Structural attributes of nucleotide sequences in promoter regions of supercoiling-sensitive genes: how to relate microarray expression data with genomic sequences

TL;DR

This study investigates how nucleotide sequence structures in E. coli promoters relate to gene expression changes caused by chromosomal supercoiling, revealing specific periodicities linked to gene regulation.

Contribution

It introduces a novel Fourier analysis approach to connect promoter sequence periodicities with supercoiling sensitivity and gene expression levels.

Findings

Sequences with ~10 nt periodicity are associated with relaxation-induced genes.

Sequences with ~11 nt periodicity are linked to relaxation-repressed genes.

Significant correlation between AT content, periodicities, and gene expression levels.

Abstract

The level of supercoiling in the chromosome can affect gene expression. To clarify the basis of supercoiling sensitivity, we analyzed the structural features of nucleotide sequences in the vicinity of promoters for the genes with expression enhanced and decreased in response to loss of chromosomal supercoiling in E. coli. Fourier analysis of promoter sequences for supercoiling-sensitive genes reveals the tendency in selection of sequences with helical periodicities close to 10 nt for relaxation-induced genes and to 11 nt for relaxation-repressed genes. The helical periodicities in the subsets of promoters recognized by RNA polymerase with different sigma factors were also studied. A special procedure was developed for study of correlations between the intensities of periodicities in promoter sequences and the expression levels of corresponding genes. Significant correlations of expression with the AT content and with AT periodicities about 10, 11, and 50 nt indicate their role in regulation of supercoiling-sensitive genes.