Friend or Foe: Transcription and RNA Meet DNA Replication and Repair

Event Report by Apoorva Baluapuri, University of Würzburg, Germany

RNA and DNA were first described by the Swiss biologist Friedrich Miescher in 1868. About 150 years later, we stand at crossroads of the two disciplines which have arisen as a result of dedicated research on both molecules. The first EMBL symposium on the connections between transcription and DNA replication/repair research was a major step forward in combining the progress from wide ranging topics, thus generating a consensus on how gene expression and DNA transactions cooperate.

The symposium, which was the second one from EMBL this year,  was scheduled just a day after International Women’s Day, and that aligned very well with the equally represented line-up of speakers and organisers!

The titular opening session was dedicated to transcription-associated genomic instability where all aspects of R-loops and ribonucleotide excision repair in transcription coupled DNA double strand break repair were covered. For example, Gaëlle Legube (CNRS – University of Toulouse, France) expanded in great detail on the influence of DSB-induced chromatin conformation and the strong potential of 3C-based technologies, while Elodie Hatchi (Dana Farber Cancer Institute, Boston, USA) explained about her recent publication in Nature concerning the impact of BRCA1, RAD52 and PALB2 on small RNA-driven DNA repair.

Eventually, we switched over to a more translational theme with Rushad Pavri (IMP, Vienna, Austria) who spoke about the relation between DNA replication timing and frequency of oncogenic translocations.

This time around, the poster presentation sessions were equally dynamic with topics being covered from role of RBMX in RNA processing (Sara Luzzi, University of Newcastle) to role of MYCN in reconciling elevated transcription levels with DNA replication (Dimitrios Papadopoulos, University of Würzburg, Germany).

To end the first day, Philippe Pasero (CNRS, France) tried to answer the old question of the chicken or the egg in terms of toxic R-loops, if they are the cause or consequences of DNA replication stress, while Andrew Deans (St. Vincent’s Institute of Medical Research, Australia) explained about fork re-modellers as a general mechanism of R-loop removal.

The second day started out on a high note by a talk on the consequences of DNA damage and heat shock on Pol II from Jesper Svejstrup. Prof Svejstrup recently moved his lab from the Francis Crick Institute in London to the University of Copenhagen (Faculty of Health and Medical Sciences).

To make things even more exciting at the symposium, Martin Eilers (University of Würzburg, Germany) spoke about conflict resolution by MYCN between “friends and foes”, i.e. Pol II and replication fork. This was followed by talk by Marco Foiani (University of Milan, Italy) who showed the role of ATR in nuclear integrity.

In between the breaks, the participants eagerly shared their setup of how they were joining the virtual conference:

Not only were the home setups on display, but we also got a glimpse of “add-on” participants at the conference:

Along with this fun, the second day’s poster session continued with equally interesting topics as the previous day. The virtual conference platform provided by Engagez came across as a handy tool in coming as close as possible to the in-person poster presentations.

Frédéric Chédin (University of California, Davis, USA) closed the day by talking about interplay between splicing and R-loops.

In the next two days, a wide variety of topics and methods were covered. For example,  Nick Proudfoot (University of Oxford, UK) dazzled with correlation between R-loops and antisense transcription while Petra Beli (IMB, Mainz, Germany) moved the focus from genomics to proteomics with èlan. She spoke about a method called “RDProx” which maps R-loop proximal proteome in a native chromatin environment.

Also, junior group leaders like Marco Saponaro (University of Birmingham, UK) answered what happens to replication when it encounters transcription and Madzia Crossley (Stanford University, USA) showed CytoDRIP-blots to probe RNA-DNA hybrids on gels which showed that SETX and BRCA1 loss, along with splicing inhibition, results accumulation of RNA-DNA hybrids in cytoplasm!

All along the talks, whichever questions (which, by the way, were in majority from younger researchers) didn’t get answered, were posted and responded to in the “Forum” section: this actually became a valuable summary of quite a few topics.

The networking options were also in abundance, be it the Virtual Bar mixer, or Meet the Editors session on the online platform. Given that editors from elite journals like EMBO, PLoS Biology etc. were present, it gave a nice opportunity for the researchers to gauge where their next big story could find a good home.

In summary, the symposium gave the feeling of being cozy without being too small and specific in terms of the topics covered, and benefited both the experienced and young researchers in an equal way. It was a common understanding and expectation among the participants that this symposium would perhaps be held in person next time if possible.

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‘From Functional Genomics to Systems Biology’ shines virtually

Event report by Jesus Victorino, PhD student at the Universidad Autonoma de Madrid, Spain.

Four Novembers ago, I arrived in Heidelberg on my 24th birthday which I celebrated carrying my first poster as a freshmen PhD student. Back in those days, a hypothesis with an outline of my future experiments was all I captured on that A0 laminated fabric poster. Four years and a PhD later, there could not be a better place to show my results right before defending my thesis than at the very same EMBL conference: From Functional Genomics to Systems Biology. Well, not exactly the same. This time we could not enter the ATC building and walk through its double-helix bridges, since the event took place virtually.

The organising committee managed to set up an online conference, enabling more than 270 participants to share their thoughts and results about genomics, proteomics and imaging. And we got to see everybody’s living room! Although the schedule differed from usual conferences in Europe (13:00-20:00 CET), it broadened the audience by allowing people from other countries to attend. And all that without taking a plane or paying for a hotel room, which significantly decreased the required budget to attend the conference and the carbon footprint we left behind.

I found several additional aspects of attending a virtual conference very exciting. On the one hand, the lack of big crowds in a large room with a single microphone and a line of researchers waiting for their turn, encouraged me to ask questions to the speakers. I simply felt more comfortable. Zoom allowed a record of the many questions asked, and those that were not answered due to time constraints were posted on a Slack channel created to coordinate the meeting. The Slack channel was incredibly helpful not only to increase the feedback with more scientific questions & answers but also to improve networking, especially for the poster session. I hope we keep using a similar virtual space that enables participants to contact other scientists even for onsite conferences.

