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

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Abstract

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) CG1 motifs (8-mers including 1 CG) are the nucleosome-binding motifs. (2) CG2 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 CG1 information during nucleosome core sequences, and linker sequences were distinguished by three CG subsets; there was a one-to-one relationship between abundant CG1 signal regions and histone positions; the sequence changing of squeezed nucleosomes was relevant with the strength of CG1 signals; and the AUC value of 0.986 was based on CG2 information when CpG islands and non-CpG islands were distinguished by the three CG subsets.

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Abbreviations

CGI:

CpG island

CGi :

The CG0, CG1, and CG2 subsets

NCS:

Nucleosome core sequence

NLS:

Nucleosome linker sequence

Non-CGI:

Non-CpG island

NSRE:

New symmetric relative entropy

Par:

Characteristic parameter

RF:

Relative frequency

RMN:

Relative motif number

Sn :

Sensitivity

Sp :

Specificity

XY0 :

8-mers without XY dinucleotide

XY1 :

8-mers including 1 XY dinucleotide

XY2 :

8-mers including 2 or more than 2 XY dinucleotides

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Acknowledgements

The authors thank Prof. Liaofu Luo for illumination discussions. This work was supported by grants from the National Natural Science Foundation of China (No. 31260219).

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  1. Hong Li

    Present address: , No.235, West University Street, Hohhot, Inner Mongolia, China

Authors and Affiliations

  1. Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China

    Yan Zheng, Hong Li, Yue Wang & Hu Meng

  2. College of Science, Inner Mongolia Agricultural University, Hohhot, 010018, China

    Qiang Zhang

  3. Biotechnology research centre, Inner Mongolia Academy of Agricultural and Animal Husbandry Science, Hohhot, 010021, China

    Xiaoqing Zhao

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  1. Yan Zheng
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  2. Hong Li
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Correspondence to Hong Li.

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Zheng, Y., Li, H., Wang, Y. et al. Evolutionary mechanism and biological functions of 8-mers containing CG dinucleotide in yeast. Chromosome Res 25, 173–189 (2017). https://doi.org/10.1007/s10577-017-9554-z

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