Best Poster Awards: Friend or Foe — Transcription and RNA Meet DNA Replication and Repair

During the second virtual EMBO | EMBL Symposium of the year three scientists were awarded a prize for their scientific poster. In this blog, we present the winners and their research.

Friend or Foe attracted 336 participants worldwide, discussing transcription and RNA and DNA replication and repair in live sessions and panel discussions. Three poster session rounds gave the opportunity for participants to view 72 digital posters and interact with the poster presenters.

After the sessions, a voting round followed and three presenters were distinguished with a best poster award by popular vote.

  1. Gianluca Sigismondo of the German Cancer Research Center in Heidelberg, Germany.
  2. Tycho Mevissen, Howard Hughes Medical Institute and Harvard Medical School, USA
  3. Sara Luzzi, Newcastle University, UK

Read our blog on how to create a prize-winning digital poster.

Chromatin dynamics during DNA repair investigated via chromatin-directed proteomics

A portrait picture of scientist Gianluca Sigismondo
Gianluca Sigismondo, German Cancer Research Center, Germany. PHOTO: Gianluca Sigismondo

Poster presenter: Gianluca Sigismondo

Authors: Gianluca Sigismondo, Lavinia Arseni, Jeroen Krijgsveld

DNA lesions predispose to genomic instability, a hallmark of cancer; therefore cells have evolved repair pathways to solve those harmful insults.

Double-strand breaks (DSBs) represent the most lethal DNA damage first marked by the phosphorylation of the histone H2A.X (γH2A.X) which triggers the recruitment of sensor proteins belonging to either the error-prone non-homologous end joining (NHEJ) or the efficient homologous recombination (HR) pathway.

It is now established that chromatin has an active role also in DNA repair, thus its characterization at DSB repair foci is essential to better understand the coordinate action of the repair mechanisms and to identify novel players participating in tumor-associated apoptotic resistance and cell survival.

Here we dissect chromatin changes upon exposure to ionizing radiations through multiple proteomics-based approaches. We applied the Selective Isolation of Chromatin-Associated Protein strategy (ChIP-SICAP; Rafiee, 2016) to investigate the interactors of core NHEJ, HR proteins and γH2A.X while bound to the DNA or in the chromatin soluble fraction.

Through a click chemistry-assisted procedure we profiled the configuration of DNA-bound proteins during DSBs repair; finally we analyzed the histone post-translational modifications (hPTMs) cross-talk at mono-nucleosomes marked by γH2A.X.

Our integrated analysis identified the dynamics of expected chromatin determinants during the DNA repair and interestingly suggested the role for new candidates specifically enriched upon DSB formation.

Validation experiments based on monitoring of DSB foci formation and resolution in AID-DIvA cells proficient or knock-down cells provided evidence of a role for novel candidates in DNA repair. FACS-based analysis of Traffic-light Reporter (TLR) isogenic cells upon silencing of proteins identified by MS characterized their functional role in NHEJ, HR or pathway choice. Furthermore, we defined hPTMs associated with γH2A.X-marked mono-nucleosomes and their dynamics during DSB resolution.

This analysis corroborated expected enrichments (e.g. H4K20me1/me2) and provided insights on new modifications specifically enriched at γH2A.X-nucleosomes.

Chromatin dynamics during DNA repair investigated via chromatin-directed proteomics

Towards transcription-coupled DNA repair in Xenopus egg extract

Poster presenter: Tycho Mevissen

A portrait of scientist Tycho Mevissen
Tycho Mevissen, Harvard Medical School, USA. PHOTO: Tycho Mevissen

This poster and abstract contain unpublished data and are not available at this moment.

Tycho Mevissen is a postdoctoral research fellow in Johannes Walter’s lab at Harvard Medical School. He had completed his PhD with David Komander at the MRC Laboratory of Molecular Biology in Cambridge, UK, where he used structural and biochemical tools to elucidate the intricate mechanisms of enzymes in the ubiquitin system, in particular deubiquitinases (DUBs).

His current research interests in the Walter lab revolve around molecular mechanisms at the intersection of DNA transcription, replication and repair.

In particular, he is interested in understanding how elongating RNA polymerase II deals with various types of obstacles – including different DNA lesions – during transcription elongation. To study this, he uses Xenopus egg extract, which is a powerful cell-free system that has been successfully used to recapitulate a wide range of cellular DNA repair pathways.


