Design principles of transcription factors with intrinsically disordered regions

Reviewer #1 (Public review):

Summary:

The authors define the principles that, based on first principles, should be guiding the optimisation of trascription factors with intrinsically disordered regions (IDR). The first part of the study defines the following principles to optimize the binding affinities to the genome in the receiving region that is called the "antenna": (i) reduce the target to IDR-binding distance on the genome, (ii) optimise the distance betwee the DNA binding domain and the binding sites on the IDR to be as close as possible to the distance between their binding sites on the genome; (iii) keep the same number of binding sites and their targets and modulate this number with binding strength, reducing them with increased strenght; (iv) modulate the binding strenght to be above a threshold that depends on the proportion of IDR binding sites in the antenna. The second part defines the scaling of the seach time in function of key parameters such as the volume of the nucleus, and the size of the antenna, derived as a combination of 3D search of the antenna and 1D "octopusing" on the antenna. The third part focuses on validation, where the current results are compared to binding probabilith data from a single experiment, and new experiment are proposed to further validate the model as well as testing designed transcription factors.

Strengths:

The strength of this work is that it provides simple, interpretable and testable theoretical conclusions. This will allow the derived design principles to be understood, evaluated and improved in the future. The theoretical derivations are rigorous. The authors provides a comparison to experiments, and also propose new experiments to be performed in the future, this is a great value in the paper since it will set the stage and inspire new experimental techniques. Further, the field needs inspiration and motivations to develop these techniques, since they are required to benchmark the transcription factors designed with the methods presented in this paper, as well as to develop novel data based or in vivo methods that would greatly benefit the field. As such, this paper is a fundamental contribution to the field.

Weaknesses:

The model assumption that the interaction between the transcription factor and the DNA outside of the antenna region is negligible is probably too strong for many/most transcription factors, particularly in organisms with a longer genome than yeasts. The model presents many first principles to drive the design of transcription factor, but arguably, other principles and mechanisms might also play a role by being beneficial to the search and binding process. Specifically: (i) a role of the IDR in complex formation and cooperativity between multiple trascription factors, (ii) ability of the IDR to do parallel searching based on multiple DNA binding sites spaced by disordered regions, (iii) affinity of the IDR to specific compartmentalisations in the nucleus reducing the search time, etc. The paper would be improved by a discussion over alternative mechanisms.

Reviewer #2 (Public review):

Summary:

This is an interesting theoretical exploration of how a flexible protein domain, which has multiple DNA-binding sites along it, affects the stability of the protein-DNA complex. It proposes a mechanism ("octopusing") for protein doing a random walk while bound to DNA which simultaneously enables exploration of the DNA strand and stability of the bound state.

Strengths:

Stability of the protein-DNA bound state and the ability of the protein to perform 1d diffusion along the DNA are two properties of a transcription factor that are usually seen as being in opposition of each other. The octopusing mechanism is an elegant resolution of the puzzle of how both could be accommodated. This mechanism has interesting biological implications for the functional role of intrinsically disordered domains in transcription factor (TF) proteins. They show theoretically how these domains, if flexible and able to make multiple weak contacts with the DNA, can enhance the ability of the TF to efficiently find their binding site on the DNA from which they exert control over the transcription of their target gene. The paper concludes with a comparison of model predictions with experimental data which gives further support to the proposed model. Overall, this is an interesting and well executed theoretical paper that proposes an interesting idea about the functional role for IDR domains in TFs.

Weaknesses:

IDR domains are assumed flexible which I believe is not always the case. Also, I'm not sure how ubiquitous are the assumed binding sites on the DNA for multiple subdomains along the IDR. These assumptions though seem like interesting points of departure for further experiments.