Sequence Structure of Hidden 10.4-base Repeat in the Nucleosomes of C. elegans |
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| Authors: | F Salih B Salih E N Trifonov |
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| Institution: | 1. Genome Diversity Center , Institute of Evolution University of Haifa , Mount Carmel, Haifa , 31905 , Israel;2. Genome Diversity Center , Institute of Evolution University of Haifa , Mount Carmel, Haifa , 31905 , Israel;3. Division of Functional Genomics and Proteomics Faculty of Science , Masaryk University , Kamenice 5, Brno , CZ-62500 , Czech Republic |
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| Abstract: | Abstract 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, 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. |
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| 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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