RBMX enables productive RNA processing of ultra long exons important for genome stability

A portrait picture of scientist Sara Luzzi
Sara Luzzi, Newcastle University, UK. PHOTO: Sara Luzzi

Poster presenter: Sara Luzzi

Authors: Sara Luzzi, Gerald Hysenaj, Chileleko Siachisumo, Kathleen Cheung, Matthew Gazzara, Katherine James, Caroline Dalgliesh, Mahsa Kheirollahi Chadegani, Ingrid Ehrmann, Graham R Smith, Simon J Cockell, Jennifer Munkley, Yoseph Barash, and David J Elliott.

The nuclear RNA binding protein RBMX has a direct role in genome repair and is required for expression of the tumour suppressor BRCA2. Here we report that RBMX controls RNA processing of key genes involved in genome maintenance in breast cancer cells.

Our data demonstrate that RBMX represses a premature polyadenylation site that would truncate BRCA2 protein, and is essential for full-length mRNA expression from other genes important for genome stability. These include ETAA1, which encodes for a key replication fork protein, where RBMX and its protein interaction partner Tra2ß efficiently suppress a weak splice site to enable ETAA1 protein expression.

More generally, we propose that RBMX facilitates correct inclusion of unusually long exons within mature mRNAs by repressing cryptic RNA processing. Our data provide new molecular insights explaining the role of RBMX in DNA repair and genome maintenance.

Poster RBMX enables productive RNA processing of ultra-long exons important for genome stability

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Bioinformatics for Biobusiness: make biodata work for you

This year EMBL’s European Bioinformatics Institute (EMBL-EBI) is teaming up with Medicines Discovery Catapult (MDC) on 22nd April to deliver an exciting new SME forum: Bioinformatics for Biobusiness (B4BB). This virtual event will promote the power of bioinformatics in driving success across the life science business sectors.

We’re welcoming all businesses engaged in using biodata to take a deep-dive into how to use bioinformatics to grow your business. The agenda has been developed in an open forum style, with a full line-up of expert speakers, including John Overington, Chief Informatics Officer at MDC, Jason Swedlow, Professor of Quantitative Cell Biology at the University of Dundee and Neil Hall, Joint Head of ELIXIR-UK). There is also an opportunity to book a 1:1 meeting with Marc Daigneault, Head of Research Funding at Medicines Discovery Catapult.

Meet in small groups with expert bioinformaticians, and like-minded SMEs using informatics to advance their businesses Explore software tools and services enabling access and analyses in various biomolecular domains Discover available support, and the diverse range of open biological data resources Hear updates on the latest developments in genomics, proteins, chemical biology and imaging Discover available support, and the diverse range of open biological data resources

The half day interactive forum will bring together a raft of information from EMBL-EBI’s bioinformatics resources that are made public and freely available to the global R&D community, and a chance to discover the support available from MDC and their work to reshape the medicines discovery community by championing innovative life science technology in the UK. 

There has been a fantastic response since the event opened for registration, and there are still places available. Visit the website for the full event information including the agenda, register your place and for a chance to view a series of preview videos presented by the experts showcasing resources at B4BB. 

For any other questions contact Effie Mutasa-Gottgens, Senior Scientific Officer or Lucie Smith, Event Organiser, in the EMBL-EBI Industry partnerships team.

       

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Join EMBL-EBI training at our Wednesday Webinars!

If you’re looking for bite-sized learning opportunities delivered by EMBL-EBI experts, then our regular series of webinars might be just what you are looking for!

EMBL-EBI’s Training team has been running a series of webinars since 2013, featuring speakers from across EMBL and beyond. Over the years we have covered a wide range of subjects, but its roots are in the resources and databases made available by EMBL-EBI, as well as related biological topics. So far in 2021, we’ve heard from members of Ensembl, RNAcentral, EuropePMC, UniProt and the European Genome-Phenome Archive, with many more to come.

The webinars were started as a way to enable a much wider audience to access our training and interact with our experts. They provide attendees with an introduction to a topic and resource, along with the all important opportunity to ask questions directly to our trainers. If you want to know more about how to use a resource, or perhaps how to analyse or submit data, these are the people with the answers! 

