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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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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Meet the Trainer – Pavel Baranov

Meet Pavel Baranov, Professor of Biomolecular Informatics at the University College Cork, Ireland. Pavel’s research group focuses on the understanding of how proteins are synthesised and how their synthesis is regulated.

Why did you choose to become a scientist?

When I was a toddler, I wanted to be a firefighter. Within a couple of years, I decided that being an astronaut would be more fun. A few more years passed, and I began to dream of becoming a scientist. I guess at that point I stopped growing and started living my dream.

What is your research focus?

My research group studies RNA translation. Translation is at the core of biology. Cells spend most of their energy on protein synthesis and the ribosome is the most abundant molecular machine in almost all cells. Ribosomal RNAs and tRNAs are the most conserved molecules across all kingdoms of life, and it is now apparent that proteins evolved earlier than DNA. Life as we know it relies on two main type of molecules not found outside of living systems – nucleic acids and proteins. It is the process of translation that connects these two chemistries together. I could hardly think of a more fundamental, interesting and challenging cellular process than translation.

Where do you see this field heading in the future?

As translation brings two chemistries together it is far more complex than other molecular process such as transcription and replication. Because of its complexity and the lack of tools to study it, studying translation is very challenging. The tools are now being developed, e.g. variations of ribosome profiling techniques, real-time single molecule imaging, cryo-EM microscopy, etc. The main change that I foresee is that translation will draw the attention of many more biomedical researchers, for better or worse.

What is your number one tip for people looking for scientific training?

Independent practice is the key in my opinion. After taking a course you may get the impression that you can do something, but it could be a false impression – you don’t really know if you can unless you have done it.

If you weren’t a scientist, what would you be?

Science is not a job for me, it is a dream. If I were not able to make my living as a researcher, I would have to find something else to make earnings, but I would not give up on my scientific interests.

You are organising the EMBO Practical Course ”Measuring Translational Dynamics by Ribosome Profiling” (3 – 9 May 2020). What is the greatest benefit of the course for the scientific community and what could the techniques in this course be used for in the bigger picture?

The invention of ribosome profiling is the most significant development in the field of protein synthesis since the deciphering of the ribosome 3D structure. Ribosomal profiling is a popular technique for measuring the rate of translation in addition to measuring RNA levels, but this was somewhat possible even before. The unique ability of ribosome profiling is the detection of which open reading frames are being translated in RNA. The application of ribosome profiling revealed that even in eukaryotes the same mRNA molecule is often used for making more than one polypeptide, and that our current knowledge of the human genome protein coding repertoire is still far from complete. In addition to detecting translated frames, ribosome profiling could be used to detect ribosome pauses.  We recently learned that such pauses could be used to regulate gene expression and other biological processes.  This course will provide trainees with everything what is needed for mastering this powerful technology, from hands-on experience in generating ribosome profiling data to bioinformatics analysis and the use of public data resources.

Interested in this course? Submit your application by 9 February!

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Meet the Trainer – Imre Gaspar

Meet Dr. Imre Gaspar, Senior Research Assistant in the Kikuë Tachibana Group at the Institute of Molecular Biotechnology in Vienna, Austria, which focuses on understanding how chromatin is spatially reorganised in totipotent cells.

What is your research focus and why did you choose to become a scientist?

I’m interested in the central dogma, that is how gene expression is regulated on the transcriptional and post-transcriptional levels and how these regulations allow development of an organism.

I became a scientist because I always fancied solving riddles – and as a scientist you get to work on solving the ultimate riddle that interests us, humans.

Where do you see this field heading in the future?

Right now, there is a boom of high-throughput and omics techniques in studying gene expression allowing us to create predictive quantitative models of regulatory networks, which will allow us to get mechanistic understanding of the processes underlying development, homeostasis and pathogenesis. Microscopy analysis is already essential for the latter and is also gaining importance also in the omics studies with the advent of high-throughput hybridisation techniques.

What is your number one tip for people looking for scientific training?

Being a microscopist, it was absolutely essential for my career to receive training in state-of-the-art imaging and image analysis technologies. Courses are important, of course, but I find that the best source of training a scientist can receive is core facilities, internal trainings, and of course close colleagues in the lab.

If you weren’t a scientist, what would you be?

I have a degree in medicine, so I probably would have become a medical software developer – that profession is closest to the work of a scientist and having a background in medicine would allow me to contribute to the development of medical instrumentation.

You are organising the EMBO Practical Course ”FISHing for RNAs: Classical to Single Molecule Approaches” (15 – 20 March 2020). What is the greatest benefit of the course for the scientific community and what could the techniques in this course be used for in the bigger picture?

We are at the onset of quantitative analysis in biology: many labs have already implemented corresponding work-flows, but this principle should be spread widely, especially in the fields working on the understanding of gene expression. I expect that the single molecule techniques we will cover during the course will serve as mind-changers to help people embrace the concept of quantitative biology.

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