Large-scale chromosome folding versus genomic DNA sequences: A discrete double Fourier transform technique

JOURNAL OF THEORETICAL BIOLOGY

卷:426

Article

Chechetkin, V. R.^1,2  Lobzin, V. V.³ 

[1] Russian Acad Sci, Engelhardt Inst Mol Biol, Vavilov Str 32, Moscow 119334, Russia

[2] Troitsk Inst Innovat & Thermonucl Invest TRINITI, Theoret Dept Div Perspect Invest, Moscow 108840, Troitsk Distric, Russia

[3] Univ Sydney, Sch Phys, Sydney, NSW 2006, Australia

关键词: Chromosome architecture;    Genome organization;    Genomic DNA sequences;    Fourier transform;    Escherichia colt;   

DOI  :  10.1016/j.jtbi.2017.05.033

来源: Elsevier

【 摘 要 】

Using state-of-the-art techniques combining imaging methods and high-throughput genomic mapping tools leaded to the significant progress in detailing chromosome architecture of various organisms. However, a gap still remains between the rapidly growing structural data on the chromosome folding and the large-scale genome organization. Could a part of information on the chromosome folding be obtained directly from underlying genomic DNA sequences abundantly stored in the databanks? To answer this question, we developed an original discrete double Fourier transform (DDFT). DDFT serves for the detection of large-scale genome regularities associated with domains/units at the different levels of hierarchical chromosome folding. The method is versatile and can be applied to both genomic DNA sequences and corresponding physico-chemical parameters such as base-pairing free energy. The latter characteristic is closely related to the replication and transcription and can also be used for the assessment of temperature or supercoiling effects on the chromosome folding. We tested the method on the genome of E. colt K-12 and found good correspondence with the annotated domains/units established experimentally. As a brief illustration of further abilities of DDFT, the study of large-scale genome organization for bacteriophage PHIX174 and bacterium Caulobacter crescentus was also added. The combined experimental, modeling, and bioinformatic DDFT analysis should yield more complete knowledge on the chromosome architecture and genome organization. (C) 2017 Elsevier Ltd. All rights reserved.

【 授权许可】

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