At least in my experience, the poster session worked out way better than expected, which was a pleasant surprise. I found myself talking with researchers (mainly PhD students) for most of the session, which I never experienced before. I took advantage of the Slack channel to advertise my poster and also to interact with the presenters of other posters I was very interested in. Magically, people were showing up in my Zoom room and I found that breaking the ice virtually was easier than in a real room, since there was no awkward moment in which you hesitate to interact with the presenter, or the presenter does not know whether you might want to know more about his/her research or are just passing by.

On the other hand, I found the platform where we should upload the posters very inconvenient. Instead of uploading our posters in PDF and being able to chat through Slack, Zoom or similar, we had to use ‘iPosterSessions’ and re-shape our posters to fit the virtual and very rigid format of the website. I found the platform non-intuitive and there were incompatibilities, at least with my computer, for the ‘chat’ and ‘contact author’ options within it. Besides, we had to provide a way to virtually meet other participants and present our posters on our own (e.g. a Zoom room or similar), which was not very straight-forward,, and not everyone might have had access to it. Having said that, this was basically the only issue I experienced during the entire meeting – the lectures worked perfectly, we discussed exciting projects and the poster sessions were very fruitful.

Another great choice from the organisers was to schedule ‘meet the speakers’ sessions. I enjoyed meeting three of the speakers together with other early career researchers where we could exchange thoughts and impressions. I think this is very important to train students on how to interact with more senior researchers and I have rarely found a dedicated spot for this at international conferences.

During the conference, all lectures and short talks were divided into four main thematic areas: quantitative genomics, quantitative proteomics, quantitative imaging and single-cell genomics. Here’s my pick from the panel of speakers that I feel represents the essence of each area.

Transcriptional enhancers were the main characters of the quantitative genomics sessions, where different labs addressed the question of how the control of gene regulation affected phenotype in a different way. The fruit fly embryo was one of the preferred model organisms and was used by the team led by Thomas Gregor to study how the spatial organisation of the chromatin affects transcription at the eve locus. Justin Crocker also showed beautiful Drosophila embryos that they used as a test tube to understand the logic of a developmental enhancer and the phenotypic impact of its mutations. With respect to this study of the genotype-to-phenotype impact but in the context of human genome variation, Bart Deplancke told us about how non-coding variants affect gene expression in immune cells unveiling implications in leukemia.

Following with genomics, we witnessed the power of sequencing technology but at the single-cell level to understand physiology and disease. In this thematic area, we learnt with Antonio Lentini about gene expression and silencing at the X chromosome and Dana Pe’er talked about its uses to study development and cancer. The work presented by Henrik Kaessmann was very impressive and stood out not only for the use of thousands and thousands of cells, but for studying spermatogenesis in twelve different mammals providing a valuable resource to study this process across evolution.

The quantitative proteomics sessions taught us about the promising years that we face since improved technology might quickly move the field forward. Bernhard Küster showed how proteomics and in vitro models can be used to investigate drug response to cancer treatments. Although the massive characterisation of the proteome is yet not comparable with the performance of sequencing technologies in the genomic field, Michiel Vermeulen’s talk illustrated how to combine genomics and proteomics to understand cancer biology and identify new important players and therapeutic targets.

The fourth thematic area was quantitative imaging in which Emma Lundberg talked about high-throughput imaging and its use to dissect the human proteome. We could appreciate the potential of the analysis of massive amounts of imaging data in the work presented by Professor Lundberg where they involved hundreds of new proteins in cell cycle and identified new putative roles for proteins they found to localise in multiple subcellular compartments. Super-resolution microscopy could not be missing at this conference and Suliana Manley nicely showed how to use it to study mitochondrial organisation and dynamics.

Outstanding science and fresh data in a very interactive environment summarises the experience at the conference, where I was glad to see that many of the projects presented were shared in the form of preprints. I collected them and included in this list of preprints at the #EMBLOmics for attendees who might want to know more about some of the talks and for those who did not attend and might want to have a flavor of this conference.

Of course, it would not have been a proper EMBL meeting without the final gathering and concert. The event ended with a fantastic concert by Lazy Fur which really put the icing on the cake –the concert is recorded here, so you can listen to their nice voices while you prepare for your next experiment. I really thank the organisers for all the effort to make the screen disappear and feel like in a non-virtual event.

Since 2020 has shaken the way we interact with people, scientists, like everyone else, have had to quickly adapt to the new circumstances. In the academic world, conferences play an important role for scientists to share their recent advances and build their contact network. While it was already under debate how to reduce the ecological impact of such a tremendous flow of researchers travelling all over the world, virtual conferences did not seem to launch. All of a sudden, the global pandemic situation has rapidly turned this will to a necessity, leaving us no other option but to evolve. The good thing is that virtual conferences seem to be reasonably meeting our expectations, providing with a more sustainable way of sharing our data and interacting with each other. They offer both advantages and disadvantages with respect to in-person events but undoubtedly have accelerated our steps towards including more virtual conferences in the calendar once we go back to a ‘normal situation’.

 About the author

I’m Jesus Victorino, PhD student working in gene regulation and member of the preLights community, a platform to disseminate science and the role of preprints in Biology.

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Evolution and ecology goes virtual – a complete run down of the conference!

From our virtual event reporter Magdalena Wutkowska, The University Centre in Svalbard / UiT – The Arctic University of Tromsø, @m_wutkowska

The EMBL conference on Molecular Mechanisms in Evolution and Ecology took place from 30 September to 2 October 2020. The meeting – which had its first iteration in 2008 as a workshop on Evolutionary and Environmental Genomics – has gained a broader context over time not limited to evolution and yeast, which was reflected in this year’s program.

