After about four years in the making, we’ve finally published our paper “A combination of computational and experimental approaches identifies DNA sequence constraints associated with target site binding specificity of the transcription factor CSL” (the title, I know!!!). Please find the PDF here.
This has been an exciting journey. About four years ago I stared at a sequence motif that I got out of motif inference from a CSL/Su(H) ChIP dataset I analysed in collaboration with Sarah Bray’s group. There were a few good reasons to believe it was legit, but Sarah wasn’t convinced at all — not in the light of a crystal structure that Rhett Kovall had published in 2004. The paper discussed why the canonical motif was such a good fit for CSL, but it didn’t offer any entry point for why other sequences might be bound as well. A couple of hours with my favourite crystallographer Ilka Müller convinced me that CSL might prefer it’s canonical motif CGTGGGAA, but she also suggested to me that the space of possible sequences that are “tolerated” by the protein might be significantly larger. I presented these thoughts at a conference that was also attended by Bobby Glen, and we soon decided to team up to tackle the question more systematically using the tools of computational chemistry. Bobby and I proposed this to Apple for an ARTS Award, who presented us with some $30k of hardware, and the rest is history…
In the meantime, Sarah Bray took over the experimental validation of our computational results and because in vivo behaviour often doesn’t tell you much about what the protein really does, the very Rhett Kovall joined forces and provided additional biophysical measurements about CSL/Su(H) binding to DNA.
A truly international and interdisciplinary team. I’m proud of having been a member of it. And well done, Eddie and Rob from my CSBC team.
The Game-of-Life is an example of cellular automata, a conceptual framework that is inspired by the interaction of living cells in a confined space over time. Computer science students learn about Conway’s classic game because it teaches them about Turing completeness, biology students may learn about it as an introduction into discrete stochastic simulations.
We’ve previously used a Game-of-Life implementation on KL25Z microcontrollers (another donation from the ARM University Programme) to provide a more haptic way for students to explore the properties of the game world. Each controller represents a cell whose survival is dependent on the neighbouring devices. However, for technical reasons the implementation relies on a serial ring bus to enable communication between the boards, which is very distinct from biological systems where all cells are in immediate contact with their neighbours.
We discussed this with the ARM University Programme, who suggested the use of wireless radio technology to communicate between our “cells”. Bluetooth Low Energy (BLE) is such an approach, and the Nordic nRF51822 mbed Kit is a low-power Cortex M0-controller with BLE on board. After a few emails with ARM, we’re now in a position to explore the properties of concurrent dynamic systems and compare them to the behaviour of living cells: A great learning experience for technical people and life scientists alike!
Better late than never, one might think. Once upon a time when I spent time in Tien Hsu’s lab, back in 2001 at the Medical University of South Carolina, I conducted a 2-hybrid experiment with the fly von Hippel-Lindau (VHL) tumor suppressor. Amongst a few other candidates, we found the nm23 tumour suppressor as interaction partner for VHL. We published a very nice paper on nm23 function in tracheal development, but never quite revealed where we had found the inspiration to chose exactly that gene to work on. Now in this semi-review article we’re finally coming clean and show about 13 years later that VHL and nm23 do stuff together. Unfortunately, pay per view in Naunyn Schmiedeberg’s Archives of Pharmacology: Interaction between Nm23 and the tumor suppressor VHL.
We are very happy to announce the submission of another article to arXiv prior to publication in a peer-reviewed open access journal:
arXiv:1404.5544: Estimating transcription factor abundance and specificity from genome-wide binding profiles
This is a rather curious story, as we had actually been working on something else! If you’re interested in determining the number of bound TF molecules or how to translate PWM scores into actual binding profiles, please have a look, send us comments and suggestions, tweet it, write about it on your blog (but let us know so we can engage in a fruitful scientific discussion!).
