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DNA Topology Lab

@dnatopologylab.bsky.social
473 followers 216 following 18 posts

DNA Topology Lab @ Department of Biochemistry University of Oxford "We adore chaos because we love to produce order." -M. C. Escher

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DNA Topology Lab @dnatopologylab.bsky.social · 27/03/2026
Great science to be discussed in a fabulous location! Apply!
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Rob Klose @robklose.bsky.social · 13/03/2026
We are excited to be recruiting into 3 Associate Professorship's in @oxfordbiochemistry.bsky.social. Come join us as a colleague and benefit from our vibrant and multidisciplinary environment. Reach out to me if you have any questions. Please repost! (tinyurl.com/48deybuu) (tinyurl.com/4pdvjaft).
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Adele Marston @marstonlab.bsky.social · 03/03/2026
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
rdcu.be
How can fast-evolving DNA retain a fundamental function in cell division? | Nature
In a dividing cell, chromosome pairs are pulled apart thanks to attachment sites called centromeres. Yeast genomes reveal key steps in how centromeres have evolved. In a dividing cell, chromosome pairs are pulled apart thanks to attachment sites called centromeres. Yeast genomes reveal key steps in how centromeres have evolved.
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Bungo Akiyoshi @bungoakiyoshi.bsky.social · 22/12/2025
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...
link.springer.com
40 years of CENP-A: the foundation of a new era of centromere biology - Chromosome Research
Chromosome Research -
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Stephan Gruber @gruberlab.bsky.social · 06/11/2025
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...
cell.com
Weaving the loops of life: DNA loading by loop-extrusion machines in plasmid defense and genome organization
Structural maintenance of chromosome (SMC) complexes organize and segregate DNA via loop extrusion, but the mechanism of the initial DNA loading was unclear. In this issue of Molecular Cell, Roisné-Ha...
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DNA Topology Lab @dnatopologylab.bsky.social · 10/10/2025
As always, bacteria light the path of discovery.
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Stephan Gruber @gruberlab.bsky.social · 09/10/2025
For the specialists: the motor units adopt a DNA-holding conformation, a proposed key state of the segment capture model
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Oxford Biochemistry @oxfordbiochemistry.bsky.social · 23/07/2025
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
bit.ly
£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)
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Rebecca Berrens @rberrens.bsky.social · 16/07/2025
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...
doi.org
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...
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DNA Topology Lab @dnatopologylab.bsky.social · 16/07/2025
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
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DNA Topology Lab @dnatopologylab.bsky.social · 16/07/2025
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.
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DNA Topology Lab @dnatopologylab.bsky.social · 01/07/2025
Many congratulations Matt!
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Matt Higgins @parasitematt.bsky.social · 01/07/2025
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!
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DNA Topology Lab @dnatopologylab.bsky.social · 07/05/2025
Is that sarcasm?
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Rhianna Pratchett @rhi.bsky.social · 28/04/2025
Happy birthday, Dad. Time to come back now, it’s all gone a bit rubbish without you. ❤️❤️❤️
Sir Terry Pratchett and his daughter, Rhianna, at the launch of Dodger.
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Deegan Lab @deeganlab.bsky.social · 15/04/2025
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...
biochemistry.org
UK DNA Replication Meeting 2026
Research in the DNA replication field is progressing at a remarkable rate. Technological innovations in biochemical reconstitution, structural biology, proteomics and DNA sequencing are helping to rap...
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Lars Jansen Lab @jansenlab.bsky.social · 04/04/2025
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.
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Anja Groth @groth-anja.bsky.social · 28/03/2025
A few days left to apply for exciting PhD and Postdoc opportunities in wonderful Copenhagen and join our efforts in understanding Epigenetic Cell Memory.
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Florian Roisné-Hamelin @roisnehamelinf.bsky.social · 18/03/2025
Fantastic teamwork with @drhonsworth.bsky.social, @taschner.bsky.social, in the @gruberlab.bsky.social with James at @dnatopologylab.bsky.social
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Honsworth @drhonsworth.bsky.social · 18/03/2025
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!