This year for the first time the conference was held virtually. Six sessions over three days encompassed vast topics such as Evolutionary Systems Biology, Systems and Synthetic Biology, Assembly and Evolution of Microbial Communities and Experimental Evolution and Evolution of Complex Traits. Between the sessions, participants could join ‘meet the speaker’ coffee breaks, poster sessions and short talks. Below are just some of the highlights from the main sessions.

SESSION 1 – Evolutionary Systems Biology

The first session on Evolutionary Systems Biology was chaired by Gianni Liti (University of Nice, France), who first outlined the history of the meetings since 2008.

Matthew Goddard

Matthew Goddard (University of Lincoln, UK) spoke about the nature of interactions between yeasts and other organisms through traits. Saccharomyces cerevisiae, just as any other organisms, evolved in the presence of other species. The existence of a trait does not have to be adaptive, and evidence of increased fitness is required to make such a statement. Goddard presented a case study of interactions between yeasts and fruit flies. Yeast produce ferments and volatiles that attract fruit flies, whereas yeast could benefit from dispersal capabilities provided by fruit flies. Some experimental evidence support the notion that the yeast – fruit fly association is mutualistic. However, recent studies showed no supporting evidence, i.e. no clear individual volatile correlated with general attraction of fruit flies. Moreover, the dispersal advantage for yeast is most likely a stochastic by-product of this interaction. Thus, the interaction is not driven by adaptation, but more likely by exaptation, which is a shift in the trait function during evolution. This talk urged us to examine the evidence for increased fitness closely, while looking for adaptive traits.

Anastasia Stolyarova (Skolkovo Institute of Science and Technology, Russia) posed the question whether epistasis shape variation within populations. Many natural populations are characterised by relatively low genetic variability; therefore, it is not possible to see strong epistatic selection between polymorphisms. Thus, to study non-random associations of alleles (linkage disequilibrium), she used the world’s most variable eukaryotic species Schizophyllum commune, which differs by up to 20% of nucleotide diversity at neutral sites. Based on 54 genomes from two distinct populations, she found that in both populations between nonsynonymous mutations were higher than between synonymous ones. Additionally, within-gene linkage disequilibrium between nonsynonymous mutations was higher when compared to that between the genes. Model simulations suggested that this phenomenon resulted from abundant epistasis.

Toni Gabaldón

Toni Gabaldón (Barcelona Supercomputing Centre, Spain) talked about ‘origin and evolution of hybrid yeast pathogens’. Novel hybrid lineages may display innovative traits that could facilitate successful colonisation and growth in new settings, including human hosts. Emergence of pathogenesis in hybrids was studied by genomic comparisons of closely related pathogenic and non-pathogenic species within Candida clade that differ in virulence. Hybrids turned out to be not only common among some clades, but they can also survive for a long time.

Aaron M. New (Centre for Genomic Regulation, Spain) spoke about deciphering how genetic variants quantitatively change protein characteristics in a long evolutionary perspective. Predicting the outcome of mutation combinations is high in additive models, but drops in sign epistasis, which is crucial for evolution. This problem was explored in a model paralog pair of yeast genes involved in galactose metabolism and signalling: GAL1 and GAL3, that differ in their biochemical properties. The study identified a mutation in GAL3 that was responsible for sign epistasis by modifying existing destabilising effect to a stabilising one on protein folding. These mutational changes in sensing/signalling proteins are of evolutionary importance for the emergence of new phenotypes.

Antonis Rokas

In his talk, Antonis Rokas (Vanderbilt University, USA) focused on ‘the evolution of the buddying yeast biodiversity’. His lab members and collaborators used buddying yeast (Saccharomycotina subphylum) to decipher genetic bases for metabolic diversity at an unprecedented scale. This research revised current understanding of drivers of evolution in eukaryotes, both in genomic and phenotypic aspects. As it turned out, the gene conservation was shown to be not universal. Losses of genes or traits were pointed out as important evolutionary forces, whereas horizontal gene transfer, although identified only a few times, had an essential effect on evolutionary trajectories.

Pedro Beltrao

Pedro Beltrao (EMBL-EBI Hixton, UK) shared novel insights on ‘evolution and functional relevance of protein phosphorylation’. Phosphorylation uses enzymes to catalyse reversible attachment of phosphoryl groups that (de)activate many types of molecules, including proteins. Phospho-regulation is of fundamental importance for post-translational protein modifications, that impacts the decision process in the cells and can be an underlying mechanism in many diseases. His research on ~500 phosphorylation-deficient mutants across 100 stress conditions explained that roughly half of them had no phenotypes and the contribution to fitness is not equal between phosphosites. Relevance of these sites for phenotypes can’t be predicted by using only one variable or feature. Advancements in understanding evolution of function of protein phosphorylation requires more insights from cell biology and mechanistic understanding.

SESSION 2 – SYSTEMS AND SYNTHETIC BIOLOGY

Kiran Patil (EMBL Heidelberg, Germany) held the second session on Systems and Synthetic Biology.

Claudia Bank

Claudia Bank (Gulbenkian Science Institute, Portugal, and University of Bern, Switzerland) discussed considerations and challenges in the process of using empirical data in fitness landscapes models in predicting evolutionary outcomes. The fitness landscape theoretical framework was proven to be a platform for testing evolutionary hypotheses. Large discrepancies in experimental data have been identified in fitness arose from single-mutations and epistasis across environments. However, it is still not clear how to reliably predict mutation effects across different environments using these models.

Jens Frickel (VIB–KU Leuven, Belgium) explained issues and uncertainties connected to mechanisms buffering mutations and its role in organisms fitness. Some gene products blur the effect of many mutations; therefore, they can act as buffer against genetic variation. The most studied buffering gene is HSP90 that assists accurate folding of mutated proteins. Genome-wide screens of yeast genes in 5000 strains allowed for identification of the gene ontology categories of genes involved in buffering activities that increase the average relative fitness. The most potent categories include chromatin binding, chromatin remodelling and unfolded protein binding. He presented directions of current and future research aiming to understand buffering mutations.

