Have you ever wondered why developmental genes are often regulated by enhancers located at long distances? In this @natgenet.nature.com perspective, we speculate that long-range enhancer positioning may provide regulatory properties essential for proper gene expression www.nature.com/articles/s41...

Mechanisms and functional implications of long-range enhancer-dependent gene regulation - Nature Genetics

Development depends on gene regulation by enhancers across long genomic distances. This Perspective discusses mechanisms enabling long-range enhancer–promoter communication and the potential advantage...

nature.com

A really cool preprint from Joanna Wysocka's lab showing that housekeeping genes use distal enhancers as dosage buffers against TF fluctuations, but only during critical cell fate transitions. Makes so much sense! www.biorxiv.org/content/10.6...

Enhancer buffering protects dosage-sensitive housekeeping genes during vulnerable developmental transitions

Housekeeping genes maintain robust expression across cell types despite dynamic transcription factor fluctuations, yet their haploinsufficiency is associated with many tissue-specific developmental di...

biorxiv.org

Thank you @natgenet.nature.com for this nice Research Briefing www.nature.com/articles/s41... on our recent paper reporting live-cell measurements of Sox2 promoter bursting kinetics when varying its genomic distance from the SCR enhancer 👉 www.nature.com/articles/s41...

The genomic position of an enhancer modulates bursting dynamics of the cognate promoter - Nature Genetics

We show that, in a genomic locus with minimal complexity, the distance between promoter and enhancer modulates the frequency of clustered transcriptional bursts. Thus, besides the nucleotide sequence,...

nature.com

Next summer's Epigenetics GRC (I'm co-chairing with Deborah Bouch'is) is shaping up nicely with an all-star lineup of speakers working on a broad range of organisms and systems and everything from molecular mechanisms to new phenomena. Apply and put it on your calendar! www.grc.org/epigenetics-...

🚨 Job Alert - Please share 🙏 Interested in 3D gene regulation in development & evolution? 🤓🧬 💥 Our lab at @cabd-upo-csic.bsky.social is expanding! ✅ 4 years fully funded PhD position 💻🧪 Experimental or computational backgrounds welcome 👇 Details below #PhDPosition #PhDOpportunity #AcademicJobs

Join us in Budapest in October! There is still time to register with an abstract. Talk and flash talk slots, a great speaker line up at an informal meeting on epigenetics, gene and genome regulation etc. in a beautiful city. shorturl.at/fOuCZ. For that to do list before the holidays!

Our latest is now out in @nataging.nature.com giving reason to celebrate! Led by talented Spiros Palikyras, it improves our preprint (posted 2 years ago!) dissecting the mechanism and functional consequences of CTCF clustering upon senescence commitment of human cells. www.nature.com/articles/s43...

Senescent cells cluster CTCF on nuclear speckles to instruct an alternative splicing program - Nature Aging

Palikyras and colleagues investigate chromatin reorganization upon senescence induction, reporting that components of nuclear speckles coordinate chromatin rewiring and a senescence-associated splicin...

nature.com

We are looking for someone to lead the new Facility for Protein Biochemistry & Biophysics at the MPI of Immunobiology and Epigenetics in Freiburg — please spread the word and apply if you are interested!

Max Planck Institute of Immunobiology and Epigenetics@mpi-ie.bsky.social · 3mo ago

🚀 Job alert: We’re starting a new Facility – and you can lead it! The MPI-IE & @mariekeoudelaar.bsky.social are hiring a Head of Protein Biochemistry & Biophysics to launch and lead a brand-new Core Facility in Freiburg 🇩🇪. Once-in-lifetime-chance. Details ⬇️ jobs.ie-freiburg.mpg.de/jobposting/b...

