Assessing in vivo the impact of gene context on transcription through DNA supercoiling.

The context of genes, particularly the arrangement of neighboring genes along the DNA, exerts an important impact on their expression. However, predicting this impact remains challenging due to the complex interplay of concurrent mechanisms. To gain a quantitative understanding, we experimentally implemented the simplest possible theoretical model, isolating a gene from its neighboring genes. This allowed us to investigate the role of DNA's mechanical and topological properties, along with the enzymes that shape these properties, including RNA polymerases and topoisomerases. Comparison of the experimental results to a mathematical model based on physical principles allowed us to parametrize the operating mode of topoisomerases. Our work paves the way towards a systematic understanding of the role of gene context in gene expression.