Author: apoorva

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:

https://twitter.com/luzzi_s/status/1369373077394644997

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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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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