(1/10) The majority of human genetic variation is located in non-coding regions. The great challenge of the post-genomic era is to assign function to these variants. We reasoned that combining haplotyping with allele-specific multiomics can help pinpoint the functional ones: rdcu.be/fgr5W. A thread:

Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning

Nature Communications - How non-coding mutations in DNA contribute to phenotypes is a largely unresolved question. Here the authors integrate personal genomics and machine learning to identify...

rdcu.be

Last day to register! TriRhena Gene Regulation Club Meeting 📍 Location: MPI-IE, Freiburg 🇩🇪 📅 Date: June 29, 2026 | 2:00-18:00 PM 🆓 Participation is free of charge, advance registration is required. Register your abstracts for 20-minute research talk. www.ie-freiburg.mpg.de/gene-regulat...

(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...

bioRxiv alert! CoPhasing resolves haplotype-specific 3D chromatin structures from GAM data, revealing extensive structural heterogeneity between human homologous chromosomes and its interplay with histone modifications and gene expression! Thanks to all coauthors! www.biorxiv.org/content/10.6...

JIT 4 summer, the latest preprint from our lab, brilliantly led by @kaitezhang.bsky.social w/ support from Collepardo lab (@juliamaristany.bsky.social / @janhuemar.bsky.social). www.biorxiv.org/content/10.6... describes a new single-molecule epigenomic method, & discoveries it enables ... (1/n)

Single-molecule nucleosome spacing coordinates chromatin fiber interactions

Nucleosome spacing influences higher-order chromatin fiber organization in vitro but how this relates to cellular chromosome structure remains contentious. To address this, we developed Ligation Analy...

biorxiv.org

Excited to share our new preprint! 🧬❄️ by brilliant @mdreimann.bsky.social and great collaborators! Using cryo-ET&EM, we reveal archaeal chromatin in a near-native state: variable-beads-on-a-string fibers shaped by growth phase and histone composition #ArchaeaSky www.biorxiv.org/content/10.6...

sPYce is now published in Nature Ecology and Evolution! sPYce is a method to integrate single-cell regulatory data across species, without requiring whole-genome alignments between species. More below ⬇️ www.nature.com/articles/s41...

Did you know that stem cells have unusually large transcription clusters, which disappear upon differentiation? Yes? You paid attention in 2018! In 2026, we show you that this process proceeds via massive, global shifts in transcriptional control. advanced.onlinelibrary.wiley.com/doi/10.1002/...

New version of our preprint, led by amazing PhD students, Zoé and Stefany: disordered-like physical properties of TPR mediated by its coiled coil (!) and negatively regulated by its disordered domain (!) triggers heterochromatin exclusion and a new permeability barrier at nuclear pore basket (!)

Disorder in coiled-coils orchestrate chromatin organization and define a new permeability barrier at the nuclear pore basket

Nuclear pore complexes are the only gateway between the nucleus and cytoplasm in eukaryotic cells during interphase. Specificity of transport is ensured by a size-dependent permeability barrier, which...

biorxiv.org

Our story about the poising and connectivity of human developmental enhancers is out! www.cell.com/cell-reports...

W3 Professorship for Plant Biotechnology // University of Freiburg www.nature.com/naturecareer... The position holder will lead a research program that combines excellent basic research with clear perspectives for biotechnological and societally relevant applications. #BotanyJobs

W3 Professorship for Plant Biotechnology - Freiburg im Breisgau, Baden-Württemberg (DE) job with University of Freiburg (Uni Freiburg) | 12859402

The future position holder will lead an internationally recognized research program that combines excellent basic research with clear perspectives for

nature.com

Join is in Budapest in October! For the 6th time, all things epigenetics, gene and genome regulation and more. A fantastic opportunity to present, to talk to speakers and colleagues in a friendly, informal setting at a great location. Please note, travel grant deadline will expire soon.

⚡New preprint from the lab⚡: A key early checkpoint in gene expression is promoter proximal pausing of RNA polymerase II. For over 20 years, we as field have not been able to recreate pausing under realistic cellular conditions. @robertovn.bsky.social shows that ELOF1 is the missing piece.

