Best Poster Awards — Chromatin and Epigenetics

The 10th edition of the EMBL Conference: Chromatin and Epigentics took place virtually this year. We welcomed more than 800 participants, from which 3 were selected best poster award winners prior to the meeting and who gave a short talk on the last day of the conference. Get a glimpse of their research.

Sequence-dependent surface condensation of pioneer transcription factor on DNA

Sina Wittmann, Max Planck Institute for Molecular Cell Biology and Genetics, Germany
Presenter: Sina Wittmann, Max Planck Institute for Molecular Cell Biology and Genetics, Germany

Abstract: Biomolecular condensates are dense assemblies of proteins that are dynamic and provide distinct biochemical compartments without being surrounded by a membrane. Some, such as P granules and stress granules, behave as droplets, have many millions of molecules, and are well described by a classic phase separation picture. Others, such as transcriptional condensates are thought to form on surfaces such as DNA, are small and contain thousands of molecules. However, the correct physical description of small condensates on DNA surfaces is still under discussion. Here we investigate this question using the pioneer transcription factor Klf4. We show that Klf4 can phase separate on its own at concentrations that are above physiological, but that at lower concentrations, Klf4 only forms condensates on DNA. Analysis using optical tweezers shows that these Klf4 condensates form on DNA by a switch-like transition from a thin adsorbed layer to a thick condensed layer that is well described as a prewetting transition on a heterogeneous substrate. Condensate formation of Klf4 on DNA is thus a form of surface condensation mediated by and limited to the DNA surface. Furthermore, we are investigating how Klf4 condensation is regulated by the property of the surface such as through DNA methylation. We speculate that the prewetting transition orchestrated by pioneer transcription factors underlies the formation of transcriptional condensates in cells and provides robustness to transcription regulation.

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Single-cell profiling of histone post-translational modifications and transcription in mouse and zebrafish differentiation systems

Presenter: Kim de Luca,  Hubrecht Institute, The Netherlands
Presenter: Kim de Luca,  Hubrecht Institute, The Netherlands

Abstract: During organism development and cellular differentiation, gene expression is carefully regulated at many levels. To that end, various epigenetic mechanisms translate cell-intrinsic and -extrinsic cues into activation and repression of the relevant parts of the genome. One of the most studied and versatile forms of epigenetic regulation is the post-translational modification (PTM) of the histone proteins around which DNA is wrapped. Histone PTMs affect the surrounding DNA by forming a binding platform for a range of effector proteins, as well as by directly modulating the biophysical properties of the chromatin. Hence, histone PTMs play a crucial role in priming, establishing, and maintaining transcriptional output and cell state. Many techniques used to study histone PTMs require thousands to millions of cells, and consequently mask the heterogeneity inherent to complex biological systems. To understand the nuanced relationship between chromatin context and transcription, single-cell and multi-modal approaches are necessary. We have previously developed a method to simultaneously measure transcriptional output and DNA-protein contacts by single-cell sequencing (scDam&T). This multi-modal method is particularly suitable for studying systems containing many transient cellular states. Here, we apply scDam&T to measure chromatin modifications by expressing the E. coli DNA adenine methyltransferase (Dam) fused to a domain that specifically recognizes a histone PTM. First, we validate this approach in population and single-cell samples by comparing the resulting data to orthogonal state-of-the-art techniques. Next, using mouse embryoid bodies as an in vitro differentiation system, we apply our method to deconvolve the lineage-specific regulation of Polycomb chromatin. Finally, we study the role of H3K9me3-marked heterochromatin in the developing zebrafish embryo.

Poster not available due to unpublished data, however, you can watch a short talk presentation here.

 

Presenter: Moushumi Das, University of Bern, Switzerland
Presenter: Moushumi Das, University of Bern, Switzerland

Poster and abstract not available due to unpublished data.

