New Online! Organization of replicated chromosomes by DNA loops and sister chromatid cohesion

🚨Our work on the impact of DNA replication on 3D genome is out in Genome Biology: replication-dependent loop extrusion by sister-forks, wave of replication, no evidence for large-scale replication factory. Great collab with @aurelepiazza.bsky.social. More here: link.springer.com/article/10.1...

Exciting new paper out! @allanaschooley.bsky.social and Sergey Venev led this project that let to the discovery of two chromosome folding programs: one inherited via mitotic chromosomes and one mitotic inherited through the cytoplasm! www.nature.com/articles/s41...

I'm guest-editing a collection on "Enhancer-promoter interactions" at Genome Biology. Please send us your exciting stories! link.springer.com/collections/...

It was a pleasure to write this News & Views article for the 4D Nucleome flagship article: www.nature.com/articles/d41... With great editorial support from @hollyasmith.bsky.social! Read the 4D Nucleome paper here: www.nature.com/articles/s41...

A major output of the 4D Nucleome project appeared today. This is the joint effort of many scientists working together and (publicly) sharing data and results for several years. We hope this is of interest to many genome biologists! www.nature.com/articles/s41...

Very happy to share our paper rdcu.be/eUImj out today in @natcellbio.nature.com 🎉🎉🎉 We uncover an unexpected role for endogenous Xist RNA in regulating X-linked genes that escape X-inactivation.

Happy to share that the major part of my postdoctoral work in @pablonavarrolab.bsky.social and Michel Cohen-Tannoudji’s labs is now out @natcomms.nature.com - with the precious help of Agnes Dubois (and many others). www.nature.com/articles/s41...

One review. Many journals. Less redundancy. Check out this conversation with our head Dr. Thomas Lemberger on the vision behind @reviewcommons.org and what it means for authors and journals alike @embopress.org @embo.org www.embo.org/people/revie...

Thrilled to share that my postdoc research is published today in @science.org! We found that DNA repair uses cohesin complexes to build new chromatin loops that guide the homology search and boost accurate repair! 1/n www.science.org/doi/10.1126/...

10/12 Our model: 🔹 Loop-forming cohesin sets a megabase-scale search radius within the TAD 🔹 Cohesive cohesin forms a local clamp that tethers DNA ends to the sister chromatid Together, they focus RAD51 sampling and enable accurate repair!

I am happy to share that my postdoctoral work in the @gerlichlab.bsky.social at @imbavienna.bsky.social is finally out 🎉! Our study reveals how cohesin guides focused and accurate homology search. Read more 👉 www.science.org/doi/10.1126/... Follow along for key insights and updates! 🧵

💥 We’re back with a bang! After a quiet six months, we’re excited to share our new collaboration : a podcast for @network-alba.bsky.social on navigating the postdoc-to-PI journey. 🎧 Listen to what happened here : thelonelypipette.buzzsprout.com/1356877/epis...

📣 I hereby make my Bluesky debut to announce that our work linking DNA binding affinities and kinetics 𝘪𝘯 𝘷𝘪𝘵𝘳𝘰 and 𝘪𝘯 𝘷𝘪𝘷𝘰 for the human transcription factor KLF1 just got published in Cell! @cp-cell.bsky.social www.cell.com/cell/fulltex... Key findings in a thread (1/6):

🧩 What breaks when you remove DNA loop extrusion? Gastruloids show it: not lineage decisions… but morphogenesis. That’s our contribution to www.science.org/doi/10.1126/... Huge thanks to the amazing @karissalhansen.bsky.social + @elphegenoralab.bsky.social for leading this fantastic work 🙌

Here is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀 Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function now revised and journal accepted at www.science.org/doi/10.1126/... 🧵👇

✨ Happy to share that our paper, “BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants,” is now online in Cell. Congratulations to everyone involved, a moment to celebrate! 🎉 🥂 #ErasmusMC, #Cell, #FunctionalGenomics #AI ##NonCodingDNA #Rotterdam

Last reminder: We’ll see you bright and early at 9:30 AM EST on the 25th to kick off #chromatin2025! Fantastic lineup of speakers with discussion to follow each talk. Don’t forget to register for this virtual meeting if you haven’t yet: bit.ly/chromatin-2025

Happy to share our latest preprint. We uncover a previously uncharacterised and evolutionarily conserved chromatin architecture in premeiotic gonadal germ cells, revealed through integrated cytological and high-resolution Hi-C approaches. www.biorxiv.org/content/10.1... Thread🧵🔽

📣 SAVE THE DATE Next X-inactivation meeting in Sapporo, Japan, 19-23 October 2026. Visit x-inactivation-meeting.org to join our mailing list. 🧬 speakers @dandergassen.bsky.social @marnieblewitt.bsky.social @heard65.bsky.social @crougeulle.bsky.social @sexchrlab.bsky.social @zhouqi1982.bsky.social

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...

Our latest paper has just been published in Cell! doi.org/10.1016/j.ce... We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.

Hi Genome Engineering peeps! When you genotype crude cell lysates after colony picking, which PCR enzyme/buffer composition works best for you for genotyping >1.5kb amplicons? KOD Xtreme is amazingly robust but so $$$😬 Thank you!

Happy to share our latest publication, in which we show that the arrangement of nucleosomes around CTCF sites contributes to higher-order organisation of chromatin into TADs: www.embopress.org/doi/full/10....

Here, we show that the unique regulatory landscape of ecDNA enables an ancient LINE to resurrect and act as an enhancer of Myc. This was so fun with @katerinakraft.bsky.social and @mattjones.bsky.social and others. www.nature.com/articles/s41...

