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Evolutionary mechanism and biological functions of 8-mers containing CG dinucleotide in yeast

文献类型： 外文期刊

作者： Zheng, Yan 1 ; Li, Hong 1 ; Wang, Yue 1 ; Meng, Hu 1 ; Zhang, Qiang 2 ; Zhao, Xiaoqing 3 ;

作者机构： 1.Inner Mongolia Univ, Lab Theoret Biophys, Sch Phys Sci & Technol, Hohhot 010021, Peoples R China

2.Inner Mongolia Agr Univ, Coll Sci, Hohhot 010018, Peoples R China

3.Inner Mongolia Acad Agr & Anim Husb Sci, Biotechnol Res Ctr, Hohhot 010021, Peoples R China

4.235 West Univ St, Hohhot, Inner Mongolia, Peoples R China

关键词： Rules of 8-mer usage;8-mer biological functions;Theoretical conjectures;Nucleosomebinding motifs;CGIs;Validation

期刊名称：CHROMOSOME RESEARCH （ 影响因子：5.239； 五年影响因子：3.918 ）

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收录情况： SCI

摘要： The rules of k-mer non-random usage and the biological functions are worthy of special attention. Firstly, the article studied human 8-mer spectra and found that only the spectra of cytosine-guanine (CG) dinucleotide classification formed independent unimodal distributions when the 8-mers were classified into three subsets under 16 dinucleotide classifications. Secondly, the distribution rules were reproduced by other seven species including yeast, which showed that the evolution phenomenon had species universality. It followed that we proposed two theoretical conjectures: (1) CG(1) motifs (8-mers including 1 CG) are the nucleosome-binding motifs. (2) CG(2) motifs (8-mers including two or more than two CG) are the modular units of CpG islands. Our conjectures were confirmed in yeast by the following results: a maximum of average area under the receiver operating characteristic (AUC) resulted from CG(1) information during nucleosome core sequences, and linker sequences were distinguished by three CG subsets; there was a one-to-one relationship between abundant CG(1) signal regions and histone positions; the sequence changing of squeezed nucleosomes was relevant with the strength of CG(1) signals; and the AUC value of 0.986 was based on CG(2) information when CpG islands and non-CpG islands were distinguished by the three CG subsets.

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