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DNA Topology Lab @dnatopologylab.bsky.social · 18/03/2025
The lab is on 🔥 Tour de force by Hon, Florian and Taschi! Bravo! Privileged to have played a tiny part in this amazing story!
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Stephan Gruber @gruberlab.bsky.social · 16/03/2025
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.
Alt : Structure of the apo Lamassu protein complex. Schematic model of the active LmuA tetramer nuclease (top right). Lamassu icon (top left).
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Stephan Gruber @gruberlab.bsky.social · 11/03/2025
We are following up on one of these features in our next paper. Stay tuned! www.biorxiv.org/content/10.1...
biorxiv.org
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.
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Stephan Gruber @gruberlab.bsky.social · 11/03/2025
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.
Side view of the structure of a monomer of type II Wadjet.
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Hasan Yardimci @hyardimci.bsky.social · 04/03/2025
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...
crick.ac.uk
Yardimci Lab | Single-molecule visualisation of the eukaryotic replication machinery
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DNA Topology Lab @dnatopologylab.bsky.social · 04/03/2025
Fantastic opportunity to work with an amazing team in a world class setting. Apply!!
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DNA Topology Lab @dnatopologylab.bsky.social · 27/02/2025
Amazing opportunity. Peter is super cool. Apply!
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Matt Higgins @parasitematt.bsky.social · 25/02/2025
A brilliant, kind, funny colleague gone too soon. We will miss you Bela. www.merton.ox.ac.uk/news/remembe...
merton.ox.ac.uk
Remembering Professor Béla Novák 1956 - 2025
With great sadness, we announce the loss of Professor Béla Novák.
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Kurianlab @kurianlab.bsky.social · 24/02/2025
*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
academicpositions.com
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...
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Anders Sejr Hansen @andersshansen.bsky.social · 16/01/2025
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...
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DNA Topology Lab @dnatopologylab.bsky.social · 20/02/2025
Are you kidding me! I look at a massive tank of liquid nitrogen every day!
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Kazuhiro Maeshima @kazu-maeshima.bsky.social · 20/02/2025
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...
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Science News @scinews.bsky.social · 20/02/2025
🎯Breaking News Enzyme used in meiosis makes the cut in vitro News www.nature.com/articles/d41... Paper 1 doi.org/10.1038/s415... Paper 2 doi.org/10.1038/s415... Paper 3 doi.org/10.1038/s415...
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Syma Khalid @sykhalid.bsky.social · 18/02/2025
Our preprint on atomistic modelling of the Campylobacter jejuni lipidome is out!
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Oxford Biochemistry @oxfordbiochemistry.bsky.social · 12/02/2025
The Barr lab @ox.ac.uk has discovered the important role of cell division timing mechanisms in the formation of cancer. The research, funded by Cancer Research UK, provides valuable insight into how damaged cells are normally stopped from growing. ⬇️ bit.ly/202502-barr
bit.ly
Cancer beats the clock
New research unveils the important role of cell division timing mechanisms in the formation of cancer
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DNA Topology Lab @dnatopologylab.bsky.social · 11/02/2025
Thanks Syma!! I am very grateful for the excellent colleagues too!!
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Di Jiang @dijiang319.bsky.social · 08/02/2025
🧬🧪🦠🧫 @science.org www.science.org/doi/10.1126/... @rkoszul.bsky.social @leameneu.bsky.social @christophechapard.bsky.social @chromozz.bsky.social @pasteur.fr @sorbonne-universite.fr @institutcurie.bsky.social + PS www.science.org/doi/epdf/10.... @gfudenberg.bsky.social @vram142.bsky.social
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Romain Koszul @rkoszul.bsky.social · 07/02/2025
Using MNAse, ChIP, ATAC, CRAC and RNA-seq, Hi-C and imaging, we characterized the composition, activity and folding of bacterial genomes of varying sequence composition introduced as supernumerary chromosomes into budding yeast. Depending on their GC%, their fate was surprisingly different.
