Woolfe et al, 2026. Decoding the mystery of ultra-conservation in developmental enhancers: a role for nucleosome positioning, DNA structure and transcription factor binding www.biorxiv.org/content/10.6... ▶️conserved non-coding elements ... favor nucleosome occupancy at their borders

Excited to share the first preprint from my lab! Transcription has been implicated in regulating SMC complex function, but how this works has been unclear. Here, we use a yeast quiescence model to examine how transcription targets condensin.

bioRxivpreprint@biorxivpreprint.bsky.social · 3w ago

Asymmetric condensin loop extrusion is regulated by RPA-coated single-stranded DNA in quiescent cells https://www.biorxiv.org/content/10.64898/2026.07.10.737861v1

Chen et al 2026. Genome-wide rotational and translational phasing of nucleosomes with human transcription factors www.cell.com/molecular-ce... ▶️ In vivo nucleosome phasing measured on the same TF-bound DNA molecule ▶️ Phasing around CTCF sites is DNA encoded ▶️ FoxA and NFIA phase adjacent nucleosomes

The paper is out which means the MD trajectories are finally available! #MolecularNodes #b3d #GeometryNodes

Jan Philipp Kreysing@jpkreysing.bsky.social · last yr.

New preprint on 3D heterochromatin architecture in human cells! Great collab with @sergiocruzleon.bsky.social & @johannesbetz.bsky.social from @hummerlab.bsky.social, @marinalusic.bsky.social & the Turoňová lab. Many thanks to my supervisor @becklab.bsky.social. bioRxiv: tinyurl.com/3a74uanv 🧵👇

We recently developed ssHiC, a broadly applicable technique to study contacts made by ssDNA in cells. Here we present ssHicstuff, an open-source package to design and analyze ssHiC data. Paper: academic.oup.com/bioinformati... GUI online: tinyurl.com/sshicstuff Github: github.com/Piazzalab/ss...

Very excited to share our new Nature study! We discovered that replication stress stabilizes CTCF-dependent chromatin loops enclosing stressed nascent DNA, where G9a-mediated heterochromatin protects it from nucleolytic degradation. rdcu.be/frzLg Huge thanks to all our collaborators and co-authors!

Replication-stress-induced chromatin loops protect fork stability - Nature

Replication stress induces the formation of transient chromatin loops that enclose de novo heterochromatin-enriched stalled replication forks.

nature.com

(1/n) Very excited to share tri-lab collab (Mirny & Zechner) led by Harvey, Henrik & Jack: Q: How do enhancers & promoters interact in space (contact vs. action-at-a-distance) and time (stable vs. transient)? A: Transient E-P contact (~25-42 nm lasting ~10-20 sec): www.biorxiv.org/content/10.6...

If you have experience in biochemistry/cryo-EM, are interested in DNA replication, and would like to do a postdoc in New York - our lab has positions available! Just DM or email me with your CV.

Excited to finally share our preprint on mapping the genetic interaction network of the DNA damage response with combinatorial knockout screens led by Sam Hayward, Alina Vaitsiankova, and Tomas Lama-Diaz! www.biorxiv.org/cgi/content/...

Mapping the genetic landscape of the DNA damage response with Cas12a-based combinatorial knockout screens

The DNA damage response (DDR) is a complex network of cellular pathways that ensures the faithful maintenance of our genomes upon a wide array of genomic insults. To elucidate the functional architect...

biorxiv.org

Everything you always wanted to know about plasmid chromatinization … but were afraid to ask

Everything you always wanted to know about plasmid chromatinization … but were afraid to ask

In this issue of Molecular Cell, Mallory et al. use single-molecule DNA methyltransferase footprinting to provide an unprecedented view of the chromatin and transcriptional state of reporter plasmid molecules in human cells.

dlvr.it

link.springer.com/article/10.1... Very happy to share the early-access version of our latest paper published in CMLS. @inserm.fr @cnrsbiologie.bsky.social @lbmcinlyon.bsky.social @ensdelyon.bsky.social

MYCN and helicases DDX17 and DDX5 have opposite effects on the production of readthrough-associated chimeric transcripts - Cellular and Molecular Life Sciences

DEAD box helicases DDX17 and DDX5 control transcription termination and the associated processing of the 3' end of pre-messenger RNAs. Here, we demonstrate that the transcriptional readthrough induced...

link.springer.com

Hello all, our lab is recruiting a PhD candidate to study how 3D genome folding impacts gene regulation in development. We're located at the Center for Integrative Genomics department of the University of Lausanne, Switzerland. Please email me if interested. #PhDPosition, #PhDOpportunity

Online Now: Deciphering the dual effects of transcription on DNA replication elongation by replication-associated Micro-C Online now:

Deciphering the dual effects of transcription on DNA replication elongation by replication-associated Micro-C

Integrating replication-associated Micro-C and the reinforcement-learning-based computational framework Fun2, Zhangding et al. profile DNA-replication elongation driven by coupled replication forks at nucleosome resolution in mammalian cells and reveal that transcription has dual effects on replication elongation. Co-directional transcription facilitates fork progression, whereas head-on transcription blocks coupled forks.

dlvr.it

Happy to share our review of the past, recent, and future applications of synthetic genomics in studying the 3D functional organization of chromosomes, a set of approaches that are gaining momentum! www.sciencedirect.com/science/arti...

