Correlations between promoter activity and its nucleotide positions in spacing region

TL;DR

This study analyzes how nucleotide positions in the spacing region of promoters influence gene expression, revealing that beyond conserved regions, other positions significantly affect promoter activity, aiding synthetic biology design.

Contribution

It provides a detailed correlation analysis between promoter activity and nucleotide positions in the spacing region based on recent experimental data, highlighting influential positions.

Findings

Nucleotides in conserved regions are influential.

Positions around -19 significantly affect activity.

Non-conserved positions also impact promoter strength.

Abstract

Transcription is one of the essential processes for cells to read genetic information encoded in genes, which is initiated by the binding of RNA polymerase to related promoter. Experiments have found that the nucleotide sequence of promoter has great influence on gene expression strength, or promoter activity. In synthetic biology, one interesting question is how we can synthesize a promoter with given activity, and which positions of promoter sequence are important for determining its activity. In this study, based on recent experimental data, correlations between promoter activity and its sequence positions are analyzed by various methods. Our results show that, except nucleotides in the two highly conserved regions, $-35$ box and $-10$ box, influences of nucleotides in other positions are also not neglectable. For example, modifications of nucleotides around position $-19$ in spacing region may change promoter activity in a large scale. The results of this study might be helpful to our understanding of biophysical mechanism of gene transcription, and may also be helpful to the design of synthetic cell factory.