Evolutionary mechanism and biological functions of 8-mers containing CG dinucleotide in yeast.
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) CG1motifs (8-mers including 1 CG) are the nucleosome-binding motifs. (2) CG2motifs (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 CG1information during nucleosome core sequences, and linker sequences were distinguished by three CG subsets; there was a one-to-one relationship between abundant CG1signal regions and histone positions; the sequence changing of squeezed nucleosomes was relevant with the strength of CG1signals; and the AUC value of 0.986 was based on CG2information when CpG islands and non-CpG islands were distinguished by the three CG subsets.
Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
Yan
Y
Zheng
Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China. ndlihong@imu.edu.cn.|, No.235, West University Street, Hohhot, Inner Mongolia, China. ndlihong@imu.edu.cn.
Hong
H
Li
Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
Yue
Y
Wang
Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
Hu
H
Meng
College of Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.
Qiang
Q
Zhang
Biotechnology research centre, Inner Mongolia Academy of Agricultural and Animal Husbandry Science, Hohhot, 010021, China.
Xiaoqing
X
Zhao
D018899:CpG Islands; D018900:Dinucleotide Repeats / Q000235:genetics*; D019143:Evolution, Molecular; D006801:Humans; D009707:Nucleosomes / Q000235:genetics / Q000378:metabolism*; D059372:Nucleotide Motifs; D012441:Saccharomyces cerevisiae / Q000235:genetics*
D009707:Nucleosomes
8-mer biological functions; CGIs; Nucleosome binding motifs; Rules of 8-mer usage; Theoretical conjectures; Validation