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where the TT and AA dinucleotides display rather out of phase behavior, contrary 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.