Synthetic chromosomes for 3D functional genomics: from principles to AI-guided design

The role of genome 3D organization for fundamental chromatin processes, such as long-range promoter-activator regulatory interactions, remains ambiguo…

sciencedirect.com

Delighted to see our work now published at the EMBO Journal! Check also this concomitant paper by the Bai and Mirny labs with an orthogonal approach that aligns well with our measurements www.nature.com/articles/s41... Great system to study how SMCs facilitate/regulate target search in chromatin!

The EMBO Journal@embojournal.org · 5mo ago

Condensin loop extrusion properties, roadblocks, and role in homology search @aurelepiazza.bsky.social et al show yeast condensin unidirectionally extrudes long chromatin loops & contributes to biasing donor selection during recombinational DNA break repair link.springer.com/article/10.1...

Excited to share my PhD work! The question: How is genome organization established? Here, we developed a low-input Micro-C method, Pico-C, and used it to map chromatin architecture across early stages of fly development. Here’s a quick Blue-torial 🙂 (1/n) www.nature.com/articles/s41...

Three-dimensional genome reorganization foreshadows zygotic genome activation in Drosophila - Nature Genetics

Pico-C, a low-input Micro-C approach, reveals that dynamic three-dimensional genome folding precedes zygotic genome activation in Drosophila.

nature.com

We just published a short conceptual review together with @angela-taddei.bsky.social on the spatial controls of homology search in both bacteria and eukaryotes. We discuss an emerging framework for homology search in cells with two main phases. Check it out: authors.elsevier.com/c/1mjyh,LqAZ...

New paper alert from the group!! 🚨: DNA flexibility tips the balance between stability and plasticity in nucleosomes One of the works from my PhD, co-led alongside @nachper.bsky.social, is finally out! Work from @rcollepardo.bsky.social & @janhuemar.bsky.social ⬇️ www.biorxiv.org/content/10.6... ⬆️

How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller? Excited to share our latest work in @science.org on a new small polymerase. 1/n

A small polymerase ribozyme that can synthesize itself and its complementary strand

The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

science.org

Interested in transcriptional regulation, enhancers and 3D genome folding? In this new study we wondered about the role of cohesin loading at enhancers for long-range transcriptional control www.biorxiv.org/content/10.6... detailed 🧵👇

Please join Andreas Ladurner and me for the GRC Chromatin Structure and Function conference to be held near Barcelona Spain from May 31-June 5! We accepting abstracts for posters and talks. The meeting is preceded by an awesome GRS. Learn more in our video below and apply www.grc.org/chromatin-st...

Come on join us! We are searching for the next technical associate to join our lab ~Summer 2026. This could be a great position for someone who is graduating this spring and is looking for 2 more years of research experience before starting their PhD: careers.peopleclick.com/careerscp/cl...

Happy to share our perspective on the DNA translocation mechanism by the CMG helicase. DNA translocation by the CMG helicase: the helical inchworm model url: portlandpress.com/biochemsoctr...

Yet another reason why butterflies and moths are so interesting! Unlike other studied organisms that organise their DNA into two forms of chromatin, silkworms have a mysterious third form of chromatin folding..

The EMBO Journal@embojournal.org · 6mo ago

How do compartmentalization & loop extrusion organize eukaryotic genomes beyond classical model organisms? Hi-C analysis of silkworm chromosomes by Drinnenberg, Muller, Mirny et al reveals new combination of these mechanisms, and a new, secluded “S” compartment link.springer.com/article/10.1...

Coming soon! PhD opening joint with @drjonbaxter.bsky.social at @gdsc-sussex.bsky.social Keep a look out and get in touch if you are interested in any and all of: Chromosomes, Genome Stability, Chromatin and DNA Topology in Mitosis and Meiosis.

a computer generated image of a dna structure

ALT: a computer generated image of a dna structure

media.tenor.com

We are hiring!

Please repost and consider applying: we work in such a fantastic context, we ask so interesting questions, and we have such a collegial and best-willing atmosphere… CRBM = Happy & Good Science

CRBM-Montpellier@crbm-montpellier.bsky.social · 6mo ago

We are hiring!

🚨 New preprint from the lab. Combining modeling and data analysis of SisterC data in yeast, we investigate cohesion of replicated chromosomes and show that sister chromatids are loosely and asymmetrically aligned in G2/M. Check the tweetorial below ⬇️ www.biorxiv.org/content/10.6...

🔔 New paper alert 🔔 www.nature.com/articles/s41... Some regions in the genome replicate early and some late, but the why and how remain poorly understood. DNA replication and 3D genome organization appear linked, raising the question if one may regulate the other? (1/n)

Excited to share my PhD work from @riscalab.bsky.social on @biorxivpreprint.bsky.social CAD-C & CADwalks –repair-free, nucleosome-resolution chromosome conformation capture with engineered TEVp-activatable CAD. CADwalks: chromosome walks of ligated CAD footprints. doi.org/10.64898/202... 1/