Our collab w. V Goel, @nicholas-aboreden.bsky.social , J Jusuf, G Blobel, L Mirny, @irate-physicist.bsky.social out in @natsmb.nature.com www.nature.com/articles/s41... Was co-submitted with @allanaschooley.bsky.social @jobdekker.bsky.social whose paper should also come out soon Brief thread 👇

The TArgeted Cohesin Loader (TACL) paper was just published. Happy that we were able to contribute to this really exciting project! If you want to learn how targeting cohesin to defined loci in the genome affects the local chromatin environment and transcription, look no further! rdcu.be/eLiT5

Ever wondered what drives enhancer-promoter specificity? Why would an enhancer activate one gene rather than another neighboring one? Check our latest preprint, led by @mmasoura.bsky.social, to find out! www.biorxiv.org/content/10.1...

What is a promoter? And how does it work? We very happy to share our latest work trying to understand enhancer-promoter compatibility. I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters www.biorxiv.org/content/10.1...

How do SMC complexes load onto DNA to get ready for loop extrusion? @roisnehamelinf.bsky.social & co discovered that Wadjet, an SMC complex involved in bacterial DNA immunity, performs some impressive molecular gymnastics 🤸‍♂️🤸‍♂️🤸‍♂️. Check out the new paper: www.cell.com/molecular-ce...

⚠️ Paper alert: Using a novel CRISPR screening approach, we mapped the entire regulatory network controlling Xist—key for X-chromosome inactivation. 👉 We discover how sex and development signals are decoded at a single gene locus. www.nature.com/articles/s41... 👇 Bluetorial

Today I am so pleased to present our work on how chromatin remodelers affect mesoscale chromatin organization. www.science.org/doi/10.1126/...

📣 New preprint from the lab - Endogenous fluctuations of transcription factor levels shape their occupancy in unexpected ways www.biorxiv.org/content/10.1...

How do enhancers activate genes? Confused about how cohesin contributes? Physics uncovers a molecular scenario that explains the biological data across labs Truly exciting findings from @lucagiorgetti.bsky.social 💪

Really excited to share our latest work led by @mattiaubertini.bsky.social and @nesslfy.bsky.social: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication. www.biorxiv.org/content/10.1... A🧵👇

Really enjoyed reading the new @lucagiorgetti.bsky.social lab preprint that makes the case that not all E-P interactions are created equal - it is the subset of long-lived extrusion-mediated E-P interactions that are most transcriptionally important: www.biorxiv.org/content/10.1...

Excited to share our first preprint! We developed an image-based pooled screen to uncover regulators of HP1 condensates and discovered a link with intronic RNA and RNA processing. 👏 Congrats to all authors, especially Matthew, Shaopu & Chris!

Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up! www.biorxiv.org/content/10.1... A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)

✨Exciting news: the main story of my PhD is out in Science! Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation. 📖 Read the full story here: www.science.org/doi/10.1126/...

Excited to share another new preprint from our lab in which we developed a cluster-based phasing strategy using long read nano-NOMe-seq data to link distinct CTCF binding states—captured at the single molecule level—to the transcriptional status of genes: biorxiv.org/content/10.1...

We’re back! Registration is NOW OPEN for the 6th Annual Meeting on Advances in Nuclear Topology & 3D Chromatin Architecture in Cancer. Don’t miss insights from leading experts in the field. Join us online on Nov 25, 2025—register for free: bit.ly/chromatin-2025 #chromatin2025

Excited to share our preprint w/Gordana Wutz, Iain Davidson, Leonid Mirny, Jan-Michael Peters www.biorxiv.org/content/10.1... Evidence that PDS5A/B limits NIPBL-cohesin life w/effects on CTCF boundaries & chrm compartments, +mechanisms of compartment-extrusion interplay & cohesin regulation by PDS5

Excitingly, the lab of Jan-Michael Peters just reported largely concordant findings: The PDS5:NIPBL balance in cells tunes the rate/velocity of cohesin loop extrusion, shaping chromosomes from loops to compartments 🚅➰ www.biorxiv.org/content/10.1...

In Brief: A new center in San Francisco will offer tailor-made CRISPR therapies to cure children with rare diseases www.nature.com/articles/s41...

Histone Acetylation Differentially Modulates CTCF-CTCF Loops and Intra-TAD Interactions https://www.biorxiv.org/content/10.1101/2025.07.29.667515v1

We all know that cancers -even from the same subtype- are highly heterogeneous right? In a new study we asked whether this was also the case for the three-dimensional organization of the genome in breast cancer. The answer: it’s complicated. www.cell.com/iscience/ful...

New preprint with @gfudenberg.bsky.social We find the rate of cohesin loop extrusion in cells is set by NIPBL dosage and tunes many aspects of chromosome folding. This provides a molecular basis for NIPBL haploinsufficiency in humans. 🧵👇 www.biorxiv.org/content/10.1...

Another paper bluetorial! Today: how does the spatial location of genes influence their function? (1/n) www.nature.com/articles/s41...

The basic sciences are HIRING at UCSF: open recruitment in the Department of Biochemistry & Biophysics. Please share and please apply! aprecruit.ucsf.edu/JPF05702

🚨New preprint from the lab🚨 🧬 What keeps certain chromatin domains anchored at the nuclear periphery? Our new genome-wide HiDRO screen uncovers a key role for RNA-binding protein hnRNPK. www.biorxiv.org/content/10.1...