Relationship between promoter sequence and its strength in gene expression

TL;DR

This paper presents a theoretical model linking promoter nucleotide sequences to gene expression strength, highlighting the importance of specific regions and nucleotide groups in determining promoter activity.

Contribution

It introduces a novel theoretical model that predicts promoter strength based on nucleotide sequences and regional effects, validated with experimental data from E. coli.

Findings

Nucleotide groups with three adjacent bases significantly influence promoter strength.

Different promoter regions have varying impacts on gene expression.

The model successfully predicts promoter strength and enables the construction of promoter libraries.

Abstract

In this study, through various tests one theoretical model is presented to describe the relationship between promoter strength and its nucleotide sequence. Our analysis shows that, promoter strength is greatly influenced by nucleotide groups with three adjacent nucleotides in its sequence. Meanwhile, nucleotides in different regions of promoter sequence have different effects on promoter strength. Based on experimental data for {\it E. coli} promoters, our calculations indicate, nucleotides in -10 region, -35 region, and the discriminator region of promoter sequence are more important than those in spacing region for determining promoter strength. With model parameter values obtained by fitting to experimental data, four promoter libraries are theoretically built for the corresponding experimental environments under which data for promoter strength in gene expression has been measured previously.