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.

View poster.

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 and Artwork Awards — VIZBI 2021: Visualizing Biological Data

The 11th international meeting on Visualizing Biological Data, best known as VIZBI, was held virtually this year. The conference was as exciting as always, filled with great discussions, an outstanding speaker line-up and of course amazing, beautiful visuals.

The participants had the chance to vote for their favourite scientific poster and artwork — a very tough choice as all of the works were truly amazing! Here, we present you the winners.

Best scientific poster

Building a whole cell in 3D

by  Martina Maritan (The Scripps Research Institute, USA) Ludovic Autin, Jonathan Karr, Markus Covert, Arthur Olson, David Goodsell.

Martina Maritan, The Scripps Research Institute, USA
Martina Maritan

Mesoscale 3D models are powerful tools for exploring structural data across the entire range of scales, from the molecular to the cellular level. We built structural mesoscale models of a whole Mycoplasma genitalium (MG) cell with the CellPACK suite using data generated from a whole-cell MG simulation. 3D models integrate structural details into a computational model of MG, highlighting specific properties of the ingredients, and creating snapshots of the cell at defined time points of the simulations. Our modeling process goes through three steps. Firstly, we assemble a recipe: a list of all the proteins of Mycoplasma associated with a structural representation. Secondly, we create a model of the genome with DNA, RNA, RNA polymerase, mRNA, and ribosomes, with user-defined location of RNA polymerase and length of transcripts. Thirdly, we assemble the nucleoid, soluble, and membrane ingredients, and relax the whole system to resolve steric overlaps. The result is a framework for interactive construction of atomic resolution mesoscale models describing a spatial view of a whole bacterial cell. Our models are the first atomistic representation of an entire bacterial cell.

Building a whole cell in 3D
Building a whole cell in 3D

View Martina Maritan’s poster
Watch lightning talk

Second best scientific poster

How to communicate cell behaviours visually

by Christian StolteCellarity, USA.

Christian Stolte, Cellarity, USA
Christian Stolte

Cellarity is pioneering a new approach to drug discovery, treating disease at the level of the cell as opposed to a single molecular target. Combining unique expertise in network biology, high-resolution single-cell sequencing data, and machine learning, the result is a new understanding of the cell’s trajectory from health to disease, and how cells relate to one another in tissues. The cell and its network of transcripts and proteins offer a more complete view of the complexity of human biology than any individual molecular target. To help communicate this, we use visualizations resembling a cityscape called ‘Cellarity maps’. Based on the UMAP dimensionality reduction technique, they use the third dimension (height) to show density. This creates landscapes where we can now use colour to encode additional dimensions, and make it easier to see different ‘cell behaviours.’

How to communicate cell behaviours visually
How to communicate cell behaviours visually

View Christian Stolte’s poster
Watch lighting talk

Best artwork

10 Hallmarks of cancer

by Karolína Kryštofová, Institute of Biophysics of the Czech Academy of Sciences, Czech Republic.

Karolína Kryštofová, Institute of Biophysics of the Czech Academy of Sciences Czech Republic
Karolína Kryštofová

A whimsical series of illustrations inspired by the hallmarks of cancer as described by Weinberg & Hanahan in their paper Hallmarks of cancer: the next generation (2011).

10 Hallmarks of cancer
10 Hallmarks of cancer

View Karolína Kryštofová’s artwork

Second best artwork

The human heart

by Philipp Dexheimer, Research Institute of Molecular Pathology, Austria.

Philipp Dexheimer, Research Institute of Molecular Pathology, Austria
Philipp Dexheimer

Inspired by Leonardo Da Vinci’s original way of depicting his science and ideas, this digital painting illustrates the 21st century research process to understand formation of such a delicate organ as the human heart. Cells are derived, self-organize into 3-dimensional organoid structures, and allow unique insight into heart development and physiology. Illustrating research described in: Hofbauer et al., BioRxiv, 2020 – Cardioids reveal self-organizing principles of human cardiogenesis.

The human heart

View Philipp Dexheimer’s artwork

If you’d like to take a look at all of the posters presented at VIZBI 2021, you can! Visit the poster gallery, dive into the science, enjoy the beautiful images and be amazed by the scientists’ visualization skills.

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Meet the EMBL Events Team: Diah

You’ve just got to meet Diah. She is one bright star whose sparkle shines when she speaks, and you’ll end up smiling every time you talk to her. She joined the Course and Conference Office in 2012, then moved to her home country of Indonesia in 2018 before re-joining EMBL in 2020 (yes, in the middle of the COVID-19 pandemic!). We are very happy she is back and can’t wait for you to meet her.