Angad P. Mehta

In his talk, Angad Mehta (University of Illinois at Urbana-Champaign, USA) focused to experimental explorations of mitochondria and chloroplast evolution. The endosymbiotic theory has been backed by molecular evidence from sequencing studies. However, the process of entering the cell by endosymbionts and coevolution with the host are not understood. He used synthetic biology tools to test experimentally investigate and evaluate evolutionary scenarios of bacterial endosymbiont evolution and transformation into organelles. Engineered S. cerevisiae (lacking mitochondrial DNA) and E. coli (thiamin auxotroph) were used as host (providing required metabolites) and endosymbionts (providing the ATP). Further research focused on the evolution of yeast – E.coli chimaeras and number of mitochondria maintained within the complex. At the moment he is involved in similar studies modelling the evolution of cells with chloroplasts using S. cerevisiae and cyanobacteria.

Kyle Fowler (University of California, San Francisco, USA) spoke on how regulons can change across evolutionary time. Transcription networks are a source of evolutionary novelty and contribute to plasticity; therefore, research in this field is crucial to understand evolutionary processes. In this talk, Fowler presented some of the results from studies on gain of function in interactions between two transcriptional regulators MATα2 and MXM1. Results showed that functional, cooperative interactions could most likely evolve with ease and explain diversity in structures in regulatory networks. Common intra-molecular epistasis expanded the permissive sequence space allowing for 9% of all sequences to be functional.

Chang C. Liu

Chang Liu (University of California, Irvine, USA) presented ‘synthetic genetic systems for continuous protein evolution in vivo’. Liu Lab and collaborators developed an error-prone orthogonal DNA replication system called OrthoRep. In this system, preselected genes can be mutated at rates 100,000-fold above the genomic mutation rates. In practice it can be employed to carry continuous in vivo evolution of the preselected genes with no off-target genomic mutagenesis. OrtoRep provides countless applications to evolve useful biomolecules (enzymes, biosensors, antibodies and many more), study adaptation (governing rules, uncovering pathways of adaptation) and perhaps predict evolution in natural systems.

SESSION 3 – ASSEMBLY AND EVOLUTION OF MICROBIAL COMMUNITIES

Sara Mitri (University of Lausanne, Switzerland) chaired the first session of the day on Assembly and Evolution of Microbial Communities.

Sara Mitri

She continued with a lecture, in which she explored co-evolutionary dynamics within small bacterial communities inhabiting highly stressful environments (metal-working fluids). In particular, Mitri elaborated on interactions and stability of these communities as well as the evolution of established interactions. High toxicity promoted positive interactions between species. These interactions, however, were not constant and could be moderated by the addition of amino acids, and interactions of toxicity with food availability. Series of experiments revealed that evolving alone led to competition and genome preservation, whereas co-evolution with other species led to neutral interaction and genetic loss. Species interaction highly depend on the environmental conditions. As species adapt to each other’s presence, these interactions may weaken over time.

Daniel Machado (EMBL Heidelberg, Germany) talked about two distinct strategies developing in co-occurring microbial communities explored by genome-scale metabolic modelling. Microbial communities showed striking polarisation at the trade-off landscape between cooperation and competition. With increasing size of microbial communities, members displaying one of these strategies differed in multiple aspects such as number of metabolic genes, nutrient requirements, metabolic dissimilarity, abundance and phylogenetic distance. Moreover, competitive and cooperative communities were shown to have distinct habitat preferences. Communities displaying either of these strategies respond differently to both abiotic and biotic perturbations in their environment.

Isabel Gordo

Isabel Gordo (Gulbenkian Institute, Portugal) explained some aspects of gut bacterial communities evolution in mice models. She focused on two main topics: evolution of a single dominant strain of E. coli and evolution of an invader strain in the coexistence with resident E.coli. Studies on the first case revealed that both balancing selection and clonal interference were wide-spread within the guts. Coexistence of populations of bacteria with increased mutation rate and population without them can last for a long time. The effect of deleterious mutations in vitro was higher than from in vivo experiments, that lead to a conclusion that probably the deleterious effect of mutations was reduced by biotic interactions and is even lower in species-rich setting. Experiments on the second scenario showed that in the initial stages of the evolution of an invader was dominated by phage-mediated horizontal gene transfer. At later stage, mutations started to accumulate. In the last part of her talk Gordo emphasised the need of long-term evolutionary studies of these scenarios and presented selected unpublished results from her lab.

Jona Kayser (Max Planck Institute for the Science of Light, Germany) described mechanisms in which mechanical forces can affect evolution in dense cellular populations. These populations are found in yeast colonies, but also biofilms, embryos or tumours. Collective motion of cells in the dense colony moves other cells with them. Slow-growing mutant populations with drug resistance can be carried to the rim of the colony by fast-growing yeast that are sensitive to drugs. In case of a treatment during infection application of the drug could stop the growth of neighbouring wild populations and caused resurgent growth of the mutants that were drug-resistant and not outcompeted by fast-growing wild types. These mechanisms may lead to increased understanding of treatment design in antibiotic resistance infections and tumours.

Wenying Shou

Wenying Shou (Fred Hutchinson Cancer Research Center, USA) talked about disentangling molecular mechanisms causing rapid evolution of new metabolic interactions in cells undergoing nutrient-growth dysregulation. Through conserved mechanisms in eukaryotic cells, nutrients control eukaryotic cell states promoting or ceasing growth. During unnatural auxotrophic limitation(s) this regulation might fail, resulting in nutrient-growth dysregulation. In this state cell growth is not arrested despite of limitation in resources. Shou presented experimental evidence that cells in this state release unusual metabolites. As a consequence, these released metabolites may provide an unforeseen way of rapid evolution of new metabolic interactions with other organisms.