 

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Best Poster Awards – The Identity and Evolution of Cell Types

The second edition of the EMBO | EMBL Symposium: The Identity and Evolution of Cell Types brought together an increased number of researchers from this growing community. 315 scientists joined the virtual meeting and enjoyed four days of talks and poster presentations streamed live. A total of 72 posters were presented at the two live poster sessions out of which three were selected as the best posters by popular vote. Take a look at the winners and their work.

Molecular fingerprinting sea anemones and jellyfish: A transcriptomic approach to characterize Cnidarian cell types
image of Alison Cole
Alison Cole, University of Vienna, Austria

Presenter: Alison Cole, University of Vienna, Austria

Abstract

Animals typically consist of hundreds of different cell types, yet the evolutionary mechanisms underlying the emergence of new cell types are unclear. Cnidarians offer advantages to studies of metazoan cell type evolution, as they are the sister group to the Bilateria and yet comprise an extremely diverse set of lineages that exhibit variable life history strategies, life spans, regenerative properties, animal-defining cell types (ie. muscles and neurons), as well as clade-specific cell types (i.e. cnidocytes). Advances in single cell RNA sequencing have opened the frontiers for molecular profiling of cell types at a genome-wide scale. Application of these technologies for comparisons across species remains in its infancy, and is largely, but not exclusively, restricted to closely related species with well-defined orthologous gene sets. Here we present a large single cell dataset derived from the anthozoan polyp Nematostella vectensis (comprising both developmental and tissue-derived samples),the scyphozoan moon jelly (Aurelia aurita; comprising all life history stages as well as medusa tissue-derived samples), and the hydrozoan Clytia hemispherica (young medusa only). The same cell complement that is identifiable from species-specific genome-wide analyses is recoverable using only a set of 1:1:1 orthologous genes in all three species. Analyses of the reduced gene matrix combining all three species robustly identifies putatively homologous cell types amongst the neurosecretory derivatives, as well as cell populations with clear species-specific transcriptomic profiles. Interpretations of these data in the light of specific cell types will be discussedin order to demonstrate that the combination of unbiased single cell transcriptomes and gene-directed validations can permit the identification of novel and conserved cell types.

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Stylophora pistillata cell atlas illuminates stony coral symbiosis, calcification and immunity
Anamaria Elek, Centre for Genomic Regulation, Spain

Presenter: Anamaria Elek, Centre for Genomic Regulation, Spain

Abstract

Stony corals are colonial cnidarians that sustain the most biodiverse marine ecosystems on Earth: coral reefs. Life cycle of these animals involves a swimming larva that settles and metamorphoses into a sessile polyp, which in turn develops into the adult stage, depositing in the process a protein rich organic matrix and extracellular calcium carbonate crystals to form a stony skeleton. Despite their ecological importance, little is known about the cell types and molecular pathways that underpin the biology of reef-building corals. Using single-cell RNA sequencing, we have defined over 40 cell types across the three life stages of a stony coral Stylophora pistillata. Among others, we characterized previously unknown coral immune cells, endosymbiont alga-hosting cells, and calicoblasts responsible for calcium-carbonate skeleton formation in both settling polyp and the adult coral. Apart from these specialized coral cell types, we identified evolutionary conserved cell types by phylogenetic integration of our S. pistillata cell atlas with three other available cnidarian species. These evolutionary conservations include neuronal and gland cell types, cnidaria-specific cnidocytes, and others. Overall, this study reveals the molecular and cellular basis of stony coral biology, and addresses the evolution of cell type programs in three major cnidarian lineages separated by 500 million years of evolution.

