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

DOI10.1016/J.JTBI.2017.05.033MaRDI QIDQ1702274zbMATH OpenOpenAlexWikidataFDO

Authors Vladimir R. Chechetkin, V. V. Lobzin

Publication date 28 February 2018

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1702.08267

zbMATH Keywords

Fourier transform\textit{Escherichia coli}genome organizationchromosome architecturegenomic DNA sequences

Mathematics Subject Classification ID

Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) (60J20) Protein sequences, DNA sequences (92D20)

Abstract: 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 Escherichia coli 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.

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Cites work

• scientific article; zbMATH DE number 3222455 (Why is no real title available?)
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Cited in

(1)

• Genomic signals of reoriented ORFs

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