Tami Lieberman (Massachusetts Institute of Technology, USA) spoke on adaptive evolution of skin commensal bacteria. In Liberman’s research tracking evolution, instead of sampling over a long period, many colonies were sampled from different pores in a single time point. Some bacterial species can adapt by de novo mutations in healthy people while in other bacteria inhabiting human face there were no signals of adaptive evolution. Mutational rate was much lower compared to rapid spreading on the face skin. Pores can be seen as separate islands, where location within the pore can predict success more than fitness does. Populations within pores most likely are descendants from a single ancestor. Some of the strains expanded and diversified rapidly on individual humans. People are colonised by multiple lineages, probably coming from multiple independent colonisation events.

Rachel Dutton

In her talk, Rachel Dutton (University of California, San Diego, USA) focused on the ecological interactions in cheese-rind communities. Dutton’s Lab uses cheese rind biofilms to deconstruction and reconstruction of the system in order to understand microbial communities. They found many species-specific effects within these communities; however, some effects were found conserved across species. Over the years, the lab brought evidence for fungi being essential players impacting bacterial biology by releasing enzymes, siderophores, volatiles, antimicrobials and by increasing bacterial mobility.

The next session was a roundtable discussion on Assembly and Evolution of Microbial Communities moderated by Jun-Yi Leu (Institute of Molecular Biology, Taiwan). The participants Maitreya Dunham (University of Washington, USA), Isabel Gordo (Gulbenkian Institute, Portugal), Gianni Liti (University of Nice, France) and Nassos Typas (EMBL Heidelberg, Germany) discussed the past, present and future of the field. They emphasised that although there have been many substantial advancements in high-throughput sequencing, there are some issues that are still lacking full understanding, for instance, mutations, gene copy numbers and its consequences for the fitness of organisms. Experiments on laboratory strains of organisms explore only a small proportion of mechanisms and genetic diversity. Thus, future research should focus beyond that. The complexity of microbial systems is high, they are impacted by many factors, and they themselves impact their surroundings and other organisms. Therefore, there is a profound need for collaboration between different scientific disciplines to produce novel cross-disciplinary approaches, efficient data integration methods and solutions to long-lasting problems. Some of the significant challenges in the field include developing efficient training programmes that would enable students to receive well-rounded education encompassing a variety of disciplines. Finally, current knowledge should be more efficiently transformed into real-life solutions and applications that could potentially tackle some of the critical global issues.

Career development

The third day of the conference started with a career development session. Guests Claudia Bank (Gulbenkian Science Institute, Portugal, and University of Bern, Switzerland) and Daniel Machado (EMBL Heidelberg, Germany) discussed critical issues in carrier development and its maintenance. Career paths can be very different and can involve switching between disciplines, between academic and non-academic sectors. Much of the discussion was focused on the application process, its stochasticity and not being discouraged by rejections. They highlighted the importance of mindful and self-compassion approach towards work, especially in academia. Keeping a work-life balance might be often overlooked, although it is an important issue that can affect well-being and also motivation.

SESSION 5 – EXPERIMENTAL EVOLUTION

Lars Steinmetz

Chaired by Jun-Yi Leu (Institute of Molecular Biology, Taiwan), the session opened with a presentation on yeasts’ synthetic genomic applications by Lars Steinmetz (EMBL Heidelberg, Germany). The talk started with a summary of discoveries and advancements in genome editing. Manipulating regulation of transcription factors were used to increase understanding of adaptation to heat in yeast. Extensive work on engineered yeast cells able to on-demand reorganisation of their genomes helped to study selection changes in transcript isoforms that can occur after these reorganisations. However, many questions in genome editing and design regarding the location of genes and design principles still remain open.

Sarela Garcia Santamarina

Sarela Garcia-Santamarina (EMBL Heidelberg, Germany) shared her research on current understanding the interplay of drugs and gut microbiome in vitro. Experimental evidence showed high prevalence of drugs affecting growth of bacterial strains, whereas bacteria can significantly alter concentration of many drugs. It is not clear if these effects observed in monocultures are consistent in communities. Comparing responses of monocultures and communities in response to different drugs showed emerging community behaviours, such as sensitisation of drug-tolerant strains and protection of drug-sensitive strains. These emergent behaviours were concentration-dependent and disappeared when concentrations increased. High levels of these stressors disrupt community protective traits. The protective properties can be partly explained by drug metabolisation.

Sinead Collins

Sinéad Collins (University of Edinburgh, UK) spoke on the use of experimental evolution to understand microbial response to climate change. Oceans’ phytoplankton is composed of diverse organisms that act as “tiny adaptor plugs” between organic and inorganic worlds. These two worlds undergo shifts due to climate changes, and by using one methodology, it is impossible to predict how would they react in short and long-time perspective. She employed microcosm experiments that provide direct links between cause and effect in manipulation studies mimicking climate change, i.e. temperature and CO2 concentrations. Using these tools, the studies explored epigenetic transmission in adaptation to changing and fluctuating environmental conditions.

Christopher Large (University of Washington, USA) spoke on genomic stability and adaptation of beer brewing yeasts during serial repitching in the brewery. Repitching (using yeast many times over multiple fermentations) serves as a method to perpetually maintain yeast populations in breweries, and it is a suitable procedure to study adaptation to the brewery environment by looking at copy number variation, mitotic recombination single nucleotide polymorphisms and insertions/deletions of bases in the genome. In these conditions brewing yeast continuously underwent domestication at a fairly rapid rate. Many related strains in different breweries adapting over time displayed the same structural variations that included mitotic recombination of specific chromosomes and aneuploidy.

