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

In this #Primer, a variety of #enzyme-tethering techniques, such as DamID, ChIC, CUT&RUN, CUT&Tag, and RT&Tag are highlighted, emphasizing their suitability for single-cell and spatial applications in biological research. 🪢🧬 www.nature.com/articles/s43...

Enzyme tethering for in situ epigenomics - Nature Reviews Methods Primers

Enzyme-tethering epigenomic methods modify DNA while cells and nuclei remain intact, making them particularly suitable for single-cell and spatial applications. In this Primer, Kami Ahmad et al. discu...

nature.com

New paper! How do RNAs "know" where to go inside a cell? We dug into the sequence elements that route RNAs to the right place. It turns out that, in mammals, they're surprisingly massive (>200 nt), multipartite, and wonderfully complicated. 🧵

New from the lab: cfDNA provides an unexpected window into telomere chromatin state and genome-wide chromatin changes that accompany telomere shortening, from a blood draw. We hope this opens a path toward monitoring telomere biology disorders with a blood test. www.biorxiv.org/content/10.6...

Come join us for a great week of science in Dublin this summer! @brianstrahl.bsky.social @vanrechemlab.bsky.social @bonalditiziana.bsky.social @garcialabms.bsky.social @metorrespadilla.bsky.social

We've got two exciting chromatin talks coming up on Wednesday next week: @epijenatics.bsky.social from @jbuenrostro.bsky.social's lab and @ambystoma22.bsky.social! register and join us: us06web.zoom.us/webinar/regi...

The registration deadline for this wonderful meeting is approaching! Be sure to reserve your spot before March 10!

Matthew Taliaferro@jmtali.bsky.social · 8mo ago

Announcing the 2026 edition of the EMBO workshop on RNA localization and local translation! This meeting will be held June 30 - July 4 near Porto, Portugal. Come for exciting updates in the field from both established investigators and trainees. See the link below for details!

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...

Unique territorial and compartmental organization of chromosomes in the holocentric silkworm - The EMBO Journal

Hallmarks of multicellular eukaryotic genome organization are chromosome territories, compartments, and loop-extrusion-mediated structures, including TADs. However, these have mainly been observed in ...

link.springer.com

Updates after feedback, so now’s the time to advertise! Our work with the late, great Charles Kirkpatrick, a force in Clin. Immunology for 60 yrs. We found that B cell immunodeficient patients of his had a hypomorphic variant in EZH2 caused by a defect in allostery. www.biorxiv.org/content/10.6...

As usual this time of year, started drafting the list of gene regulation conferences for 2026, enjoy! generegulation.org/conferences-... Know of a relevant event that’s missing? Please reply below

This went under the radar but answers a fundamental question in Epigenetics... From many hundreds of olfactory receptor genes, each neuron selects expression of only single one (near-randomly). How? Outstanding work from Mathieu Boulard and colleagues www.biorxiv.org/content/10.6...

The transcription of a single olfactory receptor per neuron is enforced by epigenetic silencing of their enhancers

The ability to discriminate thousands of odors in our environment requires each olfactory neuron to express a single olfactory receptor from hundreds of available genes. The biochemical mechanism enfo...

biorxiv.org

Our Perspective article on Computational Strategies for Cross-Species Knowledge Transfer is now published in @natmethods.nature.com! This was a collab b/w @krishnanlab.bsky.social & @fishevodevogeno.bsky.social, led by the amazing Hao Yuan @yhbioinfo.bsky.social. 🧵 www.nature.com/articles/s41...

Glad to share our latest work that came out recently. We dive into the mechanisms of how Transcription Factors (TFs) like the nuclear receptor, ERα navigate the genome to find their targets.

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

Alex Stark@alex-stark.bsky.social · 7mo ago

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)

Excited for this work by Michael Cortazar, an @JagannathanLab Postdoc, to be out as a preprint. So much hard work went into it, but it was well worth it 🤓

bioRxiv Genomics@biorxiv-genomic.bsky.social · 8mo ago

Genomic stop codon scanning reveals quantitative principles of nonsense-mediated mRNA decay https://www.biorxiv.org/content/10.64898/2025.12.20.695734v1

A thread on our latest paper from the Whitehouse lab

Axel Delamarre@axeldelamarre.bsky.social · 8mo ago

Hi all! We developed CAD-C to map chromatin organization at high res in yeast. It revealed an unexpected tight alignment: nucleosomes covering the same sequence tend to be associated across sister chromatids. www.biorxiv.org/content/10.6... #3DGenome #chromatin #Cohesin #centromere

@pravrutharaman.bsky.social got super intrigued about EZHIP/CATACOMB, previously identified as a histone H3K27M mimic of PRC2. You can read about her efforts here: www.biorxiv.org/content/10.6... We hope these analyses will help spur more analyses in this very cool gene! 1/

Dynamic evolution of EZHIP, an inhibitor of the Polycomb Repressive Complex 2 in mammals

The Polycomb Repressive Complex 2 (PRC2) is an ancient, conserved chromatin-interacting complex that controls gene expression, facilitating differentiation and cellular identity during development. It...

biorxiv.org

Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...

