Yeast Nucleosomes: Cg Dinucleotide Function And its Special Role on Nucleosome Positioning

Abstract

k-mers containing the CG dinucleotide could represent a special class, and impact the nucleosome positioning. We preprocessed two types of DNA in 16 chromosome of yeast: ‘core DNA’ and ‘linker DNA’ for motif numbers distribution of three subsets of 8-mer (XY0, XY1 and XY2) based on dinucleotides classification. As well, content differences of specific dinucleotides were analyzed in core/linker DNA of 16 chromosome. Results showed that: 1) CG dinucleotides could be a specific signal region of DNA to drive the separation of core DNA from linker DNA; 2) trimodal distribution of CG dinucleotide in core DNA showed impact on nucleosome positioning; 3) relative higher CG density in linker DNA was conducive to the improvement of transcriptional activity; 4) CA/GA/TG dinucleotides could also separate core DNA from linker DNA, but inferior to CG dinucleotide. Results are of great biological significance for nucleosome positioning and function and evolution of DNA sequences.

Keywords: CG dinucleotide, Motif number, 8-mers, nucleosome positioning, Core/Linker DNA