Our next guest post is by Radu Zabet on his manuscript (with co-workers) Physical constraints determine the logic of bacterial promoter architectures, arXived here
Earlier last year we explored the possibility of understanding ‘real biology’ using our stochastic simulation framework GRiP (http://logic.sysbiol.cam.ac.uk/grip). That software simulates how transcription factors (TFs) find their target sites in the genome, using a combination of three-dimensional diffusion around and one-dimensional walk on the DNA. This biophysical mechanism is quite well studied and is commonly termed ‘facilitated diffusion’. Unlike a homing missile, the trace of a TF molecule to its target site occurs somewhat erratic, and with many other factors around, even ‘traffic jams’ on the DNA seem possible (that and other interesting phenomena were subject of two other arXiv contributions we put online last year – see Haldane’s Sieve for more, https://haldanessieve.org/2013/04/09/our-paper-the-effects-of-transcription-factor-competition-on-gene-regulation/ and the two publications: http://dx.doi.org/10.3389/fgene.2013.00197 and http://dx.doi.org/10.1371/journal.pone.0073714).
Often times, TF binding sites are closely packed or even overlapping. In our latest paper, we explore how the spacing of binding sites along the DNA can influence the probability of a “TF traffic jam” occurring, and thereby influencing the length of a TF’s “commute” to its binding site (http://arxiv.org/abs/1312.7262). We notice that one of the promoter organisations that we predict would cause massive traffic jams is underrepresented among E. coli promoters, suggesting that this phenomenon may have an important biological role.
One of the most common approaches to predicting TF occupancy is statistical thermodynamics, which assumes that the system is in steady state. Here we show that under biologically relevant parameters, a TF might take longer than a cell cycle to arrive to its binding site when the promoter is organized in a “traffic jam” inducing way. Therefore, it is important to consider the dynamics of TF binding, rather than just the steady state.
Usually, transcriptional logic refers to the idea that the specific combinations of TFs that bind to a gene promoter control the expression level of that gene. We extend this notion of transcriptional logic by proposing that the response to multiple regulatory inputs can also depend on the dynamics of TF binding. In other words: not only the final combinatorial pattern, but also the order in which these sites are occupied matters. In this context, we suggest that the spatial organisation of the promoter encodes the logic, influenced by TF concentrations that modulate promoter occupancy dynamics in biologically relevant time scales.
Using computer simulations of the search process, we show that the logic of complex bacterial promoters can be explained by the combinatorial action of three commonly found basic building blocks: switches, barriers and clusters, whose characteristics we analyse in detail.
The precise spacing of TF binding sites plays a key role in our model, and we show that physically constrained promoter organizations are commonly found in bacterial genomes and are conserved.
Finally, we also developed a new web-based computational tool (faster GRiP, or fGRIP), which is able to generate the dynamics of promoter occupancy for bacterial systems. This tool is available at http://logic.sysbiol.cam.ac.uk/fgrip/