Gilles Fischer

Gilles Fischer (Sorbonne University – French National Centre for Scientific Research, France), talked about transient hypermutator subpopulations in yeast colonies. A continuum model of genomic evolution of cancer predicts three main ways in which aberrations (including mutations) accumulate a gradual, punctuated and catastrophic modes. Often, we think about genome evolution as a gradual accumulation of mutation. Yeast populations contain hypermutator subpopulations that originate from transient phenotypic mutator cells. These subpopulations increased in size under stressful conditions such as oxidative stress and could lead to systemic genome instabilities illustrating the possibility of the catastrophic mode of genomic evolution.

Virginia Cornish

Virginia Cornish (Columbia University, USA) spoke on ‘expanding the synthetic capabilities of yeast’. Cornish Lab uses engineered yeast capable of carrying out in vivo mutagenesis and selection steps of directed evolution. These yeasts have been engineered to perform new functions that made them useful in many applications. For instance, they were used as synthetic biosensors to create cheap colorimetric essays that can be used for detecting pathogens. This and further work in this area can lead to many therapeutic applications in the future.

SESSION 6 – EVOLUTION OF COMPLEX TRAITS

Maitreya Dunham chaired the last session of the conference, which focused on the evolution of complex traits.

Joseph Schacherer

Joseph Schacherer (University of Strasbourg, France) talked about S. cerevisiae-wide survey of the evolution of complex traits. Existing knowledge on architecture, inheritance and phenotypic expressivity of complex traits is still poorly understood. Genomes and phenotypic resources generated for over a 1000 isolates of S. cerevisiae served as a platform to select strains for pairwise crossing and examination of complex traits in resulting hybrids. These hybrids were grown under 50 growth conditions in order to obtain phenotypic distribution of the offspring. Most of the cross/condition combinations were shown to have complex inheritance. The complexity across traits was found highly variable. The expressivity of complex traits was both variable and dynamic across strains in different conditions.

Melania Jennifer D’Angiolo (Institute for Research on Cancer and Aging, IRCAN, France) talked on the origin of genomic introgressions from a yeast living ancestor. Introgressive hybridisation is an important mechanism in evolution of species across kingdoms. They were frequently identified in many yeast populations; however, it remains unclear how they appeared in reproductively isolated species. In her research, D’Angiolo found a coexistence of hybrid ancestor and its descendants inhabiting the same ecological niche. It was proposed that the underlying mechanism involved genomic instability that made possible for the hybrids to overcome sterility.

Irene Stefanini

Irene Stefanini (University of Turin, Italy) spoke about research on buddying yeasts’ associations with insects. S. cerevisiae are important components of grape berries microbiota; however, their numbers depend on presence of the grapes and fluctuate according to the seasons. They are rarely found on unripe grapes, but their number rapidly increases towards the end of the season. For a long time, it was not clear where do these organisms overwinter and how do they get back on grape berries. Yet, a complete local variability of yeasts was found in insects’ guts where they could overwinter and be transported back on the grape berries when they formed in a new season. Rarely observed yeast mating in nature was promoted in insect guts, including wasps. Recent genome-wide association of S. cerevisiae from wasp guts started to shed light on mutations important ecologically relevant fungal phenotypes.

Lucy Xie (Stanford University, USA) spoke on a newly described drug resistance mutation-independent mechanism found in Candida albicans. In contrary to mutation-dependent, the new high-frequency drug resistance called pararesistance involves epigenetic modifications. Common antifungal (fluconazole) in low doses induced pararesistance in up to 10% of cells. These numbers increased after addition of other substances. The induced pararesistance was still observed after more than 100 generations cultured in the absence of the drug. Understanding the intricacies of this mechanism could decrease medical treatment failures in fungal infections.

Tatiana Giraud

Tatiana Giraud (Evolution et Systématique Laboratoire ESE, Université Paris- Sud XI, France) spoke on “multiple convergent events of mating-type loci linkage through different rearrangements”. Giraud focused on smut fungi beneficial gene linkages called supergenes that provide adaptation advantages. Presented studies on prevalence, formation and evolution of supergenes increased understanding of this little-explored field.

Adam Feist

Adam M. Feist (Denmark Technical University) spoke on an ongoing cross-disciplinary automated project for understanding adaptive laboratory evolution. The project consists of two main components hardware for high throughput culturing and complex experimentation procedures to obtain information on mutations and conditions in which they arise and with a customised software for processing the output data. Acquired experimental data are subsequently organised, described, analysed and become part of a database (ALEdb). A multi-scale annotation framework aims to identify critical mutations at different conditions and scales (from binding sites to large aggregated features such as COGs). Feist also explained the current focus on using the data for design and engineering purposes, as well as expanding the breadth and scope in the database. ALEdb is available as a web-based platform https://aledb.org/

Kiran Patil

After the last session, Kiran Patil held a speech with closing remarks and future outlook. Attendees were given access to all the conference materials, including posters and pre-recorded talks for two weeks after the conference had ended.

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Tackling gender imbalance in academia

PHOTO: Suzanna Prosser

Event report by Suzanna Prosser, Lunenfeld-Tanenbaum Research Institute, Canada

Gender imbalance is a longstanding issue in academia, with men still more likely to progress to the highest levels. Institutional and individual biases, attitudes, and self-limiting beliefs are only some of the factors that allow this situation to persist. The Gender Roles and their Impact in Academia virtual conference served as a timely reminder of these issues, whilst also highlighting current thinking, research and practices surrounding gender, diversity, equality and academia. It was only fitting that the conference commenced on the second Tuesday of October, which is designated as Ada Lovelace Day, an annual celebration to raise the profile of women in STEM.

The opening lecture was delivered by Melvin Konner (Emory University) whose 2015 book ‘Sex, Evolution and the End of Male Supremacy’, upset a lot of people if the vitriolic reviews and commentaries it received are anything to go by. The premise Melvin presents in his book is a very simple one: “women are not equal to men; they are superior in many ways, and in most ways that will count in the future”. He explained that the similarities between men’s and women’s brains are far greater than the differences, but historically women have been believed not to have the capacity to lead. The consequence of this is that their voices have been excluded from the places where they would be most beneficial. We are now, however, living in a time where women are managing to trickle up to prominent leadership roles throughout the world, although sadly the tides of change continue to move slowly.