Diah Yulianti, Course and Conference Officer

At EMBL since: 2012 — 2018 and re-joined in 2020.
Number of organised conferences/courses: 29 conferences and 22 courses.

Favourite place in Heidelberg:
Königstuhl. The view of Heidelberg especially during sunset is so beautiful. And EMBL. It is not because I work there but the place itself and the forest and farm around it are so pretty in all seasons.

What are the challenges/differences of organising a virtual conference or course?
The learning curve in mastering different platforms and software as well as a different workflow was pretty steep. It is a challenging but also very exciting process — both rewarding and humbling at the same time.

How have you adapted your role during the pandemic?
I  try to stay connected with people as much as possible. I like to keep an open mind, be mindful and creative — even more than before!

What do you miss most about life before the pandemic?
Like everyone else, I miss meeting and talking to people in person. I am a very extroverted person so it was very difficult for me when we had to start working from home. I am used to it now. I also miss playing badminton with the team!

What have you been up to during these difficult times? 
I walk a lot. Also trying new recipes — I love cooking!

If you weren’t a Course and Conference Officer, what would you be?
I was a high school teacher for quite some time. If I were not in Europe, working for a high-level international research institute, interacting with people from all over the world, I would probably be back teaching. It is a very different world but the teaching gene runs in the family. In an alternative world, I would own a small shop selling vegetables, flowers or candy😊.

What is the strangest thing that has ever happened in a conference?
Oh one time at a conference, the keynote speaker had just started her talk when the fire alarm went off. We had to herd 300 participants out of the building to the meeting point near the woods!

If you were a superhero, what power would you like to have?
I’d like to have the power to fly, to lift off the ground by myself freely and ride the air currents — it must be so cool.

Which series have you been binge-watching that we should also definitely watch?
I just finished The Queen’s Gambit and Dark. Really good!

Which are your favourite books?
My all-time favourite books are The Glass Palace, Shantaram and of course Harry Potter!

Upcoming events Diah is organising or co-organising:

EMBO Practical Course: Measuring Translational Dynamics by Ribosome Profiling, 17 – 25 May 2021, virtual.

EMBO Workshop: Predicting Evolution, 14 – 16 Jun 2021, virtual.

EMBO Workshop: The Mobile Genome: Genetic and Physiological Impacts of Transposable Elements, 29 Aug – 1 Sep 2021, virtual

 

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Celebrating 10 years of Chromatin and Epigenetics

Our upcoming EMBL Conference: Chromatin and Epigenetics is celebrating its 10th anniversary this year! Although this year’s conference will be very different in format (yup, you guessed right: virtual!), the topics to be discussed will be as exciting as always.

We spoke to Asifa Akhtar and Geneviève Almouzni, the scientific organisers who have been there since the beginning of this conference series. Read on to find out what inspired them to organise this event in the first place, and what highlights can be expected at the virtual conference!

The Chromatin and Epigenetics conference is celebrating its 10th anniversary this year. How did it all start and how has it developed over the years?

GA: I was part of the original organisation committee when it started — 20 years ago already! A long journey already… The meeting actually started with the wish to give credit to my Postdoc mentor Dr. Alan Wolffe who had tragically passed away and was very active in the field. He was coined the “champion of Epigenetics” back then… You can see his picture in the corner of the conference image.

When I started my lab, he used to tease me about having a conference in Europe on a field that was just starting to take off. The fact is that since then it has become a major gathering of people in the field, including those actively engaged in the EC funded Network of Excellence — first the Epigenome and EpiGeneSys networks which expanded towards a broader community, including the LifeTime initiative and many friends from the 4DNucleome!  Undoubtedly, research over the past two decades has been incredibly active, leading to the deciphering of chromatin-based mechanisms, multi-scale genome organisation and the uncovering of the role of epigenetics in various human disorders with an increasing interest in studying the influence of age, environment, life style and disease states. I am really excited to hear about the latest news…

AA: I was part of the original organisation team, and being located at EMBL meant that I have been part of all the nitty gritty deals of organising this conference ever since. We have had a series of outstanding co-organisers on board, which also developed the breadth of the meeting over the last 20 years. We have kept up with the pace of the field, and this meeting is a major biennial scientific event in the chromatin and epigenetics field. The location at EMBL has been fantastic, with all the support and infrastructure available to run a big meeting like this. It continues to be a pleasure to organise this conference, and I am excited about all the possibilities that the virtual format will bring.

What inspired you to organise this conference?

GA: This meeting is dear to my heart, and it has surely brought together a wonderful community in Europe that is well linked with people worldwide. Also, from the inception we wanted to engage younger people in the organisation and serve the community. It has a unique spirit — it is collegial and friendly, and a place where new collaborations arise — and a growing network! The fact is that people always presented their most advanced work and unpublished data, thereby offering opportunities to discuss science in the making. We hope that the virtual conference version this year will retain this special touch.