In brief, being challenged by the sometimes lengthy compute times of our GRiP framework, Radu Zabet derived an analytical solution for the prediction of genomic occupancy on the basis of TF binding site preference (in the form of a PWM), DNA accessibility (from genome-wide foot printing data), TF copy number and a scaling factor that translates the PWM score into a specificity. However, when benchmarking the method to actual ChIP-seq data, we realised that the same analytical model also allows the inference of TF copy number and specificity if the other two genome-wide measurements (occupancy and DNA accessibility) are given.
This is now an alternative entry point for studies into TF copy numbers, something that our group are also interested in addressing experimentally using quantitative mass-spec.
It’s not always big news that excites us. In their recent newsletter, the Prime-XS Consortium features an article Pushing the limits of biology. It’s an introduction into the cutting-edge proteomics that the Functional Genomics Centre Zurich does for their Prime-XS partners. Under the heading Next-generation proteomics they report about their work with us on the quantification of Drosophila transcription factors. While they obviously deserve all the credit for the proteomics, we are proud of having asked the question for the next generation of MS!
A lot of the freedom that I have in my work (pursuing research in fly developmental biology, computational studies on bacterial gene regulation, and even my application of microelectronics for teaching purposes) comes from being a Royal Society University Research Fellow (URF). These fellowships give scientists between five and, under exceptional circumstances, ten years to build up a research programme, with a lot of flexibility when it comes to the nature of the work. In fact, URFs can even retrieve voluntary training in media communication, innovation and business, or policy making.
Two years ago the Royal Society has started a now biannual gathering of URFs. This year I was co-organiser of the event that saw eight keynote speakers from a wide range of topics from earth sciences to black holes to genome regulation. The echo of the conference is still visible under #urfcon14 on Twitter. Go check it out and contact any of the speakers if you find their work interesting!
We’ve had a successful 2013 and that apparently hasn’t gone unnoticed. This December alone, we’ve received more applications for summer projects than in all of lent. This is particularly true for the Amgen Scholarship, for which we have chosen a candidate, and Erasmus internships. Therefore, please, do not send any more applications until further notice. You will be ignored! For doctoral and postdoctoral scientists, please see our recommendations how to apply.
One of our most exciting stories that we’ve worked on for the past couple of months was Daphne Ezer’s project on physical constraints in bacterial promoter architecture. We analysed E. coli promoters and looked at the influence of TF affinity, TF concentration, and the relative location of TF binding sites (orientation, distance between) on gene expression, under special consideration of facilitated diffusion (the mode of TF translocation on and along the DNA, see our review). Our manuscript was accepted over the holidays, and if you’re really keen, you can get a preview on arXiv: Physical constraints determine the logic of bacterial promoter architectures.
Our manuscript “The Influence of Transcription Factor Competition on the Relationship between Occupancy and Affinity” has now been published in PLoS ONE. We summarised the main findings in a few other blog posts, and it’s not a long one, so why don’t you have a quick read of the abstract at PLoS. Just a quick note that I personally find the most striking figure of the manuscript is the comparison “SDO and ADO landscape for various cognate and non-cognate abundances”. That’s a really intuitive display for a genome gazer like myself. You’ve probably seen similar also in Mike Eisen’s paper “Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development.“. However, in contrast to their paper, we include the R code to generate the profiles in the Supplementary Material.
Our manuscript “The effects of transcription factor competition on gene regulation“ was just published in Frontiers in Systems Biology in the special issue on The origins of biological noise after a whooping 36 days between first submission and acceptance. We discuss the influence of TF abundance on the arrival time of TFs on their target sites as well as the time they stay bound to the DNA. There is an “emerging property” in cases where many molecules compete in some sort of molecular traffic jam on the DNA. This noise component may be a contributor to transcriptional noise, which we found pretty interesting.
There’s a bit of a prelude to this paper. We first published it on arXiv in late March, followed by an odyssey through a handful of journals. We were one inch close to not publishing the story at all, but encouragement from the community helped us to overcome the motivational low and push for publication elsewhere. Thank you!