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Gene family evolution underlies cell type diversification in the hypothalamus of teleosts*
Maxwell Shafer, Biozentrum, University of Basel, Switzerland

Presenter: Maxwell ShaferBiozentrum, University of Basel, Switzerland

Abstract

Hundreds of cell types form the vertebrate brain, but it is largely unknown how similar these cellular repertoires are between or within species, or how cell type diversity evolves. To examine cell type diversity across and within species, we performed single-cell RNA sequencing of ~130,000 hypothalamic cells from zebrafish (Danio rerio) and surface- and cave-morphs of Mexican tetra (Astyanax mexicanus). We found that over 75% of cell types were shared between zebrafish and Mexican tetra, which last shared a common ancestor over 150 million years ago. Orthologous cell types displayed differential paralogue expression that was generated by sub-functionalization after genome duplication. Expression of terminal effector genes, such as neuropeptides, was more conserved than the expression of their associated transcriptional regulators. Species-specific cell types were enriched for the expression of species-specific genes, and characterized by the neo-functionalization of members of recently expanded or contracted gene families. Within species comparisons revealed differences in immune repertoires and transcriptional changes in neuropeptidergic cell types associated with genomic differences between surface- and cave-morphs. The single-cell atlases presented here are a powerful resource to explore hypothalamic cell types, and reveal how gene family evolution and the neo- and sub-functionalization of paralogs contribute to cellular diversity.

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*https://doi.org/10.1101/2020.12.13.414557 


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Best Poster Awards – In Situ Structural Biology Workshop

The EMBO Workshop: In Situ Structural Biology: From Cryo-EM to Integrative Modelling was our final virtual conference of 2020, but there was no trace of Zoom fatigue amongst the 466 participants who joined us from 6 – 8 December!

80 international researchers presented their posters during the two posters sessions on the following topics:

  • Biophysical analysis in cells
  • COVID-19
  • Imaging across scales
  • Integrative modelling
  • Molecular sociology
  • Structural analysis in situ
  • Structural biology

Each of the participants had the chance to vote for their favourite poster, resulting in two posters winning the Best Poster Award kindly sponsored by EMBO Press.  Here are the winners:

New insights on the catalytic mechanism of arsenite oxidase

PHOTO: Filipa Engrola

Authors: Filipa Engrola, Márcia Correia, Teresa Santos-Silva, Maria Romao, (UCIBIO@FCT-NOVA, Portugal)

Arsenic (As) and antimony (Sb) are two metalloids that, due to anthropogenic and natural causes, pose an environmental  threat, considered as priority pollutants by the World Health Organisation and the United States Environmental Protection Agency. Although the safety guards recommend a maximum of 10 μg/L of As and Sb in drinking water, these values are exceeded in many regions worldwide, with no remediation approach that is simultaneously effective, clean and economically sustainable [1,2]. The ancient bioenergetic enzyme arsenite oxidase (Aio), from microorganisms Rhizobium sp. NT-26 (NT-26 Aio) and Alcaligenes faecalis (A.f. Aio), is currently being studied for its use as a biosensor and in bioremediation processes. Both Aio enzymes contain a large subunit (AioA) that harbours a molybdenum centre and a [3Fe-4S] cluster, and a small subunit (AioB) that possess a Rieske [2Fe-2S] cluster and have demonstrated to oxidise AsIII, as well as SbIII, into the easier to remove and less toxic forms of AsV and SbV, respectively [3,4]. Aiming to elucidate the catalysis mechanism of the enzymes, a combination of expression and purification of the proteins, crystallisation, structural analysis, enzyme kinetics and affinity tests were conducted. X-ray structures of the ligand-free form of the enzyme had been previously determined (PDB: 4AAY, 5NQD and 1G8K [3,5,6]). In our work, Aio crystals in complex with two different forms of the substrate analogue – Sb oxyanions, with a reaction kinetic 6500 times slower than AsIII [6] – diffracted up to ca 1.8 Å resolution. The structures show the reaction intermediates bound at the active site, with a μ-oxo bridge binding Sb to the Mo atom. Analysis of bond lengths and geometry of the ligands at the Mo active site allowed us to revisit the catalytic mechanism of As oxidation [7], contributing to the understanding and future biotechnological application of this family of enzymes in water treatment.