AA: Alan Wolffe was a great chromatin biologist and his sudden passing took many of us by surprise, and left great sadness. He was a wonderful mentor and was interested in young scientists, a quality which I had always admired. Co-incidentally my husband was a postdoc in Alan’s lab, just like Genevieve. In fact, Alan’s plan was to visit him during his trip that eventually led to the tragedy. Co-organising the memorial workshop in his memory was an honour and in the long run a tremendously important decision, as this meeting became a focal point for chromatin biologists and epigeneticists to meet in Europe and share the wonders of the latest science we are all doing. The chromatin and epigenetics conference originated from initial event and has grown stronger over the years.

 Could you share what the focus and highlights of this year´s conference will be?

AA: The 10th conference in a series of meetings is a really memorable event and celebrating this during a global pandemic is a major challenge. We strive for excellence and this meeting will deliver many highlights and thrilling science. I very much hope that it will bring us together to appreciate the importance and perseverance of basic science, and that we celebrate coming together even in a virtual setting and show that we are dynamic and flexible, come what may…

GA: This year the session topics cover: Heterochromatin and HP1, developmental epigenetics, chromatin regulation, nucleosomes structure and function, transcription and chromatin defects and diseases, nuclear architecture as well as chromatin and RNA modifications. This is a very exciting program with both live-streamed invited speakers and selected short talks with Q&As, as well as digital poster sessions. We will also hold meet the speakers session along with some other surprises…

Among our speakers, Caroline Dean will tell us about cold-induced epigenetic switching in plants, Karen Adelman will discuss regulation of transcription elongation in development and diseases, Luciano di Croce the advances in the distinct role of Polycomb in stem biology and cancer, Bob Kingston on chromatin compaction and phase separation in epigenetic control of development, Danny Reinberg about Polycomb, inheritance and disease, Anja Groth will speak about chromatin replication and epigenome maintenance, Peter Becker will talk about how cooperation, competition and combination contribute to the targeting of the X chromosome and its regulation, Giacomo Cavalli and Allistair Boettiger about the 3D genome folding, Rick Young on Nuclear condensates, Tom Muir on chemical approaches and a Keynote by Wolf Reik on ways to exploit multiple single cell omics to unravel early embryo development.

Interested in this conference? Register by 19 April.

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Meet the EMBL Events Team: Raili Pall

In the middle of 2020, Raili Pall joined the Course and Conference Office (CCO) team. She was the first member to start working with us remotely and it was quite a journey to get everything in place. Despite all this, she was a total hero, learned everything so quickly and started talking the CCO “language” (yeah, we kind of talk in codes for our events) within a few weeks!

Check out her interview to the end, you might want to read her favourite book🙂.

Railli Pall PHOTO: Railli Pall

At EMBL since: June 2020
Number of organised conferences/courses: 4

Favourite place in Heidelberg: 
Altstadt (Old Town). I find it really cute, full of nice cafés and restaurants.

Old Town Heidelberg Marktplatz (2017). PHOTO Achim Mende/Heidelberg Marketing GmbH

First thing you do before a conference/course starts and first thing you do after it finishes:
Before the conference/course starts I’ll go through my checklist to be sure I didn’t forget anything. After a conference/course finishes I say a big thank you to the scientific organisers, speakers and the participants for making it all possible.

What are the challenges/differences of organising a virtual conference or course?
The most challenging is probably the social aspect – working out how to increase the audience interaction and keep them engaged during the virtual event.

What do you miss most about life before the pandemic?
Travelling. I love travelling and discovering new cultures, food and people. I can’t wait to start planning some trips & travel as soon as it’s safe again.

If you weren’t an event organiser, what would you be?
I’d love to be an interior designer. I can spend hours in design shops and reading design & décor magazines. I find it incredible how simple elements can change the look and feel of a space.

If you were a superhero, what power would you like to have?
I would like my superpower to be able to speak all the languages in the world. I find languages fascinating and it would be amazing to be able to communicate with anyone in their language.

Favourite:
Recipe: I love Indian food, so I’d probably choose butter chicken. I recently learned how to cook it myself and am very proud of it😊 .

Book: „On nagu pole“ (“It is like it isn’t”) by Estonian author Alan Adojaan. I read it quite long time ago, but it’s one of the most funny and inspiring travel-books I’ve ever read.

Film: I love to watch movies, so it’s difficult to choose one. I like Paolo Sorrentino (‘La Grande Bellezza’, ‘Youth’, ‘Loro’) and Quentin Tarantino movies. One of the recent highlights was ‘Parasite’ by Bong Joon-ho that I finally managed to watch.

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