Role of 10-11bp periodicities of eukaryotic DNA sequence in nucleosome positioning

Abstract

10-11bp repeating patterns of the particular dinucleotides were suggested in positioning nucleosomes in eukaryotes. In order to assess the role, the 10-11bp periodicities of the dinucleotides were examined both in human well-positioned nucleosome DNA sequences and in promoter DNA sequences of eight species. Our results indicated that the periodical occurrence of the particular dinucleotides correlates to positioning nucleosome. The signals of 10-11bp periodicities are more pronounced in the nucleosome DNA sequences than in the linker DNA sequences. Near the transcription start site, the signals reveal a similar feature that the nucleosome organization exhibits. But, it seems that the species do not share the same dinucleotides patterns. Furthermore, the dinucleotides patterns are dominant at the specific region of genome, indicating their diverse roles in forming and organizing nucleosomes. Moreover, the 10-11bp periodicities signals near the translation start negatively correlate with gene expression, demonstrating a vital role in transcription regulation. Our study reveals some details about the roles of DNA sequence in positioning nucleosomes.