The notion that men are superior to women has perpetuated in part due to biological evidence perceived in such a way so as to support this thinking. Against this, Gemma Puixeu (IST Austria) very eloquently argued that while biology can justify the differences between the sexes, it cannot justify gender binarism nor gender inequality. Acknowledging that there are many other players aside from chromosomal sex defining systemic sex, allows us to appreciate that gender expression is multifactorial, leading to a continuum that is influenced by non-biological factors. Indeed, gender binarism can only be explained by cultural enforcement. For gender inequality, traditional evidence states that sexual selection is stronger in males, as male traits are superior and that evolution is male-driven. On the other hand, alternative evidence says that there is no power inequality between the sexes, and questions what are male and female traits, and why we value them differently. Furthermore, one sex does not evolve in spite or at the expense of the other. So, if male supremacy is not explained by biology, why has science failed us? First, it is subjective – if performed by men, it is for men and suffers from unconscious bias. Second, arguing women are subordinate by nature justifies socio-politico-economic interests.

Talks by Cordelia Fine (University of Melbourne), Ijeoma Uchegbu (University College London) and Stephen Curry (Imperial College) covered why gender diversity matters in the work place, strategies to approach equity and diversity in academia, and how to ensure science is built by men and women. Evidence provides overwhelming support for diversity on teams and panels leading to better decision-making processes, outcomes and productivity. Indeed, diverse teams make superior decisions as they focus more on facts and process them more carefully. Depending on field, over 50% of graduate students are female, however often less than 10% of professors are women. Reasons why women fall out of the academic pipeline are varied but, as Heather Metcalf (Association for Women in Science) explained, intersectionality is a crucial dimension, with reasons being very different for women of different backgrounds.

Women are frequently encouraged to adopt more male-associated traits, such as confidence. However, Suzanne Doyle-Morris (InclusIQ) informed us that women that display overt confidence tend to be penalized with negative labels such as bossy, difficult, and strident. And the inherent confidence women possess to occupy space in fields dominated by men often goes unacknowledged. Furthermore, over-valuing confidence disadvantages people from groups, genders and cultures in which self-promotion is criticised, and risks hiring and promoting the wrong people. Instead, panels need rigorous training in preparation for conducting evaluations so as to see through confidence to get to competence. It is important to value competence over confidence, as competence as a trait works for a wider range of people when looking for leaders in academia. In addition to hiring committees, this is particularly important in research funding decisions, as obtaining funding serves as an indicator and requirement for career success. However, systemic inequality also exists in grant allocation, to the detriment of women. Claartje Vinkenburg (CJ Vinkenburg Advies) described how panel members believe in their own ability to objective evaluate proposals based on merit, but that panel members’ implicit associations and explicit expectations around the ‘ideal scientist’ and ‘ideal career’ affect how they evaluate and discuss applications. In addition, the requirement to ‘sell science’ (high risk, high reward) creates an additional layer of gendered complexity to the decision process.

In the final keynote lecture of the conference, Jo Handelsman (Wisconsin Institute for Discovery) discussed gender bias in academic science. Unconscious bias describes the underlying attitudes and stereotypes that people unconsciously attribute to others that affect how they understand and engage with them. Unfortunately, many scientists believe they don’t display unconscious bias as they are trained to be objective, however study after study proves this to be untrue. In one such study, participants were more likely to hire whichever application had a man’s name on it, then provided post-choice justifications, like citing whichever strength was present, for their biased behavior. Worryingly, those who believe they aren’t biased are those that apply biases the most. Fortunately, there are tangible steps that can be taken to overcome unconscious bias, including: promotion of self-awareness of biases, understanding the nature of bias, providing opportunities to discuss bias to create accountability, and the provision of training sessions to promote bias literacy. Indeed, earlier in the meeting, Ansgar Büschges had described the use of unconscious bias training as a prerequisite for participation in faculty search committees at the University of Cologne for the active recruitment of women. In addition, the identification of hiring criteria before the evaluation of candidates can abolish bias in selection participants. Jo also advised female scientists to give their referees as much information as possible about themselves (accomplishments, career goals etc.), as the less information people have available the more likely they are to fall back on biases.

Gender imbalance in science hasn’t occurred due to not having suitably qualified women, but rather the structures that are in place which prevent them from taking their rightful place in the higher echelons. Instead of helping women do better, we need to eradicate the barriers that prevent them from succeeding and provide them with the same level of support and mentorship that men receive. We need affirmative action, targets and quotas to reach gender equality, alongside a rethinking of criteria and assessment. While the problem is a chronic under-representation of women in research, men need to be part of the conversation. Indeed, the drive for gender equality is not an attack on men to prevent them from succeeding, but the provision of space to allow women to succeed as they deserve.

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14th EMBL Conference: Transcription and Chromatin

Event Report by Apoorva Baluapuri, University of Würzburg, Germany

As it happens frequently in life, there is always something good that comes out of a bad situation. The scientific world seems to be in the midst of such a situation, where all possibilities to share exciting discoveries and network among peers in person have disappeared, thanks to a 200 nm wide particle of protein. However, the good thing that has come out of it was the ability to virtually participate in conferences and talks at a reduced cost, and also without raking in carbon footprint.

The 14th Transcription and Chromatin conference at EMBL showed how such virtual hosting can be done in an excellent manner. While the new format took some getting used to, such a minor inconvenience was a small price to pay for making the new science accessible to researchers around the world – and many of them who would not have joined a conference in a different continent in person, tuned in from the comfort of their homes and offices.

