Coexistence of different base periodicities in prokaryotic genomes as related to DNA curvature, supercoiling, and transcription

Abstract

We analyzed the periodic patterns in E. coli promoters and compared the distributions of the corresponding patterns in promoters and in the complete genome to elucidate their function. Except the three-base periodicity, coincident with that in the coding regions and growing stronger in the region downstream from the transcriptions start (TS), all other salient periodicities are peaked upstream of TS. We found that helical periodicities with the lengths about B-helix pitch ~10.2-10.5 bp and A-helix pitch ~10.8-11.1 bp coexist in the genomic sequences. We mapped the distributions of stretches with A-, B-, and Z-like DNA periodicities onto E. coli genome. All three periodicities tend to concentrate within non-coding regions when their intensity becomes stronger and prevail in the promoter sequences. The comparison with available experimental data indicates that promoters with the most pronounced periodicities may be related to the supercoiling-sensitive genes.

WEB-server for search of a periodicity in amino acid and nucleotide sequences

“…This period could not be identified using the entire previously developed software programs, such as TRF [12], T-REKS [9], Mreps [13], ATR hunter [14], TRStalker [3], Repfind [15], as well as the other developed methods and algorithms. This also applies to the spectral approaches developed in certain woks [16][17][18].…”

Detection of Large-Scale Noisy Multi-Periodic Patterns with Discrete Double Fourier Transform

“…The direct calculations for the independent Gaussian variables {Δx n } provide the related generating function The generating function (33) corresponds to the multi-variable Rayleigh probability for the intensity harmonics (6) ( ) ( )…”

Bacterial genomes lacking long-range correlations may not be modeled by low-order Markov chains: The role of mixing statistics and frame shift of neighboring genes

“…It is well known that the periodicity of 10/10.5/11 is the second strongest periodic signal in DNA sequences (Trifonov and Sussman, 1980;Trifonov, 1998;Herzel et al, 1999;Kravatskaya et al, 2011), and it can be both related to a periodicity in protein sequence (Herzel et al, 1999) or a nucleosome positioning signal (Trifonov and Sussman, 1980;Salih et al, 2008Salih et al, , 2014Sosa et al, 2013).…”

“…5, sometimes after 9 bases, other times after 12 bases. The existence of longer periodicity after periodicity-3 signal being removed (here by examining only the RF1, RF2, RF3 subsequences) has been studied before (Korotkov et al, 1997;Cohanim et al, 2006;Cohanim and Haran, 2009;Kravatskaya et al, 2011).…”