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