Known for decades: DNA sequence drives nucleosome "rotational positioning" (which face of DNA contacts histones) But: How does this persist when remodelers & transcription constantly mobilize nucleosomes? Our new preprint 1/ : www.biorxiv.org/content/10.6...

Calling all archaeal enthusiasts! 🔬🔥 From molecular machines to microbial communities, Archaea never fail to surprise us! We are excited to announce the 2026 EMBO Workshop on the Molecular Biology of Archaea, 6–10 July in Cambridge, UK! Sign up here: meetings.embo.org/event/26-arc... #ArchaeaSky

New online: Evolution of promoter-proximal pausing enabled a new layer of transcription control

Evolution of promoter-proximal pausing enabled a new layer of transcription control

Nature Structural & Molecular Biology, Published online: 15 December 2025; doi:10.1038/s41594-025-01718-yHere, the authors generated and analyzed run-on sequencing data to observe transcription in species across the tree of life to uncover the origins of the promoter-proximal pause.

go.nature.com

Rotational settings quantize nucleosome movement by chromatin regulators https://www.biorxiv.org/content/10.64898/2025.12.12.693854v1

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.

bioRxivpreprint@biorxivpreprint.bsky.social · 8mo ago

CUT&ID for simultaneous profiling of protein-DNA and protein-protein interactions https://www.biorxiv.org/content/10.64898/2025.12.11.693662v1

Took us a bit, but proud of this published version. We now examine the genetic interaction of phosphorylation with oligomerization and where bulk and phospho-Swi6 localize. Wonder if chromatin affinity tuning to enable Suv39 H3K9me3 spreading is a conserved mechanism ? doi.org/10.1093/nar/...

Phosphorylation of HP1/Swi6 relieves competition with Suv39/Clr4 on nucleosomes and enables H3K9 trimethyl spreading

Abstract. Heterochromatin formation in Schizosaccharomyces pombe requires the spreading of histone 3 (H3) Lysine 9 (K9) methylation (me) from nucleation ce

doi.org

Al-Sady lab@al-sadylab.bsky.social · 2y ago

A preprint from the lab led by graduate student Dana R Kennedy. doi.org/10.1101/2024... Over 20 years ago, the Eissenberg lab showed that phosphorylation of HP1 is important for its silencing function. Why? Key observations from our study in fission yeast:

Excited to share that this work is now published in its final form! link.springer.com/article/10.1...

TDP-43 directly inhibits mRNA accumulation in neurites through modulation of mRNA stability - The EMBO Journal

The subcellular localization of many mRNAs to neuronal projections allows neurons to efficiently and rapidly react to spatially restricted external cues. However, for most of these RNAs, the mechanism...

link.springer.com

Matthew Taliaferro@jmtali.bsky.social · last yr.

Excited to share our latest work! We asked if and how TDP-43 regulates RNA transport in neurons and if this is misregulated in ALS. We found that it works to keep RNAs *out* of neurites, and that loss of TDP-43 activity results in specific RNAs aberrantly accumulating there.

Very happy with the final version of this work showing menin-MLL is a vulnerability in liver cancer and an interesting re-localization of NF-Y in response to menin inhibition. Menin-MLL1 complex cooperates with NF-Y to promote hepatocellular carcinoma survival: Cell Reports doi.org/10.1016/j.ce...

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

Histone H3 lysine 4 trimethylation (H3K4me3) at gene promoters is thought to play a central role in gene transcription. H3K4 methylation is deposited by the SET1 (A/B) and MLL (1-4) multi-protein comp...

biorxiv.org

Giovana Breda Veronezi, who also earned her PhD this year, was first author on a research article doi.org/10.1016/j.ce...

🔔This Wednesday , in #FragileNucleosome seminar, we are excited to host @ishtiaqueh.bsky.social of Pastor lab and Prof. Sarah Teichmann, @teichlab.bsky.social, to tell us about their exciting studies! 🗓️Register here for upcoming session and the entire series: us06web.zoom.us/webinar/regi...