Roberto Vázquez Núñez@robertovn.bsky.social · 4mo ago

🚨 New preprint: GATO-seq did it again! ELOF1 is the missing promoter-proximal factor that confers RNA Pol II resistance to TFIIF. Including ELOF1, DSIF, and NELF in GATO-seq reactions recapitulates promoter-proximal pausing in vitro at physiological conditions for the 1st time. tinyurl.com/ELOF1

Help please! We need to do some large(ish) cell culture inhibiting E-cadherin with a monoclonal antibody. Does anyone have the DECMA-1 hybridoma cell line so we could purify our own antibody? or a similar monoclonal that would do the job. Any help greatly appreciated, just DM me. Please repost!

I am very grateful and excited about this opportunity! Big thank you to our fantastic team who have made this possible and to many supportive mentors 🙏

Max Planck Institute of Immunobiology and Epigenetics@mpi-ie.bsky.social · 4mo ago

We are over the moon! 🎈 Dr. Marieke Oudelaar joins the MPI-IE as a new #MaxPlanck Director, heading the newly established Department of Genome Biology She studies how the 3D folding of DNA controls gene expression – more details below ⬇️ Welcome to #Freiburg, @mariekeoudelaar.bsky.social!

📣 Preprint alert! We developed a method to analyze concurrent interactions between multiple chromatin regions at single alleles at sub-nucleosome resolution (multi-way Micro-Capture-C, mwMCC) & used this to study structural synergy within super-enhancers. 1/14 www.biorxiv.org/content/10.6...

How do sperm and egg fuse? Surprisingly, we still don’t fully know… Our field has uncovered many pieces of the fertilization puzzle, but not how they fit together. We identify ✨ SPARK ✨ - a conserved sperm complex that couples sperm-egg binding to fusion. tinyurl.com/34cm4xat Read on! 🧵👇

Now out @natbiotech.nature.com ! Do lncRNAs commonly bind 1000s of genomic sites? Maybe they do, but the dozens of studies that report genomic binding maps of lncRNAs are deeply flawed, with probes binding suprious DNA sites rather than RNA-bound ones.

Igor Ulitsky@igorulitsky.bsky.social · 11mo ago

A preprint‼️that's bound to ruffle some 🪶 "Widespread DNA off-targeting confounds studies of RNA chromatin occupancy" led by our Micah Goldrich and Louis Delhaye from Pieter Mestdagh in Ghent. TL;DR we show that many of lncRNA chromatin occupancy obtained are flawed www.biorxiv.org/content/10.1...

Excited that Della Syau's PhD work is now available as a NAR Breakthrough article: academic.oup.com/nar/article/.... Della's work clarifies how IWS1 engages the transcription elongation complex, stimulates transcription, and controls association of other factors such as RECQL5.

Structure and function of IWS1 in transcription elongation

Abstract. Transcription elongation by RNA polymerase II is a tightly regulated process that requires coordinated interactions between transcription elongat

academic.oup.com

Our preprint on how variant U1 snRNAs control transcriptional and splicing homeostasis of hiPSCs is now officially out in @natcomms.nature.com and accessible via this link: www.nature.com/articles/s41... This has been the culmination of our work as part of the SPP1935 program funded by @dfg.de 1/n

Akis (Argyris) Papantonis @akispapantonis.bsky.social · last yr.

In our latest preprinted work, Yajie and Kostas combine computational analysis with precision KO of single variant U1 snRNA genes in human iPSCs to find pronounced deregulation of both gene expression and splicing that seem to affect the cell cycle and the differentiation potency of stem cells. 1/n

Registration open. Top-notch lineup of speakers from Europe, the US and beyond, covering chromatin biology, genome maintenance, cancer plasticity and evolution, and metabolism www.atoutcom.com/cancer-epige...

Why can't we explain enhancer action despite 2 decades of chromosome conformation technologies? 😬 Our new study spearheaded by Leonid Mirny's group points to a flaw in our assumptions, and to a solution from physical principles By @timothyfoldes.bsky.social 💻& @karissalhansen.bsky.social 🧪 🧵👇