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

Our new study shows a CHD-family remodeler can nucleate and spread H3K9 methylation de novo, inverting the canonical hierarchy between writers and remodelers. www.biorxiv.org/content/10.6...

Nucleosome remodeling by a CHD enzyme promotes H3K9 methylation establishment and spreading via remodeler-writer feedback

In Schizosaccharomyces pombe , the conserved CHD remodeler Mit1 function within the SHREC remodeler-deacetylase complex (a homolog of the metazoan Mi-2/NuRD complex), which is essential for H3K9 methy...

biorxiv.org

Happy to share the final version of our study on the evolution of chromatin states across eukaryotes, out today in @natgenet.nature.com Led by @crisnava.bsky.social and @seanamontgomery.bsky.social www.nature.com/articles/s41... Some highlights below

Diversity and evolution of chromatin regulatory states across eukaryotes - Nature Genetics

This study introduces iChIP2, a low-input chromatin immunoprecipitation followed by sequencing method that profiles histone post-translational modifications (hPTMs) simultaneously across diverse eukar...

nature.com

Our study published today @science.org shows that X-chromosome inactivation (XCI) attracts L1 mutations to the human X chromosome: doi.org/10.1126/scie... With outstanding Perspective from @aurelien-doucet.bsky.social & @retrogenomics.bsky.social: doi.org/10.1126/scie...

RNA-seq tells us how much RNA is present in the cell. But to understand gene regulation, we need to easily measure the synthesis and decay rates driving this abundance. We introduce AIR-seq: analog intrinsic recoding sequencing. (1/6) www.biorxiv.org/content/10.6...

Analog intrinsic recoding measures RNA dynamics without chemical conversion

Steady-state RNA abundance measurements mask the synthesis and decay rates that shape gene expression. Analog intrinsic recoding sequencing (AIR-seq) repurposes the base-pairing properties of N4-hydro...

biorxiv.org

New paper in @natphys.nature.com! We uncovered a stress adapation mechanism where keratin intermediate filaments in stretched epithelia undergo a supracellular bundling transition that uncages the nucleus. www.nature.com/articles/s41... @ibecbarcelona.eu, @upc.edu @qmul.bsky.social

Facing federal science budget cuts, biologist Daniel Blumstein resorted to uploading marmot videos to OnlyFans to raise funds for his marmot research. However, when he uploaded his driver’s license for verification, OnlyFans informed him that his appearance didn’t match the marmots in the videos.

‘OnlyMarms’: Marmots Are on OnlyFans to Raise Money for Research (Gift Article)

A team of scientists uploaded videos of the squirrel-like rodents in the wild on the adult-content site OnlyFans to raise money amid government budget cuts.

nytimes.com

Excited to share our recent preprint (biorxiv.org/content/10.6...), where we show that each of HP1α's binding partners (CAF-1, LBR, and Sgo1) tunes its phase separation differently, while electrostatic interactions ultimately dominate how phosphorylated HP1α forms condensates.

The role of electrostatic interactions in the phase separation of HP1α and its protein binding partners

Heterochromatin protein 1α (HP1α) is an intrinsic component of heterochromatin domains where it is involved in a diverse set of functions including heterochromatin spreading and organization, chromati...

biorxiv.org

🚀🔬 Can cell shape, signal and movement tell us about a cell's future? #DeepLearning studies now predict cell fate from #microscopy. Together w Rita, @mariodelr.bsky.social, @inesmcunha.bsky.social, @juliettegriffie.bsky.social + @guijacquemet.bsky.social👇 www.preprints.org/manuscript/202607.1414/v1

In their Review, Alexandra Edwards and Elizabeth Finn discuss how genome organisation underlies evolution and development. journals.biologists.com/jcs/article/...

The STRAIGHT-IN (Dual) kit is now available via @addgene.bsky.social! 🧬 A complete 24-plasmid toolkit for installing up to two orthogonal CLYBL landing pads, DASIT-based enrichment without FACS, and efficient large DNA integration in human cells. Link: www.addgene.org/kits/gallowa... 🧵

Now online! Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context

Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context

Using an in situ genome-rewriting platform, Zhou et al. demonstrate that precise transcriptional regulation of the NMU promoter is governed by a 3D regulatory hub comprising a core retroviral LTR enhancer, a decoy LTR promoter, and activity-boosting “facilitator” elements.

dlvr.it

Excited to see this collaboration now in print. Dye chemistry meets AI-designed proteins. Three small, orthogonal tags; lifetime modulation; split versions. Request the free dyes at dyes.janelia.org www.science.org/doi/10.1126/...

De novo design of orthogonal far-red, orange, and green fluorophore-binding proteins for multiplexed imaging

Fluorescent proteins and small-molecule dyes offer complementary advantages for biological imaging: proteins are amenable to genetic tagging, whereas dyes provide superior brightness and photostabilit...

science.org

I'm excited to share that Corgi is out in @natcomms.nature.com! We refine context-aware sequence-to-function models by using FiLM to condition the model on trans-regulator expression levels. This way Corgi can generalize to unseen cell types. www.nature.com/articles/s41... 🧵Thread 1/n

Context-aware sequence-to-function model of human gene regulation - Nature Communications

This study introduces Corgi and Corgi+ , biology-inspired deep neural network models of regulatory DNA sequences that can generalize to unseen cell types. They accurately impute epigenomic d...