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Allosteric hotspot in the main protease of SARS-CoV-2

PHOTO: Léonie Ströhmich

Authors: Léonie Strömich, Sophia N Yaliraki, (Imperial College London, UK)

Since the beginning of 2020 we have seen the coronavirus SARS-CoV-2 causing a global pandemic with almost 34 million cases and over 1 million deaths worldwide [as of 01.10.2020] [1.] As a result, we have seen a surge in research efforts to develop effective treatments for the underlying disease, COVID-19. One approach is to target the main protease (Mpro) of SARS-CoV-2 as it is essential for virus replication in an early step of the viral life cycle [2.] Most efforts are centred on inhibiting the orthosteric binding site of the enzyme. However, considering allosteric sites on the protein allows for more selective drug design and widens the chemical search space. Here, we report an allosteric hotspot in the SARS-CoV-2 Mpro dimer by using novel atomistic graph theoretical methods: Markov transient analyses follow the propagation of a random walker on a graph and have been shown to successfully identify allosteric communication in catalytic proteins [3.] We further score the so identified allosteric hotspots against random sites in similar distances and thus identify a statistically significant putative allosteric site in the SARS-CoV-2 Mpro. We then simulate a binding event at this hotspot region using data from a recent XChem fragment screen by the Diamond Light Source [4.] which provides a starting point for rational drug design. This study uses highly efficient network theoretical models to shed light on allosteric communication and uncovers putative allosteric sites in the SARS-CoV-2 main protease. This provides a valuable contribution to the ongoing efforts to find a cure against COVID-19 by broadening the horizon for drug discovery efforts.

Image: Léonie Ströhmich

References:
[1.] Official World Health Organization COVID-19
dashboard: https://covid19.who.int (Accessed: 01.10.2020).
[2.] Hilgenfeld, R. (2014). FEBS Journal, 281(18), 4085-4096.
[3.] Amor, B., Yaliraki, S. N., Woscholski, R., & Barahona, M. (2014) Molecular BioSystems, 10(8), 2247-2258.
[4.] Douangamath, A., Fearon, D., Gehrtz, P., Krojer, T., Lukacik, P., Owen, C. D., … Walsh, M. A. (2020) Nature Communications, 11, 5047.

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How to present a memorable flash talk in 12 easy steps

Flash talks are a great way to give an introduction to your work, and whet people’s appetite for your research.

Generally flash talks last for 1 to 2 minutes, and presenters are normally allowed one simple PowerPoint slide or, in the case of virtual events, a 1 – 2 minute pre-recorded video. But is it really possible to present something really memorable within such limitations?

Here are some things to take into account when preparing your flash talk to make sure the audience remembers you, and contacts you after the session to find out more. Because that’s the goal, right?

1. Keep it brief

You should definitely start by giving a very brief introduction that makes people understand why your work is interesting, and ends by saying how people can contact you afterwards. Of course you can say where you’re from and your affiliation, but the critical thing is to attract to people’s attention.

2. Cover the basics

Answer the following questions:

  • Why is it interesting?
  • What is it about?
  • How did you do it?
  • With whom did you carry out the work?

3. Connect with the audience

For live events be sure to always look at the audience – don’t lose eye contact. Keep scanning the room for the duration of your talk, and definitely do not turn your back to them. In the case of a pre-recorded video, treat your camera like an audience and talk directly to it.

 4. Leave the audience asking for more

Try to build up the anticipation and attention of the people who are listening and watching– put out something you’ve investigated but don’t tell them the whole story. You want to leave them hanging and intrigued enough to want to find out more.

5. Be dynamic

Your flash talk is going to be short so your audience will generally be paying attention to you. Build up to something where you clearly emphasise one or two points. These are the sort of things that are going to bring their attention to the most important parts. Be enthusiastic – if you show that you’re really into your science people will come along and want to know more.

6. Don’t be afraid to use visual tools

If it’s relevant, there is no problem with using props in your flash talk. Alternatively, make your talk visually memorable by using dynamic diagrams, graphics and images. Videos will normally not be possible for live flash talks, so don’t rely on these.

