Loss of SUMOylation drives aberrant PRC1 clustering and 3D genome rewiring independent of H3K27me3 https://www.biorxiv.org/content/10.64898/2026.02.05.704038v1

Now published in @science.org www.science.org/doi/10.1126/...

New preprint from the lab! We identify the ZnF protein Mulberry as a condensation-dependent structural regulator of genome topology that organizes “multi-way regulatory hubs” in early Drosophila embryos. www.biorxiv.org/content/10.6...

Nature research paper: Regulatory grammar in human promoters uncovered by MPRA-based deep learning go.nature.com/3ZQcb6Q

H3K79me2/3 is sufficient to antagonise PRC1 www.nature.com/articles/s41...

BRD4 represses developmental and neuronal genes through interactions with polycomb complexes https://www.biorxiv.org/content/10.64898/2026.01.31.702994v1

The role of cohesin loading at enhancers in the flux of loop extrusion and long-range transcriptional control https://www.biorxiv.org/content/10.64898/2026.01.20.700462v1

🔔 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)

ICYMI: New Online! PIONEARing how DNA sequence composition tunes TF–nucleosome interactions

New online: Interplay between cohesin and RNA polymerase II in regulating chromatin interactions and gene transcription

Our work on #RegulatoryTrajectories is out today in Nat. Comms: www.nature.com/articles/s41... Led by @raquelrouco.bsky.social, this study establishes a new framework to study how enhancer landscapes act sequentially at developmental loci and are silenced to shape gene expression patterns. (1/n)

Did you ever wonder how gene expression, once activated, it's maintained for a precise period of time before being decommissioned? Happy to present the final version of our manuscript on the discovery of regulatory trajectories, just published in Nat. Comms: www.nature.com/articles/s41... 1/14

Online Now: Chromatin folding principles underlying the generation of antibody diversity Online now:

New online: A negative feedback mechanism controls histone gene expression

New online: Cell-cycle-dependent repression of histone gene transcription by histone H4

🧬 @science.org A SWI/SNF-specific Ig-like domain, SWIFT, is a transcription factor binding platform | Science www.science.org/doi/10.1126/... @ckadoch.bsky.social @danafarber.bsky.social @harvardmed.bsky.social @broadinstitute.org @hhmi-science.bsky.social 🔬 #chromatin #transcription #cancer 🧫

Very proud of this collaboration with Elly Tanaka and Elad Bassat. Jorge Peña @jpenap.bsky.social from our lab skillfully conducted our contributions. @regen-hearts.bsky.social #HeartRegeneration

Our preprint "Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo" is on bioRxiv: www.biorxiv.org/content/10.6... . Amazing collaboration by @shenzhichen1999.bsky.social, Vincent Loubiere (@impvienna.bsky.social,@viennabiocenter.bsky.social),... (1/2)

Not that long ago, in vivo mouse enhancer design was a dream. Today, it's a reality! Using transfer deep learning to design de novo synthetic embryonic enhancers active in the heart, limb, and CNS. Great collab with @alex-stark.bsky.social lab! @ucibiosci.bsky.social @impvienna.bsky.social

Improved short nascent strand sequencing (iSNS-seq) enhances DNA replication origin detection and reduces non-origin biases https://www.biorxiv.org/content/10.64898/2025.12.22.696044v1

This is now a published peer-reviewed paper, in which we show, for the first time (to my knowledge) an interaction and co-operation between SALL4 and BAF (SWI/SNF). Together, they induce neural crest fate early on, by priming thousands of enhancers in the neuroectoderm. doi.org/10.1242/dev....

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...

Why it's silenced to allow broad K27me3 patterns in naive ESCs is still a mystery to me, but it's clearly more important in the germline than in this context. Paper here if you're interested! (fig 2 and ext 4) (2/2) www.nature.com/articles/s41...

Can one map the genome-wide binding (1) and its protein partners (2) simultaneously from the same sample? Yes, one can. with CUT&ID ✂️🪪 Spearheaded — singlehandedly — by @annanordin.bsky.social No need of transgenesis, cloning and overexpression. Check it out, it's fast and its works.

Excited to share our new preprint from the Klose lab, where we investigate how SET1/MLL complexes shape H3K4me3 and regulate transcription in mouse ES cells. www.biorxiv.org/content/10.6...

An early Christmas present for those interested in chromatin and transcription! Fantastic work from @au-ho-yu.bsky.social and @aleksszczurek.bsky.social . Thanks to Inge and Michiel for their help. Please repost! www.biorxiv.org/content/10.6...

