We just posted it on biorxiv here http://disq.us/t/38qjs6b so it is almost like Evgeny’s work is published… hmm… Comments are welcome as we are just kicking off the submission process.

In any case, I think this is an important piece of work. As we said in the conclusion: “Our work demonstrates the importance of measuring protein concentration dynamics. Previous genetic studies showed that Rb and p107 deletion, as well as cyclin D or E overexpression, reduced cell size, and genome-wide screens have identified additional regulators involved in size homeostasis including Largen and p38 MAPK 7–12,40. However, while deletion and overexpression change the concentration of these key regulatory molecules to affect cell size, these experiments do not imply that the concentration of these molecules change in wild type cells as they grow through G1. Our studies of protein concentration dynamics therefore complement the previous genetic studies by identifying the key regulators whose concentrations are in fact changed by cell growth in G1 to drive cell cycle progression, such as Rb and p107.

Conceptually, our work shows how cell size signals can originate in any part of a pathway or network. For a protein to be a ‘size sensor’ all that is required is that the protein’s concentration changes with cell size, and that this concentration change influences cell cycle progression. Here, we identified the size sensors Rb and p107, which are two cell cycle inhibitors in the middle of the mammalian G1/S regulatory pathway. Following similar logic, we previously identified the cell cycle inhibitor Whi5 in budding yeast as a cell size sensor. While Whi5 is functionally similar to Rb, in that both proteins inhibit transcription factors at the core of the G1/S transition, they share no sequence similarity and have a different evolutionary origin 21. That both these transcriptional inhibitors serve as size sensors by being diluted by cell growth demonstrates a deep conservation of the systems level logic at the core of cell cycle control.”

It really is amazing how useful studying yeast has been, even when it has no right to be. Here, we are simply studying the analogous circuit, which uses completely different proteins (see work from the Buchler lab, e.g., Medina et al in eLife). It is just so exciting to see that circuit ideas are useful and conserved, even when protein constituents of those circuits are not. Next, we need to figure out how this works in live growing animals since that may, of course, be different than the tissue culture models we examined here. Again, cell line studies have been informative, even when they really have no right to be… I know what model my money is on, but, of course, we could well be wrong. We have to do the experiments. Exciting times!

Rb dilution+Figs-1.png
Posted
AuthorJan Skotheim

https://www.biorxiv.org/content/early/2018/08/21/397448

Despite all the work so for on cell cycle control, we  don't know too much how cyclins, the specificity subunit of cyclin-dependent kinases, find their targets. Surprisingly, this is also true for cyclin D, which launches the human cell cycle, at least in part by phosphorylating the retinoblastoma protein, Rb. We should know how cyclin D recognizes Rb, and now we do... it might actually be important for human health. The cyclin D-Cdk4,6-Rb pathway is just now becoming an important cancer therapeutic pathway with a new series of drugs in clinical trials targeting the ATP binding pocket of Cdk4,6. That these Cdk4,6 inhibitors have significant off-target activites raises the possibility that a new class of drugs targeting cyclin substrate recognition based on our helix docking mechanism could improve cancer therapy (seriously).

On another note, there is something interesting about the cyclin D recognition mechanism. Other cyclins recognize short linear motifs in unstructured regions of the target proteins, while we observe a cyclin recognizing a structural element (an alpha-helix that resides within a previously reported unstructured region) in the C-terminus of Rb. This expands our understanding of structural elements responsible for determining cyclin-dependent kinase targets to drive the many facets of cell division.

Finally, much remains to be done, for example, we still don't know all the mechanisms cyclins E or A use to recognize Rb too... and we should understand that since these are interactions at the very core of the eukaryotic cell cycle.

Posted
AuthorJan Skotheim

Also, everyone needs to post preprints too, so we did that too. First time for me. Anyway, Ali, Antonia, Marius, Stanley and I wrote this manuscript describing Ali and Antonia's work using catalytically inactivate Cas9 to block transcription factor binding at specific sites. This give a quick way to check the function of particular TF binding sites. It works because guide RNAs are longer than TF binding sites so flanking sequence can be used to generate specificity.

Check it out here! https://www.biorxiv.org/content/early/2018/03/15/282681

Posted
AuthorJan Skotheim