DNA Topology Lab
@dnatopologylab.bsky.social
DNA Topology Lab @ Department of Biochemistry
University of Oxford
"We adore chaos because we love to produce order." -M. C. Escher
University of Oxford
"We adore chaos because we love to produce order." -M. C. Escher
Reposted by DNA Topology Lab
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...
"Weaving the loops of life: DNA loading by loop-extrusion machines in plasmid defense and genome organization"
Molecular Cell www.cell.com/molecular-ce...
November 6, 2025 at 6:41 PM
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...
"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
October 10, 2025 at 8:12 AM
As always, bacteria light the path of discovery.
Reposted by DNA Topology Lab
For the specialists: the motor units adopt a DNA-holding conformation, a proposed key state of the segment capture model
October 9, 2025 at 2:49 PM
For the specialists: the motor units adopt a DNA-holding conformation, a proposed key state of the segment capture model
Reposted by DNA Topology Lab
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
£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)
bit.ly
July 23, 2025 at 2:48 PM
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
Reposted by DNA Topology Lab
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...
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...
doi.org
July 16, 2025 at 4:55 PM
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...
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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!
Congratulations to #KavliOxford Professor Matt Higgins on his election to EMBO Membership for 2025! 🎉
kavli.web.ox.ac.uk/article/matt...
kavli.web.ox.ac.uk/article/matt...
Matt Higgins Elected to EMBO Membership for 2025
kavli.web.ox.ac.uk
July 1, 2025 at 5:57 PM
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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Happy birthday, Dad. Time to come back now, it’s all gone a bit rubbish without you. ❤️❤️❤️
April 28, 2025 at 10:27 AM
Happy birthday, Dad. Time to come back now, it’s all gone a bit rubbish without you. ❤️❤️❤️
Reposted by DNA Topology Lab
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...
www.biochemistry.org/events-and-t...
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...
www.biochemistry.org
April 15, 2025 at 10:30 AM
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...
www.biochemistry.org/events-and-t...
Reposted by DNA Topology Lab
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.
April 4, 2025 at 10:22 AM
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.
Reposted by DNA Topology Lab
A few days left to apply for exciting PhD and Postdoc opportunities in wonderful Copenhagen and join our efforts in understanding Epigenetic Cell Memory.
🚨𝐌𝐚𝐣𝐨𝐫 𝐉𝐨𝐛 𝐀𝐥𝐞𝐫𝐭!🚨The Groth @groth-anja.bsky.social, Mailand, Nilsson @nilssonlab.bsky.social & Krietenstein @nilskrietenstein.bsky.social labs are hiring 𝟔 𝐏𝐡𝐃&𝐩𝐨𝐬𝐭𝐝𝐨𝐜𝐬 to join the new Center for Epigenetic Cell Memory (EpiC) in Copenhagen, Denmark. Apply here: tinyurl.com/yvd93na2 & please share!
6 Postdoctoral and PhD positions in Center for Epigenetic Cell Memory (EpiC)
The Center for Epigenetic Cell Memory (EpiC) is a new Center of Excellence that will be established based on funding by the Danish National Research Foundation.
tinyurl.com
March 28, 2025 at 3:51 PM
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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Fantastic teamwork with @drhonsworth.bsky.social, @taschner.bsky.social, in the @gruberlab.bsky.social with James at @dnatopologylab.bsky.social
March 18, 2025 at 8:15 AM
Fantastic teamwork with @drhonsworth.bsky.social, @taschner.bsky.social, in the @gruberlab.bsky.social with James at @dnatopologylab.bsky.social
Reposted by DNA Topology Lab
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!
March 18, 2025 at 8:03 AM
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!
Yet another preprint from the lab—this one is personal. During my PhD, I ended up working on the cohesin SMC hinge, showing its role in sister chromatid cohesion and proposing it as a DNA entry gate in the SMC ring. But the details have remained mysterious and controversial.
March 18, 2025 at 10:37 AM
The lab is on 🔥 Tour de force by Hon, Florian and Taschi! Bravo! Privileged to have played a tiny part in this amazing story!
Reposted by DNA Topology Lab
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.
March 16, 2025 at 9:15 AM
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.
Reposted by DNA Topology Lab
We are following up on one of these features in our next paper. Stay tuned! www.biorxiv.org/content/10.1...
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.
www.biorxiv.org
March 11, 2025 at 9:22 AM
We are following up on one of these features in our next paper. Stay tuned! www.biorxiv.org/content/10.1...
Reposted by DNA Topology Lab
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.
March 11, 2025 at 9:22 AM
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.
Reposted by DNA Topology Lab
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...
www.crick.ac.uk/careers-stud...
Yardimci Lab | Single-molecule visualisation of the eukaryotic replication machinery
www.crick.ac.uk
March 4, 2025 at 11:39 AM
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...
www.crick.ac.uk/careers-stud...
Fantastic opportunity to work with an amazing team in a world class setting. Apply!!
March 4, 2025 at 6:33 PM
Fantastic opportunity to work with an amazing team in a world class setting. Apply!!
Amazing opportunity. Peter is super cool. Apply!
Postdoc or PhD working on C. elegans? Interested in applying C. elegans techniques to understand the astonishing world of epigenetics in parasitic nematodes? Apply to our Wellcome Trust funded postdoc position, joint between my lab in Oxford and Mark Viney's in Liverpool:
tinyurl.com/5y6cpvcv
tinyurl.com/5y6cpvcv
Job Specification
tinyurl.com
February 27, 2025 at 8:29 PM
Amazing opportunity. Peter is super cool. Apply!
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A brilliant, kind, funny colleague gone too soon. We will miss you Bela.
www.merton.ox.ac.uk/news/remembe...
www.merton.ox.ac.uk/news/remembe...
Remembering Professor Béla Novák 1956 - 2025
With great sadness, we announce the loss of Professor Béla Novák.
www.merton.ox.ac.uk
February 25, 2025 at 4:41 PM
A brilliant, kind, funny colleague gone too soon. We will miss you Bela.
www.merton.ox.ac.uk/news/remembe...
www.merton.ox.ac.uk/news/remembe...
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*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
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
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...
academicpositions.com
February 24, 2025 at 3:14 PM
*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
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
Reposted by DNA Topology Lab
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: are generally rare (2.3%)
www.biorxiv.org/content/10.1...
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:
www.biorxiv.org/content/10.1...
January 16, 2025 at 1:35 PM
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: are generally rare (2.3%)
www.biorxiv.org/content/10.1...
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:
www.biorxiv.org/content/10.1...
Reposted by DNA Topology Lab
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...
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...
February 20, 2025 at 11:15 AM
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...
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...
Reposted by DNA Topology Lab
🎯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...
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...
February 20, 2025 at 6:21 AM
🎯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...
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...
Reposted by DNA Topology Lab
Our preprint on atomistic modelling of the Campylobacter jejuni lipidome is out!
Atomistic modelling of lysophospholipids from the Campylobacter jejuni lipidome https://www.biorxiv.org/content/10.1101/2025.02.13.638095v1
February 18, 2025 at 6:52 PM
Our preprint on atomistic modelling of the Campylobacter jejuni lipidome is out!