Promoters proximity as a regulatory mechanism in single cell protein numbers statistics

Closely spaced promoters are pervasive in all kingdoms of Life. It remains unclear whether their expression dynamics has unique features when compared to ‘individual’ promoters [1].
We studied their single-cell statistics on the prokaryote model organism Escherichia coli using a YFP fusion library to observe a significant portion of its native tandem promoter pairs with single cell sensitivity by flow-cytometry [2].
We find that the distance between the promoters’ transcription start sites (TSS) in tandem formation is a key regulator of the mean, variability, and asymmetries (as measured by skewness [3]) of the single-cell distribution in protein numbers.
Interestingly, reducing RNA polymerase concentration causes the asymmetry relationship to become weaker, suggesting that such asymmetry emerges directly from interference between RNA polymerases.
Meanwhile, we did not find clearly distinct behaviors between overlapping and non-overlapping promoters, suggesting that the dynamics of DNA-bound RNA polymerases, prior to commitment to open complex formation, is diffusive, rather than static.
Finally, we show that both the squared coefficient of variation, as well as the skewness of the single cell distribution of protein numbers decrease with the average single-cell protein numbers.
Overall, these results suggest that the distance between closely spaced tandem promoters is a key regulatory variable of their dynamics. Given the sensitivity to RNA polymerase numbers, this is likely due to stochastic mechanical interference between RNA Polymerases, caused by their 1-dimensional diffusive behavior centered around the transcription start sites, prior to open complex formation.
References
[1] Häkkinen, A. et al. (2019). doi: 10.1098/rsif.2019.0507
[2] Taniguchi, Y. et al. (2010). doi: 10.1126/science.1188308
[3] Startceva, S. et al. (2019). doi: 10.1016/j.bbagrm.2018.12.005