SET1/MLL complexes control transcription independently of H3K4me3 https://www.biorxiv.org/content/10.64898/2025.12.08.692985v1

Excited to see the latest from the Klose lab out this morning! Our brilliant PhD student Alan, now Dr Au, has dissected how SET1/MLL complexes shape H3K4me3 and shows they regulate transcription independently of their cat activity. He teamed up with Aleks to explore how. A few surprises!

Sign up now for EMBO Workshop "#LimbDevelopment and #regeneration: Quantitative, ecological and diversification studies" in #Tokyo, JP, 23–27 March 2026. Registration by 23 Jan 2026 Abstract submission by 15 Dec 2025 https://meetings.embo.org/event/26-limb-dev#LimbDevelopment#regeneration#Tokyo#EMBOLimbDev #GeneSky #EMBOevents 🧪

Cell cycle-resolved Hi-C reveals unexpected plasticity of A/B compartments across interphase https://www.biorxiv.org/content/10.64898/2025.12.06.692720v1

Looping specificity of Polycomb response elements requires GAF and a combinatorial code of looping factors https://www.biorxiv.org/content/10.1101/2025.11.28.691166v1

Bah, who needs cohesin if you're at the right place (near). Grover once taught us the difference between near and far (my favourite Sesame Street piece), and now amazing work from @elphegenoralab.bsky.social led by @karissalhansen.bsky.social shows us how: www.science.org/doi/10.1126/...

Register now for the EMBO Workshop "Limb development and regeneration: Quantitative, ecological, and diversification studies" in #Tokyo, Japan, 23–27 March 2026. Abstract submission/Registration deadline: 12/15 December 2025 https://meetings.embo.org/event/26-limb-dev#Tokyo#EMBOLimbDev #EMBOevents 🧪

Pervasive binding of the stem cell transcription factor SALL4 shapes the chromatin landscape https://www.biorxiv.org/content/10.1101/2025.11.14.688441v1

Fabulous talk by Haruhiko Koseki today @oxfordbiochemistry.bsky.social followed by a fun dinner with Neil Brockdorff and @aleksszczurek.bsky.social ! Thanks for visiting Haruhiko!

Ultra-long-range Polycomb-coupled interactions underlie subtype identity of human cortical neurons https://www.biorxiv.org/content/10.1101/2025.11.05.686502v1

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

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...

Nascent CUT&Tag captures transcription factor binding after chromatin duplication https://www.biorxiv.org/content/10.1101/2025.10.13.682212v1

Enhancer-promoter compatibility is mediated by the promoter-proximal region https://www.biorxiv.org/content/10.1101/2025.10.14.682013v1

Derivation of embryonic stem cells across avian species - @stemcell.keck.usc.edu go.nature.com/4gLAGcZ

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🧵👇

We published a detailed protocol for our Plate-CUT&Tag method on @protocolsio.bsky.social to accompany our recent preprint (www.biorxiv.org/content/10.1...) give it a try! Feedback welcome! dx.doi.org/10.17504/protocols.io.n2bvjed5wgk5/v1

Our work exploring a new explanation for the regulation of Hoxd genes and the #fin-to-limb transition. 🧪 It was an absolute joy working on this w/ @aurhin.bsky.social and @homeobox.bsky.social @denisduboule.bsky.social @neilshubin.bsky.social #evo-devo #InHoxWeTrust

Are digits modified fins, or evolutionary innovations? Read how we tackled this old question from a new angle🧪 A story with @chasebolt.bsky.social, @homeobox.bsky.social and myself, coordinated by @denisduboule.bsky.social from @college-de-france.fr and published in @nature.com today! #InHoxWeTrust

Out today. 🙏 again to everyone for this wonderful piece of work, in particular to Aurelie @aurhin.bsky.social Chase @chasebolt.bsky.social and Brent @homeobox.bsky.social. 🙏 also to the Harris lab @fish4walking.bsky.social and @neilshubin.bsky.social @biology-unige.bsky.social @college-de-france.fr

CUT&TIME captures the history of open chromatin indeveloping neurons https://www.biorxiv.org/content/10.1101/2025.08.29.673195v1

#Preprint alert! 📣 We are thrilled to share the work led by Lara Zorro-Shahidian and Lucio di Filippo, in which we show that #MLL2 controls gene expression in both #ESC and upon #differentiation by facilitating the #enhancer like activity of #LINE1 elements www.biorxiv.org/cgi/content/...

MLL2 facilitates long-range gene regulation through LINE1 elements https://www.biorxiv.org/content/10.1101/2025.08.10.669526v1

Online Now: Single-stranded DNA-binding proteins are essential components of the architectural LDB1 protein complex Online now: