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 a similar bad situation, where all possibilities to share exciting discoveries and network among peers in person have disappeared, no thanks to a merely 200 nm wide particle of protein. However, the good thing that came 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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Meet the EMBL Events Team: Rianne

We are very happy to welcome Rianne Moes to the Course and Conference Office marketing team! Rianne, her husband and her son just arrived to Heidelberg from Utrecht, in the Netherlands, a couple of months ago. New job, new house, new house again, taking care of a baby boy, all of this in the middle of a pandemic — you go girl!

At her previous job, she was a Communications Officer at the public library in Utrecht, with the responsibility to promote about 150 cultural events a month at the 13 library buildings scattered around the city.

Rianne Moes PHOTO: Rianne Moes

You just arrived in Heidelberg and settling down is certainly hectic. Do you already have a favourite place in Heidelberg where you go to relax?
I live near the Rohrbach area right now, and I really like the Rathausstrasse. It’s like a little village, with the town hall and some nice restaurants, bars and a bakery. It is nice to sit down on the Rorbach terrace with a drink or grab an ice cream at Illegally Tasty (they have great pasta too!).

What are the challenges of starting a new job in times of a pandemic?
First of all, I had my job interview virtually and I had never been to Heidelberg before. So, I didn’t really know what to expect. But I like a bit of an adventure!

And now, working mostly from home, it is a different vibe. Especially in the first weeks, you have so many questions that you just want to quickly ask your colleagues, instead of sending them emails or putting meetings in their calendar. But luckily, I get to go to the office quite a lot and have now also met most of my colleagues!

If you weren’t a Marketing Officer, what would you be?
A teacher probably. Maybe I will become a teacher one day, who knows! It has some similarities to marketing, because you really need to be able to place yourself into someone else’s shoes (or head, actually) and see their view on things. Also, I believe in simple, straightforward and appealing content, and explaining things to students should also be simple, straightforward and appealing.

If you were a superhero what power would you like to have?
The ability to read minds. I would love to know what everyone is thinking.

What’s your favourite:
Recipe: Melanzane alla parmigiana, that’s an Italian dish with fried eggplant, tomatoes and lots of mozzarella and parmesan cheese. Wouldn’t mind eating this every day.

Book: I actually worked in a library (as a marketing officer though), so I should be able to answer this. Maybe I should promote the first Dutch writer that (just) won the Booker prize: Marieke Lucas Rijneveld (1991) with their (Marieke identifies as both male and female) book the Discomfort of Evening.

TV Series: The Wire. I think everyone should watch this. And really, keep watching, it took me a few episodes to get into the slang and the story, but this is really the best series I have ever watched.

 

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Ada Lovelace Day 2020 – The women of computational biology today

Ada Lovelace. Source: Suw Charman-Anderson on Flickr
Ada Lovelace as depicted by Suw Charman-Anderson on Flickr

Ada Lovelace is often regarded as the first to recognise the full potential of computers and as one of the first computer programmers. 

In honour of Ada Lovelace Day 2020we are shining the spotlight on some of the remarkable women that we have met during our training courses this year. 

 


Who? Hema Bye-A-Jee
Job title: Senior Scientific Database Curator, EMBL-EBI
Where to find her? Hema is delivering the webinar ‘A Guide to UniProt for Students’ via the EMBL-EBI training website tomorrow (14 October 2020). It is full, but the recording will be available the next day.

PHOTO: Hema Bye-A-Jee
PHOTO: Hema Bye-A-Jee

Tell us a bit about your work, what are you researching currently? 
I am a scientific curator for the UniProt team and I primarily sift through scientific publications to annotate C.elegans proteins, but I get to find out about lots of proteins in many organisms. Engaging with scientific and non-scientific communities is a very important aspect of what we do. Not only does my role feed my scientific curiosity, but it also enables me to help others to look at their data in different ways; we prepare specialised workshops and webinars, such as the “guide to UniProt for students” which I shall be presenting tomorrow.

What does it mean to you to be a woman in STEM today?
It means a lot because I know that many struggles and injustices have been endured, and it is unsettling that battles are still ongoing in many respects. I believe that science is for everyone and earning a place at the discovery table shouldn’t be based on gender, age, race, or even who shouts the loudest. If you can see beyond what’s right in front of you and can question it, surely you should at least be deserved of an invitation to be in the same room as the table!

What are your aspirations for your career in the future? 
I am very fortunate because I get to read about something new every day. I hope to continue working at the forefront of scientific discovery and innovation and take forwards my skills in communicating complex scientific principles, and wish to help others achieve the most from their data in the intellectual property law field.


