This year’s EMBO Conference From Functional Genomics to Systems Biology (November 10-13 2018) took place in the super sciency Advanced Training Centre next to the European Molecular Biology Laboratory (EMBL) in Heidelberg, a city hosting the oldest university of Germany. The conference was organized by a local team (Eileen Furlong, Arnaud Krebs, Mikhail Savitski), which accomplished the tough job of compiling a very broad scientific program covering topics under the umbrella of systems biology. This breadth was exemplified by the opening words of E. Furlong who advised everybody to be taken out of their comfort scientific area to try to see their studies from another perspective.
At the introductory session covered most of the topics of the conference such as genomic and proteomic methods, some curious model organisms, developmental biology and single-cell genomics. The meeting ended on a Tuesday with a half-day session mostly focused on the transnational aspects of systems biology.
The conference was a good opportunity to meet many people in the field, establish contacts, reinforce pre-existing ones and check out what’s new. The schedule was jam packed, but ensured enough time to digest the talks and visit the posters in coffee breaks or during the lunches and dinners up in the “EMBL canteen”. There were moments of fun as well, like the party on the rooftop of the ATC and a lunch run organized in the autumnal forest surrounding EMBL!
High throughput yeast library generation for comparative cell analysis
Michael Knop, Heidelberg university
Knop started with the description of a high throughput PCR tagging method to generate a yeast library. But when his group submitted this paper, there was a lot of interest about the potential applicability of the technology to mammalian cells, therefore they invested some efforts to optimize this. Indeed, they choose Cas12a to create cuts and a PCR encoding for the tag of interest obtained with two oligos including homology sequences to the region that needs tagging and the crRNA for Cas12. By adding few tricks and improvements such as an antibiotic selection marker, the efficiency of endogenous tagging improves to 60%. Well, if this got you curious, wonder no more, as the authors deposited this on BiorXiv few weeks ago.
Nascent transcription profiling in single cells by intron seq FISH
Long Cai, Caltech, USA
Long Cai wanted to address the issue of tissue heterogeneity, and as an alternative to RNAseq and single cells RNAseq, introduced a new technology he developed to collect spatial genomic information. Among the disadvantages of the conventional technologies is the need to dissociate the tissue to capture the mRNA (more stable than the transcripts and therefore less dynamically regulated) and the need to produce a reverse transcript and a library. His solution is an innovative and high throughput method which allows the profiling of more than 10,000 genes: intronseqFISH. It is a microscopy based in situ method which allows the detection, through subsequent rounds of probe hybridization and computational decoding, of nascent transcripts. He showed that actively transcribed regions are at the edge of chromosome territories and he can narrow it down a 10 min window. Adding pulse chase with 5-EU, this approach can detect low and high transcriptional states in many cell lines, showing a 2 hour period correlated to the expression of Hes1 in stem cells.
Thermal stability and solubility in molecular biology
Mikhail Savitski, EMBL Heidelberg, Germany
Mikhail Savitski started off his talk with a broad introduction to 2DTPP (2-dimensional thermal proteomic profiling) which is the direct evolution of the thermal shift assay extended to a proteome-wide level. Here, protein stability is assessed at multiple temperatures and compound concentrations. He applied the technology to ATP and other metabolites, moving it from its conventional use to map small molecule interactions towards larger metabolism applications. He retrieved a large number of binders, as expected for such an important molecule like ATP, which could be destabilized and thus validated by modulating the concentration. He concluded the talk with the fascinating description of the observed effect of ATP as a hydrotope molecule, able to increase the solubility of the proteome, performing even better than some detergents.
Genome-wide analysis of protein-DNA interactions
Jussi Taipale, Karolisnka Institute, Sweden
Jussi Taipale presented much of his labs work on predicting gene expression by combining experimental and computational data. In order to do this, it is necessary to identify transcription factor binding sites, regulatory elements, and possible sources of errors. With the help of high throughput and automated technologies, his lab has identified hundreds of TF binding sites and TF cooperativity. With Patrick Cramer, he dissected the rule that governs the binding of TF to nucleosomes depending on gyre, periodicity, dyad or orientation. These experiments can be brought inside of living cells where stronger binders will dominate in a concentration and tissue dependent manner. He concluded the talk noting that open chromatin defines cell types while the gene expression defines temporal response to a stimulus and to a given position within tissue.
Multiplexed protein maps link subcellular organization to cellular states
Lukas Pelkmans, University of Zurich, Switzerland
The closing lecture of the meeting was given by Lukas Pelkmans on his work to link and quantify subcellular organization to cellular states. At any time in a given cell population there are patterns, single cell variability, and single molecule stochasticity. To try to measure all these parameters, his laboratory developed an imaging method called 4i (iterative indirect immunofluorescence imaging) which can be applied to 40 conditions in subsequent antibodies hybridizations rounds. With 20,000 single cells and different drug treatments this is definitively something on the system biology scale. In the near future he would like to refine this method to be both high throughput (100-150 conditions) and include 3D samples (paraffine blocks) or blood samples.
For more exciting development in the field in only two years from now we will have the possibility to broaden our minds again at the next Functional Genomics to Systems Biology meeting.
Thanks to Melania Zauri for this summary