nature.com

MIT ACCESS is an opportunity for undergraduates to explore cutting-edge research and graduate education in science and engineering. See for yourself what grad life is like at MIT! Applications due Aug 1: access.mit.edu @mitcheme.bsky.social @mitchemistry.bsky.social

Big conferences are impressive. But how often do you actually meet someone there? 🤔 The Epigenetics Meeting was created differently. We have a great line-up of speakers with exciting research topics, ample time for discussion, and very familiar setting. Join us now: events.ie-freiburg.mpg.de

📣 #JobAlert The Faculty of Biology of @uni-freiburg.de invites applications for a Professorship (W3) for Bioinformatics and Molecular Genetics. ❗ Application Deadline: 15 August, 2026 🔗 kurzlinks.de/roi8 #Biology #Bioinformatics #MolecularGenetics

HHMI released the official 2027 Gilliam Fellowship details, and a lot changed. Deadline's earlier this cycle: Oct 27. Int'l & MD-PhD students now eligible. Stipend up to 50K. New postdoc pathway adds up to 7 yrs of support. No Journal names!!!! www.yaelcourtney.com/resources-an...

2027 HHMI Gilliam Fellowship: New Deadline, Eligibility, and Award Changes — Ya'el Courtney

HHMI's 2027 Gilliam Fellowship guide is out. What changed: an earlier October 27 deadline, expanded eligibility, a higher stipend, and a new postdoc pathway.

yaelcourtney.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 · last mo.

🚀 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...

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

Our latest is out in Nature Genetics with @soumyakundu.bsky.social @anshulkundaje.bsky.social and @sbmontgom.bsky.social ! We built a resource of predicted variant effects on chromatin accessibility, and FLARE to identify disease variants with extreme effects. www.nature.com/articles/s41...

Decoding common and rare noncoding variant effects across cellular and developmental contexts - Nature Genetics

This study contributes a resource of predicted effects of noncoding variants on chromatin accessibility and a method to identify noncoding variants with extreme regulatory effects, with application to...

nature.com

Since the 1960s, the genetic code has been used to predict protein sequences from DNA and mRNA sequences. Our @nature.com article demonstrates that these predictions miss thousands of protein sequences present in human tissues. www.nature.com/articles/s41... 1/

Nikolai Slavov@slavov-n.bsky.social · 2y ago

We report many proteins not predicted by the genetic code. They are stable & abundant O( 10³ ) copies / cell. Generative mechanisms include codon-anticodon mismatches & RNA modifications. Their abundance depends on codon frequency & protein stability. www.biorxiv.org/content/10.1...

If you’ve built DNA-barcoded antibody panels, you know the pain: every barcode means another conjugation. In our new preprint we introduce UnO, which transforms antibody conjugation problem into a universal barcode conversion workflow, enabling rapid panel generation. www.biorxiv.org/content/10.6...

Universal oligo adapters for high-efficiency DNA-barcoded antibody panel generation

DNA-barcoded antibodies are central to a broad range of spatial and dissociative assays and applications, including multiplexed imaging, single-cell profiling, and proximity detection. Direct modifica...

biorxiv.org

How does aging reshape a tissue that must continually rebuild itself hundreds of times? Our latest: Using spatial transcriptomics, we find that ovarian aging disrupts the coordination of cells across space and time before reproductive cycles stop. #OvarianAging

Nature Aging@nataging.nature.com · 2mo ago

Online now! Spatial atlas of aging mouse ovary shows that reproductive decline reflects progressive loss of spatiotemporal coordination #OvarianAging #WomensHealth @hattaca.bsky.social @davidsebfischer.bsky.social @akochersberger.bsky.social @jennifergarrison.bsky.social doi.org/10.1038/s435...

First pre-print from the lab, a collaborative effort led by Jess Bourn @bournsupremacy.bsky.social, a fantastic PhD in my group. We resolve a key problem in development + evolution: how do we quantify heterochrony and link temporal variation to phenotype? www.biorxiv.org/content/10.6...

Quantitative mapping of heterochrony to species-specific phenotypes

The genetic program of animal development is conserved, but its rate of execution varies across species. Heterochrony, shifts in the relative timing of developmental events, generates phenotypic varia...

biorxiv.org

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

Sub-cellular architectures arise through integrating signaling and structure. @edenchang.bsky.social and @zjmaggiexu.bsky.social show how coupling reaction-diffusion signaling to protein condensation provides a tunable, regulatable landscape for sub-cellular structure www.biorxiv.org/content/10.6...

Let's step inside a neuron together, and ask, "how did all this get here?" 🤔 In this review, I trace the history and transformations of a neuron's molecules, pay homage to major discoveries in brain development ... and make a call to action for neuroscience. www.annualreviews.org/content/jour...

The Translation of Genetic Information in Neurodevelopment

Neurodevelopment is the transformation of genetic information into diverse neuronal phenotypes. Developmental signals initiate patterns of gene transcription and translation that drive progenitors tow...

annualreviews.org

Mitochondria tethered to the nucleus secure its energy supply

Mitochondria directly interact with the nuclear pore complex - Nature

Mitochondria interact directly with the nuclear pore complex via VDAC1–RANBP2 binding to sustain nuclear ATP levels.

nature.com

1/🧵 Can transcription factor condensate formation be explained without phase separation? Our new preprint introduces SPARK, a simulation tool that reproduces condensate behavior (clustering, fusion, FRAP) from diffusion & binding kinetics alone. Movie: 60 sec FRAP sim www.biorxiv.org/content/10.6...