Exploring our upcoming webinar listings provides an overview of subjects to be covered. For the majority of webinars the only thing required is an interest in the topic, though some may be aimed at a more specific audience.

The Training team’s Scientific Training Coordinator, Sarah Morgan, at the first webinar of 2021, introducing EMBL-EBI’s resources and the training available.

The series is currently organised by my colleague Ajay Mishra and I. One of us is on hand at every webinar, introducing the speakers and making sure everything runs smoothly. As well as ensuring questions are answered, we also provide an opportunity for all attendees to give feedback, so if you join us, please let us know what you think. You can also tell us if there’s a topic you are keen to see covered in the future. 

 

EMBL-EBI’s webinars are currently run by Anna Swan and Ajay Mishra.

Over the years we have run a number of focused webinar series, including programmatic access of EMBL-EBI resources and data management. From April this year, we will be running a new focused series, “A guide to…”, where we will introduce some concepts in bioinformatics and how they link to some of the EMBL-EBI resources. This series is aimed particularly at students and early-career researchers, but anyone with an interest will be welcome. We will be kicking off the series with topics such as “A guide to exploring genes and genomes with Ensembl” and “A guide to RNA families”. The first webinars in the series are available for registration now, but keep an eye out for future topics in this series, including drug discovery and pathway analysis. 

If you are ever unsure about joining a webinar, you can always contact the team at webinars@ebi.ac.uk and we’ll happily answer any questions you may have. We’re also always thinking about what to include next in the programme, so let us know if there’s something you would like to see.

Finally, if there is a webinar that has taken place in the past or there’s one you cannot attend, it is not a problem! We record them all and make them available, along with the slides, in the on-demand section of our website. We always include details on how to get in touch with the trainers and their teams so you can ask the experts a question anytime. We also encourage other trainers to use our recordings and materials in their own training – check out these details on re-use of our content for further information.

We look forward to seeing you at a webinar in the future.

 


Written by 
Anna Swan.

Anna Swan – Scientific Training Officer (e-learning) – EMBL-EBI Training

Anna joined the Training Team at EMBL-EBI in March 2019 as a Scientific Training Officer (e-learning). She has a PhD in Bioinformatics from the University of Nottingham, where she focused on the bioinformatic identification of biomarkers of osteoarthritis. Following her PhD, Anna worked as a medical writer, spanning many therapeutic areas and working both on promotional and educational content for clinicians. Returning to bioinformatics, Anna worked as a data wrangler for the International Mouse Phenotyping Consortium at the project’s data coordination centre based in the Medical Research Council’s Harwell Institute.

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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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Looking back on a year of organising virtual events

Exactly one year ago, the Covid-19 pandemic hit Europe. All on-site events had to be cancelled and we had to rethink our entire program. Our Course and Conference Officers worked really hard to create a virtual equivalent of EMBL’s on-site training offering.  We successfully launched our first virtual conference and many more followed. 

The learning curve was steep and so was the stress level. But when the going gets tough, the tough get going. Two of our Conference Officers, Nathalie and Diah, share with us their experience from being in the eye of the storm, the lessons they have learned and some tips for organising a virtual meeting.

Conference Officers Nathalie and Diah
Conference Officers Nathalie (left) and Diah

How does organising a virtual event compare to organising an on-site event?

Diah: “It is a different world, but equally fun! Organising a virtual event is harder than people think and often more challenging. Not getting to see anyone in person and mastering all sorts of virtual platforms can be quite tough.”

Nathalie: “Some of the milestones we have are the same, for example: preparing the website, programme, opening registration, emails with participants and invited speakers, abstract review and selection… But a huge bulk of the work is totally different: instead of booking buses and ordering catering, we are setting up Zoom webinars and populating the virtual platform.

The massive change has been adapting to the new tasks we have to do and how we should do them consistently for all our events. In our team we have numerous working groups looking at areas of event organisation and creating guidelines, procedures and templates that will help us all. It really is a whole team effort!”

Read: Why do we charge fees for virtual events?

What kind of feedback do you get from participants, speakers and organisers?

Nathalie: “The feedback I have received from speakers and participants has been great: they are so happy we converted our event to virtual instead of cancelling/postponing it. Initially a few speakers were disappointed for the event to turn virtual but the same people commented afterwards that they were impressed with how well it went. What is wonderful is that it is still so beneficial for them in their continued research.”