A word cloud composed of the titles of the talks from Day 1 showcases the range of topics in focus.

In fact, thanks to the intuitive features of Zoom, many more questions were asked following the talks at the conference, with intense rigour and enthusiasm particularly from the younger participants. Due to the considerations of time-zone differences, the meeting was restricted from 14:00-22:00 CEST (approx.) and consisted of 15-20 minutes long talks, which turned out to be very fruitful in terms of keeping things concise while maintaining the interest.

The titular opening session was dedicated to mechanisms of transcription in eukaryotes. The range of speakers truly covered every end of the spectrum in all respects. While seasoned scientists like Patrick Cramer (Max Planck Institute for Biophysical Chemistry, Germany) showcased the lessons learnt in transcription initiation, promoter-proximal pausing and elongation from Pol II structural biology, young scientists like Kinga Kamieniarz-Gdula (Adam Mickiewicz University, Poland) also dazzled with new insights into transcription termination.

Similar trend was noted in the area of chromatin topology with Ana Pombo (Max Delbrück Center for Molecular Medicine, Germany) showcasing Genome Architecture Mapping which found variable 3D topology in brain cells at both short and long genomic distances, and integrated it with single-cell RNA-Seq data to get cell-type specific gene expression. Display of new technologies was relentless with Kyle Eagen (Northwestern University, USA) showing how BRD4-NUT (which recruits P300 histone acetylase) drives interactions to form a specific nuclear subcompartment, and how a PROTAC against it abolished the subcompartment interactions.

In times when scientists are mostly working from home, Steve Henikoff (Fred Hutchinson Cancer Research Center, USA) took the concept to a new level by showcasing a new protocol for CUT & RUN called CUT&Run @ Home, which can actually be performed in your own garage. This was truly inspirational!

However, regulation of X chromosome was not left behind, and Asifa Akhtar (Max Planck Institute of Immunobiology and Epigenetics, Germany) H4K16ac and X chromosome regulation. It was shown in really exhaustive detail how histone acetylation is not just a way to open the chromatin structure, but it’s also a much more elaborate and elegant system controlling gene expression in both Drosophila and mouse.

As usual, what was very obvious was the affinity of the speakers towards incredible puns and double entendre! While Alistair Boettiger (Stanford University, USA) mentioned that he thinks of TADs as more like “dancers”, rather than architects of nucleus, Karolin Luger (University of Colorado Boulder, USA) showed cool structural data indicating how SPT16 CTD “hugs and protects” exposed DNA binding surfaces on nucleosomes.

When it comes to transcription in the 2020s, the phenomenon of phase separation cannot be ignored. Thanks to Bob Kingston (Harvard Medical School, USA), who showed the functional role for phase separation in a system, where PRC1 subunit CBX2 CaPS domain drives phase separation in cells; and David Gilmour (The Pennsylvania State University, USA)  who explained the consequences of too short and too long consensus Pol II CTDs, it was clear that the phenomenon has clear and present relevance in transcription.

However, the core mechanistic session related to Pol II was not neglected either: Steve Buratowski (Harvard Medical School, USA), showed that Pol II CTD phosphorylation cycle is all about time and not distance on genes. Using single molecule imaging system, he showed two modes of Pol II association on promoters: short duration via Mediator in contrast to long duration via PIC. Amazingly, he found time to talk about Elongation Factor dynamics as well.  It turns out that elongation exchange can happen on moving Pol II as well, and was shown for SPT5 that it actually disassociates while Pol II remains bound, with a new SPT5 binding event being recorded later.

That being said, this conference was not just about basic science and mechanisms – but included lessons learnt from applying the mechanistic understanding into the translational aspects of science. For example, Ali Shilatifard (Northwestern University Feinberg School of Medicine, USA) showed that inhibiting Super Elongation Complex (SEC) by small molecule inhibitors reduces Pol II speed (in terms of kb/min by FP-4sU-Seq, and not pSer2 Pol II ChIP-Seq – no sloppy work shown at this conference !!) and helps in recovery of MYC driven tumours in mice.

Towards the last session of the conference, there was a nice mix of talks covering transcription elongation and termination, with Hanneke Vlamming (Harvard Medical School, USA) (one of the few post-doctoral researchers who delivered the talks!!) showing that for Pol II, the elongation potential is encoded in DNA sequence. She also indicated that mRNA sequences are not only easier to transcribe for Pol II, but also for maintaining steady state RNA and protein levels. At the same time, Torben Heick Jensen (Aarhus University, Denmark) showed the effects of depleting Integrator, indicating that Integrator depletion causes decrease OR increase of transcriptional read-through, depending on the genes if they are multi or mono-exonic. What seemed really striking was also the report that heat shock triggers increased elongation rates of Pol II while inducing premature termination – as shown by Jesper Svejstrup (now at University of Copenhagen).

Finally, the conference wrapped up with Shelley Berger summarizing the new findings from her lab changes in foraging behaviour of ants based on epigenetics, with the cool finding that HDAC inhibitors induce changes in “caste” of ants.

In many ways, this conference was a first for a lot of people. The ease with which young scientists could ask questions in Zoom and interact with the speakers on Slack was definitely the highlight – but left some scope for improvement in terms of how poster presenters interacted with the audience. In the words of a few presenters, it seemed extra work to upload the data in parts when some of the other conferences allowed them to upload just the PDFs of their posters. Nevertheless, the Zoom sessions were still adequate for the individual poster sessions.

What was truly enjoyable and an upgrade from in person socialising at conferences was the Social Mixer Event! It was an amazing experience to meet so many new people (and say hello to a few old acquaintances) during the speed networking. Hope this is a recurring theme in the years to come.

This bring us to introspect the utility of virtual conferences when the emphasis to reduce the carbon footprint has been on the rise. Maybe alternating between virtual and in-person conference, or a hybrid model with virtual and in-person talks in the future would be that way to go.

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