Read all about it here https://www.sciencedirect.com/science/article/pii/S1097276519302813?dgcid=author

Ali shows that targeting dCas9 to specific transcription factor binding sites can be used to inhibit those sites function. Basically, dCas9 outcompetes the TF to block binding. This worked in all the cases we looked at and resulted in increased and decreased transcription depending on the site blocked. As a case study, we examined the pluripotency network in embryonic stem cells and found that an Oct4 site on the Nanog promoter drove positive feedback to maintain pluripotency, and that a Nanog site in the Nanog promoter had the opposite effect and provided negative feedback. This method can be used to individually delete links in transcriptional networks to asses their function without deleting the transcription factor hubs. It was a nice collaboration with Marius Wernig (stem cell inst) and Stanley Qi and Antonia Dominguez (bioengineering). Thanks everyone for making this such a fun collaboration.

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AuthorJan Skotheim

Read all about it here https://www-cell-com.stanford.idm.oclc.org/molecular-cell/fulltext/S1097-2765(19)30224-2

It is a great paper and a great collaboration with the Sage and Rubin labs (thanks to everyone involved for being excellent). But, don’t let the number authors fool you… Ben did a heroic amount and performed a range of complex and different experiments to address this historic problem of how cyclin D finds its main target, the retinoblastoma protein, to inactivate it via phosphorylation (we think).

Posted
AuthorJan Skotheim

Daniel Berensen defended this thesis last Thursday. Congratulations! It is always so nice to see work reach its conclusion and achievements rightly earned and awarded. We also got excellent reviews for his paper which we should turn around in a week or so (a small miracle - much appreciated). Then he will continue the next phase of his education in the MD program at Stanford. We wish him all the best in his future endeavors (just finish those last experiments for the Rb dilution manuscript first).

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Posted
AuthorJan Skotheim

Measuring the size of human cells is hard, or requires fancy equipment most people don’t have. Our tool makes it much easier. Our preprint is available here on bioRxiv http://disq.us/t/3cykkni

We express a fluorescent protein from a constitutive promoter so that its amount is proportional to cell size, then measure total fluorescence by flow cytometry or widefield microscopy. We show that these measurements correlate well with those from other established methods including flow cytometry, protein-binding dye, nuclear volume, and dry mass. Crucially, we also show that our fluorescence measurements are more robust and less dependent on image segmentation than is the commonly-used measurement of nuclear volume. Moreover, our straightforward technique, requiring only a wide field fluorescence microscope, does not require equipment unavailable to most cell biology laboratories and is compatible with commonly used live cell imaging methods. Finally, use of two colors allows estimation of the concentration (ratio of your favorite protein to the size reporter) of the second fluorescently tagged protein. Thus, our reporter can be used to facilitate concentration measurement using simple wide field instrumentation available in most cell biology labs.

Nice work Daniel!

Posted
AuthorJan Skotheim

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!

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Posted
AuthorJan Skotheim