Analysis On The Evolutional Separations And The Functions Of 8-Mer Motif Usage In Yeast Genome Sequence

Based on the phenomenon of the tri-modal distribution of 8-mer relative appearence with their frequencies in human intergenic sequence, we analyzed the unimodal distribution of 8-mers in yeast genome and discussed the evolutional separation and functions of 8-mers usage. We classified all 8-mers into three subsets accordeding to XY dinucleotide classification and analyzed the using differences of m-mer (m=3,4) in 8-mers among the three 8-mer subsets. We proposed the biological functions of 8-mer including 1CG and 2CG. All the study is consist of four parts and the details shows as follows:First, previous studies have found that the distribution of κ-mer (k>6) relative appearence with their frequencies in human intergenic sequence showed a tri-modal distribution, distribution is more clear and stable when κ=8. So we selected intergenic sequence of chromosome 1 of human, geted the tri-modal distribution of 8-mer relative appearence with their frequencies. Based on the number of contains XY dinucleotide in 8-mers, make all 8-mer motif classified, we found that 8-mers containing 2CG、1CG and OCG formed an independent unimodal distribution in CG subsets, and the 2CG、1CG and OCG distribution strictly corresponding with the peak1, peak 2 and peak3 distribution, the center of OCG distribution is consistent with the distribution center of random sequence, and frequencies of 1CG and 2CG distribution is much smaller than frequencies of random distribution or away from the random center. Indicated the usage of 8-mers containing OCG was the result of random evolution, the usage of 8-mers containing 1CG and 2CG was the result of directed evolution. And that the most probable relative appearence of 1CG distribution more then OCG distribution. Combining analysis of features of these 8-mers sequence and experimental comparison, we proposed three theoretical conjecture:(1) the 2CG motif constituted the core motif of CpG island sequences, (2) the 1CG motif was functional fragment what was interaction with histone, which we called that binding motif of nucleosome, (3) using separate of three kinds of motif respond the evolutionary relationships between organism genomes, the fundamental cause of difference in all kinds of genomes sequence. Therefore, this article will research the phenomenon of evolutional separations of 8-mer usage in yeast genome, base on the using rule of 8-mer in the human genome.Second, the paper analyzes the distribution of 8-mer relative appearence with their frequencies in yeast genome sequence. Found that all of the 8-mer distribution is unimodal distribution, the CG content decreased with the increases of using frequency. Combined with the tri-modal distribution of the human intergenic sequence, we classified all 8-mers into 16 kinds of XY subsets, then we found that only in CG classified sub-set had the most probable relative appearence of 1CG higher than OCG, accorded with human distribution, the result of unimodal phenomenon of 8-mer distribution was caused by nearly distribution center of 0CG、 CG and 2CG. From the view of biological evolution, starting from yeast has been displayed evolutional separation of CG motif in lower eukaryotes, we believed that the phenomenon of separation is universal in eukaryotes. Calculated the relative frequency of m-mer (m=3,4) in 0XY、1XY and 2XY subsets in the yeast genome sequence after XY classification and compared with the relative frequencies of m-mer in all 8-mer. We found that the using separation of m-mer in 2XY subsets was maximum,1XY subsets followed, the separation of m-mer in OXY subsets was minimum, in XY category. The using separation of m-mer in CG and GC subsets was maximum, showing this kinds of motif was directly evolved, in 1XY and 2XY subsets. The using separation of m-mer in CG/GC/CC/GG subsets was minimum, showing this kinds of motif was randomly evolved, in OXY subsets.Third, applied new symmetric relative entropy to quantitatively describe the separational distance of the m-mer usage. Compared with m-mer in all 8-mer, about OXY subsets, we found that the new symmetric relative entropy of m-mer in OCG subsets was minimum, indicated that the 8-mers containing OCG was minimum separation from all 8-mer. In the 1XY subset, we found that the new symmetric relative entropy of m-mer in 1 CG subsets was maximum, indicated that the 8-mers containing 1CG was maximum separation from all 8-mer. About the 2XY subset, we found that the new symmetric relative entropy of m-mer in 2CG subsets was maximum, indicated that the 8-mers containing 2CG was maximum separation from all 8-mer.Fourth, applied analysis of radian difference and analysis of distance difference calculated the separational distance of m-mer usage in 16 subsets and all 8-mers. The result accorded with the result of new symmetric relative entropy, but there are differences for some XY subsets. Carefully analysed the define of three parameters found that resulting the evolutional separations of OCG subset was the using preference of m-mer in OXY subsets. About 1XY subsets, resulting evolutional separations of 1CG subset was not only the using preference of m-mer, but also the using deviation of m-mer what have few relative frequency was important. In 2XY subsets, resulting the evolutional separations of 2CG subset was the using deviation of m-mer. These conclusions have important value for we will predict nucleosome positioning and CpG island sequences.