Regulation of bacterial genomes
In bacteria, genetic context is more evolutionarily conserved than transcription factors. How does it regulate gene expression? How to predict its impact?
What are the units of regulation in bacteria? Analysis of hundreds of genomes reveals synteny segments – sets of consecutive genes whose proximity along the DNA is evolutionarily conserved. They define units of co-expression at the 10-20 kilobase scale, beyond operons. We have shown that this length scale is universal for bacterial genomes.
- I. Junier, O. Rivoire (2016). Conserved units of co-expression in bacterial genomes: an evolutionary insight.
- I. Junier, P. Frémont, O. Rivoire (2018). Universal and idiosyncratic characteristic lengths in bacterial genomes.
- A. F. Schober, A. D. Mathis, C. Ingle, J. O. Park, L. Chen, J. D. Rabinowitz, I. Junier, O. Rivoire, K. A. Reynolds (2019). A two-enzyme adaptive unit in bacterial folate metabolism.
In vivo gene regulation from the bottom-up
To understand how gene context impacts gene expression in vivo, we designed and analyzed an experimental system where a single gene is isolated from other genes, instantiating a theoretical model proposed in the 1980s to illustrate how the over or under twisting of the DNA molecule – supercoiling – is affected by and impacts transcription. A first-principle biophysical model explains our results and highlights an antagonistic role of topoisomerases in the regulation of DNA supercoiling.
- I. Boulas, S. Rimsky, O. Espeli, I. Junier, O. Rivoire (2022). Assessing in vivo the impact of gene context on transcription through DNA supercoiling.
With Lisa Bruno, Olivier Espeli & Ivan Junier, we develop our bottom-up experimental and theoretical models to describe and predict how the transcription of a gene is influenced by the transcription of its neighbors.
With Marion Chauveau & Ivan Junier, we build statistical models of genome content and organization to identify the constraints to which bacterial genomes are subject.