Who? Rea Antoniou-Kourounioti
Job title: Postdoc at the John Innes Centre
Where to find her? Rea was a recent speaker at the EMBL-EBI Mathematics of Life: Modelling Molecular Mechanisms virtual course. You can find her slides on our ftp site.

Rea Antoniou-Kourounioti
Rea Antoniou-Kourounioti

Tell us a bit about your work, what are you researching currently?
My work combines mathematical modelling and experimental biology to understand how temperature affects when plants decide to flower. I am currently part of the groups of Martin Howard and Caroline Dean, and our work focuses on the gene FLC, which is epigenetically silenced in response to cold. We recently discovered one of the temperature sensing mechanisms that affect this gene and compared plants adapted to different climates. We found that the levels of the gene in autumn are very important for their different responses, and we are now trying to understand the mechanism that determines these levels.

Who or what inspired you to enter a career in STEM? 
I was fortunate to grow surrounded by academia, because both my parents were at the University, my mother specialising in biology and my father in maths. Therefore, I had many role models, though the pattern of women in biology/men in maths was prevalent in my environment. However, I was very close to a woman mathematician (the first female professor of Mathematics in Greece) who would give me puzzles to solve at all the grown-up parties. Solving puzzles was my passion then, and so it remains, and there are so many unsolved puzzles in biology!

What do you hope the future of working in STEM looks like?
More focus needs to be put towards understanding the complex reasons that women leave science at all career stages such as a different perception of worth, both from the outside and the inside. Hiring and assessment procedures favour characteristics associated with men, e.g., I still remember the lack of confidence I have had to battle to make my voice heard in meetings. This is deeply rooted in the differently promoted values for boys and girls and needs to be battled there and in its consequences. Events such as the Nobel prize recognising women this year helps girls to see that science is (also) for women and gives them inspiring role models like I was lucky to have.


Who? Zuzana Jandova
Job title: Postdoc at Utrecht University
Where to find her? Zuzana is a speaker at the upcoming BioExcel Winter School on Biomolecular Simulations event. Applications are currently open.

PHOTO: Zuzanna Jandova
PHOTO: Zuzanna Jandova

Tell us about your work, what are you working on right now?
As a part of the HADDOCK team at the Utrecht University, I focus on dissemination and training of our software as well as my own research. In training, we prepare tutorials, organise workshops and summer/winter schools, answer questions on public forums and make software easier and more approachable to users. In my own research, I look at how the combination of a traditional docking approach with molecular dynamics simulations and machine learning can improve the prediction of protein-protein interactions. This is then applied in areas like antibody design, where we can engineer antibodies in pharmaceutical research.

What are your aspirations for your career in the future?
I would like to stay in the biomedical field, where I also started when I decided to study pharmacy. Working in research, more specifically academia gave me a lot such as critical thinking, data management and project planning which I would like to take further into a more applied area. Thus, working in a pharmaceutical company or research institute where I could focus on not only the first theoretical stages of drug development but also on the further use of the drugs and biologics on the market would be a good option for me.

What does it mean to you to be a woman in STEM today?
To be honest I have never thought about my gender as a key element for my career choice. However, I realise that women are still somewhat underrepresented in computer or technical sciences in general. This is also why I think it is important that we talk more about women in science which can be a great example and inspiration for younger generations. And the more recognition we get, the more it becomes a norm to take women as an equal, respectable and knowledgeable part of the society. 


Name: Alessandra Villa
Job title: Senior Researcher at KTH Royal Institute of Technology
Where to find her? Alessandra is a speaker at the upcoming BioExcel Winter School on Biomolecular Simulations event. Applications are currently open.

PHOTO: Alessandra Villa
PHOTO: Alessandra Villa

Tell us about your work, what are you working on right now?
I was educated as a chemist. Early in my career, I realised that I was very interested in solving biophysical problems, thus I decided to do it using molecular modelling and computer simulation. My work focuses on improving molecular models to better describe how macromolecules interact. This can deepen our understanding of their function. Higher-education teaching has also played a key role in my career. Currently, I am working at the European Center of Excellence BioExcel, applying my expertise to promote and improve the use of advanced scientific tools.

What are your aspirations for your career in the future?
My aspiration is to contribute to building a lively environment that combines high-level teaching and research and to move to a coordination role with more decision power.  

What does it mean to you to be a woman in STEM today?
To be a scientist in STEM means to be able to understand, to contribute, to deepen our knowledge and to teach/disseminate on how nature (in my case molecules) function. In addition, it also means to be able to critically evaluate any new information and to be curious about things in general.  To be a woman in STEM is to be a scientist in STEM.