7. Avoid special effects

It is possible to make something visually memorable without going overboard on big special effects such as PowerPoint animations. If your science is good it doesn’t need any fireworks.

8. Do the unexpected

If it fits with your character, you can try to make people laugh. Doing something that the audience is not expecting can be very effective. We’ve seen everything from interpretive dance to a guitar-accompanied talk – anything is possible! Just make sure it matches to who you are so that it appears natural.

9. Include your poster number

Definitely, definitely, definitely include your poster number during your flash talk! It will make it much easier for people to come and find you later on at the poster session.

10. Be a slide minimalist

As already mentioned, diagrams, graphs and images are great when you have only 1 or 2 slides at your disposal. Make sure though that there is a minimum of information on your slides to try to bring people into the main message – focus on the thing that you want them to remember.

11. Practise!

Like all talks, you need to practise beforehand! Even if you want to bring across that you’re relaxed and everything is quite informal there is no way around it – you’ve got to practise to be prepared.

12. Stick to the time limit

With a flash talk this is so important – the time limitations are extremely strict, and you will be moved off the stage when your time is up, or your video won’t be uploaded to a virtual event platform. So make sure you have condensed everything into the time provided, and don’t go over or you may be stopped mid-sentence!

Check out these examples of great flash talk slides!
Single-slide flash talk by Fariha Akter
Multi-slide flash talk by Pablo Gonzalez-Suarez

Original video with Dr. Cornelius Gross, EMBL Rome, and Dr. Francesca Peri, University of Zurich

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Expanding the Druggable Proteome with Chemical Biology – Best Poster Awards

The 2020 conference season at the EMBL Advanced Training Centre kicked off with the EMBL Conference: Expanding the Druggable Proteome with Chemical Biology (5 – 7 February 2020). Meet the three poster prize winners from the conference – Patrick Zanon, Enric Ros and Rens de Vries.

Identification of novel antibiotic targets using covalent inhibitors and residue-specific proteomics

PHOTO: Patrick Zanon

Authors: Patrick Zanon (1), Stephan Hacker (1)

Bacterial resistance towards all marketed antibiotics poses an imminent threat to global health. In order to overcome this antibiotic crisis, drugs with novel mechanisms-of-action are desperately needed. Covalent inhibitors are especially promising in this regard as they are already prevalent as antibiotics (e.g. β-lactams and fosfomycin), allow targeting protein pockets that are hard to address with non-covalent interactions alone and hold the promise to overcome some mechanisms of resistance development.[1] Furthermore, covalent inhibitors are uniquely suited to identify new binding pockets on proteins using residue-specific proteomics and in this way to broaden the scope of targetable protein targets.
The vast majority of covalent inhibitors so far either hijack the enzymatic activity of the protein by modification of catalytic serines and tyrosines or address cysteines through their inherent outstanding nucleophilicity. Nevertheless, the number of potentially addressable proteins in the bacterial proteome is significantly limited by the requirement for these amino acids to be present in target proteins. By developing electrophilic groups that are selective for other amino acids (e.g. lysine), we strive to expand the number of exploitable interaction sites for covalent inhibitors in the bacterial proteome. Furthermore, to assess the reactivity and selectivity of covalent inhibitors and to streamline the discovery of novel antibiotic targets, we develop new methods for residue-specific activity-based protein profiling.[2,3] In this way, we are convinced, that we will be able to make important contributions to overcome the antibiotic crisis.

References:
[1] R. A. Bauer, Drug Discov. Today 2015, 20, 1061–1073.
[2] K. M. Backus et al., Nature 2016, 534, 570.
[3] P. R. A. Zanon, L. Lewald, S. M. Hacker Angew. Chem. Int. Ed., doi: 10.1002/anie.201912075.

