A question of dynamics

Enoch B. Antwi (1,2,3), Yassine Marrakchi (2,4), Özgün Çiçek (4), Thomas Brox (2,4,5), Barbara Di Ventura (2,3)

1) Heidelberg Biosciences International Graduate School (HBIGS), University of Heidelberg, Heidelberg, Germany

2) Centers for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Freiburg, Germany

3) Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany

4) Department of Computer Science, Albert-Ludwigs-University, Freiburg, Germany

5) BrainLinks-BrainTools, Albert-Ludwigs-University, Freiburg, Germany.

Abstract

Cells respond to external stimuli and developmental cues mostly with changes in gene expression. Gene expression is often regulated by transcription factors (TFs), proteins that bind DNA in a sequence-specific manner at so-called response elements and recruit the general transcription machinery at the promoter to start transcription. TFs have been shown to display different dynamics, that is, the shape of the curve that describes the TF activity over time is not always the same, but depends on the type of stimulus the cell receives. Different dynamics have been, in turn, implicated in the activation of specific sets of target genes. In light of these findings, it is proposed that the same TF starts different gene expression programs purely depending on its dynamics and not its total abundance. This would imply that promoters be able to decode TF dynamics. In this lecture, I will present our work combining optogenetic experiments, automated image analysis and mathematical modeling to understand which elements on a mammalian promoter play a role in decoding TF dynamics. I will first describe LINuS, a light-inducible nuclear localization system developed by us, then show how, by imposing various TF dynamics with blue light and reading out the response from a library of synthetic promoters built with well-studied and defined elements, we find that sustained and pulsatile activation are distinguishable provided the coupling between TF binding and transcription pre-initiation complex formation is inefficient. Additionally, we show that the efficiency of translation initiation affects the ability of the promoter to sense TF dynamics. Using the knowledge acquired, we built a synthetic circuit that allows us to obtain two gene expression programs (proteins A and B both highly expressed versus protein A highly expressed and protein B only very weakly expressed) depending solely on TF dynamics. Taken together, these results help elucidate how gene expression is regulated in mammalian cells and open up the possibility to build synthetic circuits that respond better to determined TF dynamics.