In the later stage of my career, I have realised that as a woman in STEM I always had to really demonstrate what I know. I was evaluated for what I did and not for what I could do, and further steps in my career may be full of “unpredictable” obstacles.


Name: Molly Gasperini
Job title: PhD Scientist, Octant
Where to find her? Molly was a speaker at a recent EMBL-EBI Industry Programme virtual workshop: High Throughput of Assessment of Functional Human Mutations. EMBL-EBI Industry programme members can download the slides from the members area.

PHOTO: Molly Gasperini
PHOTO: Molly Gasperini

Tell us a bit about your work, what are you researching currently?
I am developing high throughput functional assays to screen drugs against neuropsychiatric receptors at a scale and speed never before achieved. Find out more.

What does it mean to you to be a woman in STEM today?
I am extremely fortunate to be a part of science at a time where women generations before me (like Ada) have broken down many previous gender-based barriers. Though improvement is still required, most parts of science are largely welcoming for female scientists. Now, it is our responsibility to break down existing barriers for scientists who don’t identify with the racial, sexual-identity, or economic majority of the scientific community.

What are your aspirations for your career in the future?
I have always struggled with whether to climb the traditional ladder of leadership, though such job advancement takes you further from the bench and Rstudio, and into more meetings! Fundamentally, I hope to always continue working on thrilling tech dev as part of a rigorous and fun team.


Follow #ALD20 on Twitter to celebrate even more women, advocates and educators in STEM.


Authors

PHOTO: Michelle Mendonca
PHOTO: Michelle Mendonca

PHOTO: Rebecca Nicholl
PHOTO: Rebecca Nicholl

PHOTO: Emily Pomeroy
PHOTO: Emily Pomeroy
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EMBL’s Corporate Partnership Programme celebrates 10 years of impact

As EMBL’s Advanced Training Centre passes its 10th anniversary, Corporate Partnership Manager Jonathan Rothblatt reflects on the ATC Corporate Partnership Programme and how it promotes training for outstanding scientists.

Jonathan Rothblatt, Corporate Partnership Manager at EMBL. PHOTO: Jonathan Rothblatt

Since its opening in March 2010, the EMBL Advanced Training Centre (ATC) has served as a forum for the scientific exchange of new ideas, data, approaches and tools. An important component of this is the ATC Corporate Partnership Programme (CPP), which aims to connect companies with the latest developments in molecular biology and build successful long-term relationships between EMBL and corporate partners.

EMBL Advanced Training Centre built in 2010. PHOTO: KARL HUBER FOTODESIGN

Supporting outstanding scientists

The support that industry partners provide through their membership in the CPP, ensures that outstanding scientists – from PhD students to established investigators – are not excluded from attending a course or conference, or working in an EMBL laboratory as a visiting scientist, because of a lack of funds to cover conference fees or travel expenses. Since 2010, CPP funding has provided fellowships covering registration fees and travel costs to more than 2,100 participants from over 90 countries, attending more than 350 EMBL or EMBO courses, conferences, or symposia.

In addition to the significant impact of their financial support, the engagement and collaboration of corporate partners is crucial in the development and delivery of EMBL’s courses and conferences. For example, of the 33 training courses held at EMBL Heidelberg in 2019, 11 were co-organised with CPP partners. Another example is the EMBL Conference ‘Expanding the Druggable Proteome with Chemical Biology’, which took place in February 2020. This conference, co-funded by the CPP, explored advances at the interface between academic and industry research. The scientific organisers included two CPP partners alongside academic leaders in the field (read the interview with one of the organisers Gerard Drewes here and check out the winning posters here).

Building mutually beneficial relationships

The strong involvement of EMBL scientists at all levels is another crucial factor in enabling the CPP to establish and develop mutually beneficial relationships with its corporate partners. The alliance of the CPP with its corporate partners is one facet of EMBL’s engagement with industry – in particular the life sciences business sector. This compliments the activities of EMBL’s technology transfer partner EMBLEM, the EMBL Course and Conference Office, the EMBL-EBI Industry Programme, and direct interactions with industry partners by EMBL group and team leaders and heads of core facilities.

With two new partners joining the CPP in 2019 and another already this year, the CPP has grown to 19 members, bringing together EMBL and global leaders in a range of business sectors, including biopharmaceuticals, diagnostics, information technology, research and clinical instrumentation, and laboratory products.

Members of the EMBL ATC Corporate Partnership Programme

We look forward to seeing the programme continue to evolve and grow in future years, always striving to deliver outstanding value and maintain its impact on the future of science.

For further information, contact Jonathan Rothblatt (jonathan.rothblatt@embl.de, +49 6221 387 8799), or visit embl.org/cpp.

This article was originally published in Issue 95 of EMBLetc. magazine.

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