Diah: “Very humbling! Many agree that onsite face-to-face events are somehow irreplaceable but at the same time they are amazed at the number of benefits virtual events offer too! They give you more flexibility: you don’t have to travel across the world. Also, some people feel more comfortable asking questions in the virtual format. ”

What is the most important lesson you have learned about organising virtual events?

Nathalie: “It’s been necessary for us to turn to virtual events but the lessons we have learned are that virtual events are effective, valuable and have many advantages! We’ve noticed that participants feel more comfortable asking questions during Q&A, that virtual talks have had a wonderful response, that virtual networking works well and you can meet different people from all over the world just at your desk!

On a bigger scale, virtual events mean less travel and a lower carbon footprint and they are more inclusive as they allow some people to participate who couldn’t have done so before. This is hugely important and is a very positive outcome of this difficult situation and it will have an impact on how events are organised in the future.”

What do you miss most about on-site events?

Diah: “The buzz when everyone arrives and the ATC is full of people is very exciting – after all the planning, everyone is there! And my favourite moment is the end of the conference: everyone is smiling and happy and you wave goodbye to the buses that leave EMBL. That sense of relief and accomplishment at the same time. I miss that!”

Nathalie: “Parties! One of the best things about the onsite events is meeting the speakers and participants you’ve been in touch with for months and when it comes to the conference party, it is really fun to see everyone let their hair down and enjoy themselves! And taking silly pictures at the Photobooth with people is something I loved and a really cute memento of the conference. That is a small thing I miss too!”

What in your opinion makes virtual events better than on-site events?

Nathalie: “The inclusiveness: more participants can take part as there is not the same financial barrier (travel, accommodation) and people can join from anywhere in the world.”

Diah: “Virtual events are resilient. There is no need to cancel an event because of the weather or a disaster. Participants can attend the event from anywhere!”

Conference Officer Diah wearing a face mask in an empty auditorium during a virtual event
Conference Officer Diah working a shift in an empty Auditorium

A common criticism is that networking doesn’t work well in the virtual world. What is your experience with virtual social events?

Nathalie: “I think it is great to see how Zoom breakout rooms allow people to mix in small groups or 1-to-1. Particularly the speed networking translates very well.”

Diah: “It’s my favorite part of the programme and I am amazed at how well it has been accepted and running so far. We have had live-streamed concerts and participants love it. At one conference some of the scientific organisers even stayed for the whole duration of the social session and wanted to continue mingling even after it had finished.”

Read our blog on virtual speednetworking.

Top tips to keep in mind while organising a virtual event?

Nathalie: “First of all – be open-minded. There are so many new technologies out there and different things you can try!

Have clear guidelines and templates: you use so many different apps and systems that saving time when setting things up can be a lifesaver!”

Diah: “I would also say: Test, test and test. Glitches are always likely to happen, so be prepared and stay calm.”

Read our blog for more tips on how to organise a virtual event

How do you see the future of EMBL Events?

Nathalie: “I hope we will embrace this new world of virtual events and have effective hybrid events in the future: allowing for face-to-face interaction for those who want to come on-site, but also giving the opportunity for those who prefer to join virtually and get the benefit of being part of the event without having to leave their home!”

Diah: “I think hybrid events will take a central place in the format of EMBL Events in the future. But whatever the format will be, we will keep improving and finding the best way to support the scientific community.”

Looking back in general, what are your thoughts?

Diah and Nathalie: “It has been very rewarding during the last year to see how we at EMBL have been able to adapt to the situation we have found ourselves in and been able to ensure that we can still provide a platform for scientific exchange. The aim of EICAT is to provide excellent training to scientists, and, despite the challenges, this is being achieved virtually for the first time! We are really proud of being able to provide opportunities for this exchange of knowledge and research.

Personally, this time has also been one of continuous learning for all of us on the team. We have developed our skills and experience in a number of ways and massively increased our knowledge of online platforms and tools! It has truly been a time of teamwork as we have adapted into the virtual event world and we are grateful to everyone involved: our marketing team, our Photolab technicians, designers and scientific organisers. It has been a challenging but very valuable learning experience!”

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