DNA Topology Lab

I had fun writing this N&Vs on two fascinating new papers on centromere evolution in yeast. If you’re interested in how centromeres adapt yet stay functional, here’s my take. rdcu.be/e6DD0 @nature.com @gautamdey.bsky.social @gsherloc.bsky.social @helsenjana.bsky.social @maxhaase.bsky.social

40 years of CENP-A: the foundation of a new era of centromere biology - Chromosome Research Chromosome Research -

Put together by Simona Giunta, @tatsuofukagawa.bsky.social, @roneilllab.bsky.social and myself. Big thanks to all the authors who contributed to this collection!
link.springer.com/article/10.1...

Very nice Preview by @bramkamplab.bsky.social on the SMC DNA loading paper by our @roisnehamelinf.bsky.social

"Weaving the loops of life: DNA loading by loop-extrusion machines in plasmid defense and genome organization"

Molecular Cell www.cell.com/molecular-ce...

As always, bacteria light the path of discovery.

For the specialists: the motor units adopt a DNA-holding conformation, a proposed key state of the segment capture model

£840,000 award from the Wolfson Foundation to enhance Oxford’s proteomics research State-of-the-art mass spectrometer to be installed at the University’s Advanced Proteomics Facility (APF)

Great news for the Advanced Proteomics Facility based here in Biochemistry @ox.ac.uk ! The Wolfson Foundation is supporting the acquisition of a state-of-the-art mass spectrometer – the first of its kind in the UK – opening up possibilities for breakthroughs in human health ⬇️ bit.ly/202507-apf

Long-read RNA sequencing of transposable elements from single cells using CELLO-seq - Nature Protocols Single-cell long-read RNA sequencing enables the high-fidelity mapping of single-cell expression data from highly sequence-similar transposable elements to unique genomic loci by correcting errors fro...

Very happy to share our protocols paper for CELLO-seq. This will make single cell long read RNA-seq more accessible and provides analysis guidelines. We hope this helps the #transposon #TEsky community and folks working on #singleCell isoform and allelic #gene expression. doi.org/10.1038/s415...

The fact that we believe it is true inside us is an extrapolation that may or may not be true. We are trying to find ways to test if chromosomal DNAs do get trapped inside Cohesin rings

Very spicy question indeed! All we can say are the following: we can detect sisterDNAs of 2.3 kb plasmids trapped inside Cohesin rings (we call them catenated diners CDs). Every mutation that we know affects cohesion of chromosomes also affects CDs. That is the limit of concrete evidence.

Many congratulations Matt!

Honoured to be elected an EMBO member. Looking forward to being part of this wonderful organisation that does so much for European science. Also thanks to Kavli Oxford for always using a picture which makes me look 20 years young. I own you guys!

Is that sarcasm?

Sir Terry Pratchett and his daughter, Rhianna, at the launch of Dodger.

Happy birthday, Dad. Time to come back now, it’s all gone a bit rubbish without you. ❤️❤️❤️

3rd edition of the fantastic UK DNA replication meeting is happening next September in Edinburgh. Don't miss out 🧬🏴󠁧󠁢󠁳󠁣󠁴󠁿

www.biochemistry.org/events-and-t...

Fresh of the press! rdcu.be/egmY0 We discovered key chromatin modifications that are heritably maintained through mitotic cell divisions in the absence of continued transcription. These hold a memory of past exposure to interferon-gamma, priming cells for future activation of gene expression.

A few days left to apply for exciting PhD and Postdoc opportunities in wonderful Copenhagen and join our efforts in understanding Epigenetic Cell Memory.

Fantastic teamwork with @drhonsworth.bsky.social, @taschner.bsky.social, in the @gruberlab.bsky.social with James at @dnatopologylab.bsky.social

Very pleased to share our new story on SMC complexes, a great team effort from @roisnehamelinf.bsky.social, @taschner.bsky.social in the GruberLab and James of @dnatopologylab.bsky.social We find that SMC hinge domains are ssDNA gates to facilitate obstacle bypass during DNA loop extrusion!

The lab is on 🔥 Tour de force by Hon, Florian and Taschi! Bravo! Privileged to have played a tiny part in this amazing story!

Alt : Structure of the apo Lamassu protein complex. Schematic model of the active LmuA tetramer nuclease (top right). Lamassu icon (top left).

Glad to share the work of @yli18smc.bsky.social and co on Lamassu, a bacterial defense system related to Rad50/Mre11 (RM). While RM carefully trims DNA ends for repair, Lamassu chops up the host chromosome. Our study reveals how it is regulated to minimize damage, activating only during infection.

Structure of a Type II SMC Wadjet Complex from Neobacillus vireti Structural Maintenance of Chromosomes proteins are essential DNA-folding motors that facilitate critical cellular functions, including chromosome segregation and DNA repair. Wadjet systems are prokaryotic SMC complexes specialized in cellular immunity against plasmids. Type I Wadjet systems restrict plasmids via a DNA extrusion-cleavage reaction. Two other Wadjet types (II and III) have also been identified, however, their molecular characteristics are unclear. Here, we reconstituted a representative type II Wadjet system from Neobacillus vireti. We show that this system shares substrate selection and cleavage properties with type I but exhibits distinctive structural features, including a long elbow-distal coiled coil, a channel-less hinge, and a tandem KITE subunit. These features help identify the common and distinguishing architectural elements in the family of Wadjet systems and raise intriguing questions about the evolution of prokaryotic SMC complexes. ### Competing Interest Statement The authors have declared no competing interest.

We are following up on one of these features in our next paper. Stay tuned! www.biorxiv.org/content/10.1...

Side view of the structure of a monomer of type II Wadjet.

Happy to share the beautiful structure of a Wadjet SMC complex by @roisnehamelinf.bsky.social, with support from the DCI and @drhonsworth.bsky.social ! This is a type II Wadjet with unique characteristics including a tandem KITE subunit, distinct coiled coil architecture and a deviant hinge.

A new PhD position is available in my lab to explore DNA replication mechanisms using single-molecule approaches. Apply by 19th of March:

www.crick.ac.uk/careers-stud...

Fantastic opportunity to work with an amazing team in a world class setting. Apply!!

Amazing opportunity. Peter is super cool. Apply!

Remembering Professor Béla Novák 1956 - 2025 With great sadness, we announce the loss of Professor Béla Novák.

A brilliant, kind, funny colleague gone too soon. We will miss you Bela.
www.merton.ox.ac.uk/news/remembe...

Professorship in genetics and molecular cell biology (W3) (f/m/d) - Academic Positions The University of Cologne is one of the oldest and largest universities in Germany. With its six Faculties covering a broad spectrum of disciplines and its i...

*Tenured full Professorship in Genetics and Molecular Cell Biology* at the University Of Cologne, Germany

It's an opportunity to rebuild the place that used to be home to luminaries including Benno Müller-Hill, Max Delbruck, Campos-Ortega, Diethard Tautz Maria Leptin, Thomas Langer

Excited to share James Jusuf's preprint:

By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%)

We quantify mESC 36k loops: <loops> are generally rare (2.3%)

www.biorxiv.org/content/10.1...

Are you kidding me! I look at a massive tank of liquid nitrogen every day!

Our new review on how the #chromatin domain is formed in the cell is now available @Curr Opin Struct Biol.📄✨
We critically discuss the domain formation mechanism from a physical perspective, including #phase-separation and #condensation.
📥 Free-download link:
authors.elsevier.com/a/1keGn,LqAr...