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(1) Technical University of Munich, Germany


Incorporating 1,2,4,5-tetrazines into proteins: A method for targeted drug release

PHOTO: Enric Ros

Authors: Enric Ros (1), Antoni Riera (1), Lluís Ribas de Pouplana (1)

Bioorthogonal reactions, namely reactions that can take place under biocompatible conditions, are having a major impact in the development of new research tools and novel therapeutic strategies. In the latter case, the discovery of the reaction commonly referred to as “click-to-release” (CtR), which triggers the liberation of a given cargo (normally a drug or a fluorophore), has led to several applications in drug delivery. This reaction happens between a 1,2,4,5-Tetrazine (Tz) fragment and certain alkenes or alkynes and, in order to achieve drug delivery specifically at the site of action, one of the two reactant counterparts should be conjugated to a biomolecule acting as a carrier, ideally a protein.
We have synthetized the previously unreported 3-bromo-1,2,4,5-tetrazine and used its excellent reactivity to attain chemoselective protein labelling onto lysines. Due to the chemical features of the formed amino-Tz. The resulting labelled lysines can undergo fast CtR reactions with trans-cyclooctenes, thereby releasing a desired cargo under physiological conditions. To showcase the applicability of this approach, we have labelled the monoclonal antibody Trastuzumab (anti-Her2) and demonstrated the specific release of the cytotoxic drug doxorubicin upon reaction in a mammalian cell culture context, resulting in a decrease in cell viability.
Additionally, we have also used 3-bromo-1,2,4,5-tetrazine to synthetize an amino-Tz containing non-natural amino acid and used it to achieve protein labelling through its genetic incorporation by amber codon suppression in Escherichia coli. The resulting site-selectively labelled proteins can also trigger fast, high yielding CtR reactions.
To summarize, we have successfully applied a new compound, 3-bromo-1,2,4,5-tetrazine, as a reagent to achieve either chemoselective or site selective protein labelling. We have applied the bioconjugated proteins to demonstrate their potential use for targeted drug delivery in a relevant cellular model, opening new therapeutically useful methodologies.

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(1) IRB Barcelona, Spain


Modulation of nuclear receptors through ligand architecture

PHOTO: Rens de Vries

Authors: Rens de Vries (1), Femke Meijer (1), Luc Brunsveld (1)

Nuclear receptors (NRs) have been one of the primary drug targets over the last decades for their ability to regulate gene expression. The traditional approach of modulating NRs is to design small synthetic molecules that interact with the ligand-binding domain (LBD) of the NR. Ligands can thereby either enhance or inhibit gene transcription. Apart from the effects on transcription, recent research shows that minor changes in the ligand scaffold can have a significant impact on the behavior of the NR. In this research, we show how small-molecules can change both the dimerization behavior of NRs and the recruitment of allosteric modulators.
The Retinoic X Receptor α (RXRα) is known as a master regulator among NRs through its ability to heterodimerize with, and thereby modulate, other NRs. We show, using a novel NanoBIT complexation assay, that small directed changes in the RXR ligand scaffold can lead to selective formation of specific hetero- and homodimers. Using our structural data and focused compound library, a model was developed to help to understand this effect of the ligand. This information can serve as a blueprint to design small-molecules that selectively target specific NRs via RXR. This makes RXR as an exciting and versatile target for NR modulation, especially when classical modulation of the partner NR is not possible.
Recently, small-molecules have been found to bind to allosteric sites of NRs. Allosteric ligands are of interest since they do not compete with the endogenous ligand of the NR and often shown an increased selectivity towards their target. We show, using X-ray crystallography and biochemical assays, that there is communication between orthosteric and allosteric ligands in the RAR-related orphan receptor γ t (RORγt). We successfully solved eleven new ternary crystal structures of RORγt in the presence of both orthosteric and allosteric ligands. These structures mechanistically show how binding of the orthosteric ligand leads to positive cooperative binding of the allosteric ligand.

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(1) Eindhoven University of Technology, The Netherlands


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