GC% of bacterial genomes characterized in yeast
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Romain Koszul @rkoszul.bsky.social · 07/02/2025
Our latest work: how can compartmentalization emerge in a eukaryotic genome lacking canonical heterochromatin? By investigating bacterial genomes put in yeast, we show that the presence or absence of transcription is sufficient! #chromatin #3Dgenome #generegulation www.science.org/doi/10.1126/... 👇
science.org
Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus
In eukaryotes, DNA-associated protein complexes coevolve with genomic sequences to orchestrate chromatin folding. We investigate the relationship between DNA sequence and the spontaneous loading and a...
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DNA Topology Lab @dnatopologylab.bsky.social · 07/02/2025
Why do different DNA molecules occupy different places in the nucleus? What drives chromatin compartmentalisation? Read this amazing paper to find out www.science.org/doi/10.1126/... Many congratulations to all the authors of this brilliant work! @rkoszul.bsky.social
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AlphaFold Unofficial @alphafold.bsky.social · 29/01/2025
Does anyone else agree? We do: “Bluesky is much better for science. There is much less toxicity, misinformation, and distractions,” wrote one respondent. My feed is almost entirely scientists and I actually get updates on research that is relevant and timely” www.nature.com/articles/d41...
nature.com
Bluesky’s science takeover: 70% of Nature poll respondents use platform
Roughly 6,000 readers answered our poll, with many declaring that Bluesky was nicer, kinder and less antagonistic to science than X.
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The Dunn School, Oxford @dunnschool.bsky.social · 22/01/2025
ICYMI We are recruiting a new Associate Professor in cell and molecular biology, with a preference for immunology, inflammation and/or infection - all defined broadly Come and be our colleague! Deadline 28 Feb, please spread the word! www.path.ox.ac.uk/vacancy/asso...
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Syma Khalid @sykhalid.bsky.social · 26/01/2025
Some exciting news, folks. @timcoulson.bsky.social and I have a new science podcast launching soon. Please do follow the account for updates. More details coming very soon!
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Rob Klose @robklose.bsky.social · 23/01/2025
Fabulous work from our colleagues in the Barr lab showing how the CPC binds the nucleosome! www.biorxiv.org/content/10.1...
biorxiv.org
A pivot-tether model for nucleosome recognition by the chromosomal passenger complex
Spatial restriction of Aurora B to centromeres during prometaphase and metaphase enables it to phosphorylate proteins necessary for spindle assembly checkpoint signalling and biorientation of chromoso...
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Multiscale Genome Organisation @mgo-bps.bsky.social · 24/01/2025
Friendly reminder of our webinar next Tuesday! See you all there!
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Aleksandra Galitsyna @agalicina.bsky.social · 24/01/2025
Three-dimensional organization of amoeba Dictyostelium discoideum has fascinating features! Very prominent dots at between convergent gene positions, something never really seen for other species. More about the puzzle and how the team of my PhD colleagues resolves it: doi.org/10.1093/nar/...
doi.org
Convergent pairs of highly transcribed genes restrict chromatin looping in Dictyostelium discoideum
Abstract. Dictyostelium discoideum is a unicellular slime mold, developing into a multicellular fruiting body upon starvation. Development is accompanied b
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Cees Dekker @ceesdekker.bsky.social · 23/01/2025
Radical blow to biomedical science in the US due to Trump administration decrees: www.science.org/content/arti...
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Grainger Lab @graingerlab.bsky.social · 21/01/2025
If you're interested in chromosome biology (DNA folding, gene regulation, replication, polymer modelling and more) we're organising the below this autumn. It'd be great to see you there. Please share if you can. :-)
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taschner.bsky.social @taschner.bsky.social · 23/01/2025
The plasmids described in our recent ‘4G-cloning’ paper for multi-subunit complex expression (www.life-science-alliance.org/content/8/1/...) are now available from @addgene.bsky.social (www.addgene.org/search/catal...). Thanks to Addgene for distribution in this convenient and affordable format!
life-science-alliance.org
4G cloning: rapid gene assembly for expression of multisubunit protein complexes in diverse hosts
Multisubunit protein complexes are central to many cellular processes, and studying their activities and structures in vitro requires reconstitution via recombinant expression and purification. Obtain...
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