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

DOI10.1016/J.JTBI.2017.05.033zbMATH Open1381.92068arXiv1702.08267OpenAlexW2614634492WikidataQ38759387 ScholiaQ38759387MaRDI QIDQ1702274FDOQ1702274

Authors: Vladimir R. Chechetkin, V. V. Lobzin 

Publication date: 28 February 2018

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

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.

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

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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)

Cites Work

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• Upstream curved sequences in \textit{E. coli} are related to the regulation of transcription initiation

Cited In (1)

• Genomic signals of reoriented ORFs

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