Intrigued by a long-standing conundrum in small RNA biology—how nuclear Argonaute proteins silence transposons when they *need* target transcription for their own recruitment—we studied the piRNA pathway. And found a hidden RNA-decay axis from Piwi to the RNA exosome.

Ladies and gentlemen... the weekend. (also: you are important and are not alone 🧡)

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...

Very happy to share our paper rdcu.be/eUImj out today in @natcellbio.nature.com 🎉🎉🎉 We uncover an unexpected role for endogenous Xist RNA in regulating X-linked genes that escape X-inactivation.

@science.org🧬Cohesin guides homology search during DNA repair using loops and sister chromatid linkages | Science www.science.org/doi/10.1126/... @fedeteloni.bsky.social @danielgerlich.bsky.social et al.

Oh hey, looks like I can upload longer videos here now! Here’s my most recent one covering the latest findings on ecDNA retention mechanisms from the Chang & Mischel labs.

Oxidative phosphorylation complexes contain subunits encoded by both the nuclear and mitochondrial genomes. How do cells coordinate the synthesis and assembly of these complexes at the inner membrane? We teamed up with Martin Ott (@mitolab.bsky.social) to address this in two recent papers.

We just released IRIS (7+yrs project), a tech we believe will transform cell biology by pairing high-resolution cell images with matched #scRNAseq, letting us interpret cellular form by its molecular ground truth. Huge tx to @JohannesBues, @JoernPezoldt, @CamilleLambert et al. shorturl.at/zgY8Z

Here is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀 Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function now revised and journal accepted at www.science.org/doi/10.1126/... 🧵👇

Man it would be so cool if, in the year 2025 of our lord, we could all just be chill and celebratory about nice professional things being announced for our colleagues in molecular biology. Unrelated, anyone reading absolute Batman? Bc it slaps.

We are looking for a postdoctoral fellow to work on induced proximity 🤜🤛 and functional genomics! Join our team in Toronto 🇨🇦 to tackle major challenges in oncology and neurodegeneration. www.nature.com/naturecareer...

Unpause! I'm super happy to now be able to share the published version of our paper at Science Advances showing that: 1) active histone mods occur independently of transcription 2) transcription coordinates histone deacetylation at active promoters www.science.org/doi/10.1126/...

Read my full story here! Psychedelics and immortality: Nature went to a health summit starring RFK and JD Vance www.nature.com/articles/d41...

Today in @nature.com, in work led by @adititm.bsky.social, we report the ability to prompt Evo to generate functional de novo genes. You shall know a gene by the company it keeps!

Very excited to present OpenCGChromatin🔥🔥🔥 A new coarse-grained model that probes full chromatin condensates at near-atomistic resolution to reveal the molecular regulation of chromatin structure and phase separation Brilliantly led by @kieran-russell.bsky.social, with the Rosen and Orozco groups

Major new direction in the lab: hacking human cell biology with pathogen effectors (eORFs) - amazing collaboration with @miketilapia.bsky.social lab. Huge congrats to first authors Tomas & He & all co-authors! Check out the pre-print on @biorxivpreprint.bsky.social www.biorxiv.org/content/10.1...

Excited to share Nona: a unifying multimodal masking framework for functional genomics. Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM). Can these be unified under a single paradigm? 1/15

Stoked to share our latest work entitled: “Large-scale discovery of neural enhancers for cis-regulation therapies” shorturl.at/H3Qww This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon. Bluetorial below.

(1/10) How do diverse leukemia mutations converge on the same molecular program? In #RibackLab first manuscript @cp-cell.bsky.social, collaboration with @goodell-lab.bsky.social shows that disparate mutations rewire shared protein networks to form nuclear condensates called C-bodies.

RNAs outside of cells?! How did they get there? (Thread coming soon 👀) www.biorxiv.org/content/10.1...

1/ Excited to share our new study with @brumbaugh-lab.bsky.social, out in @natbiotech.nature.com! P-bodies selectively sequester RNAs encoding cell fate regulators, often from the preceding developmental stage. Releasing these RNAs can drive changes in cell identity. 🧵 www.nature.com/articles/s41...

Now published in PLOS Biology! We found new retron containing bacteria in the wild, figured out defense mechanisms, and turned them into genome editors. From a cupful of dirt to new parts for genome editing in one story! journals.plos.org/plosbiology/...

The Skok Lab is recruiting an experienced computational scientist to lead single-molecule epigenomic and 3D genome analysis. We integrate long-read sequencing with Hi-C/Hi-ChIP, scmulti-omics, and machine-learning to explore chromatin topology, and gene regulation.

Been working on a really strange retron bacterial immune system, here's the preprint: www.biorxiv.org/content/10.1... Type VI retrons are unlike any other. Phage infection triggers reverse transcription of a DNA fragment that activates translation of a toxin to kill the infected cell.

🚨 🚨 🚨 New preprint alert!!! 🚨 🚨 🚨 In the past, we have learnt that Oct4 can induce nucleosome breathing on the mono-nucleosome level. But what happens when you have a fibre of multiple nucleosomes? www.biorxiv.org/content/10.1... @rcollepardo.bsky.social @juliamaristany.bsky.social

Our collab w. V Goel, @nicholas-aboreden.bsky.social , J Jusuf, G Blobel, L Mirny, @irate-physicist.bsky.social out in @natsmb.nature.com www.nature.com/articles/s41... Was co-submitted with @allanaschooley.bsky.social @jobdekker.bsky.social whose paper should also come out soon Brief thread 👇

Hello Boston! The lab is delighted to be at #ASHG25🧬 Check out our talks over the next few days - all unpublished stories. Kicking things off is @michaelherger.bsky.social presenting "Saturation mutagenesis of 37 human splicing factor genes with pooled prime editing". Today @2pm, Rm205abc Also 👇

Super excited about first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to the brilliant Chase Suiter (not here) & @greenahn.bsky.social on the work! Preprint here: www.biorxiv.org/content/10.1...

Lab’s 1st preprint! Menstruation is understudied due to societal taboos + a biological challenge: mice (a key system for research + drug discovery) don’t menstruate. @cagricevrim.bsky.social made menstruating mice + used them to discover early events in menstruation. He is on the job market!

I’m thrilled to share my postdoc work and the first paper from the McKinley Lab! 🎉 @karalmckinley.bsky.social We built the first transgenic model of menstruation in mice. We used it to uncover how the endometrium organizes and sheds during menstruation. 🧪 www.biorxiv.org/content/10.1... 🧵

Congratulations @karalmckinley.bsky.social & lab on their groundbreaking recent preprint establishing + characterizing a chemically inducible model of menstruation in mouse: www.biorxiv.org/content/10.1... My jaw dropped when I heard this presented earlier this year. Incredible.

New paper: Hepatic ceramide synthesis links systemic inflammation to organelle dysfunction in cancer Liu, Miao, Wang, Ezequiel, Kim, Zhang, Sun, Binari, Asara, Yanhui Hu, Goncalves, Janowitz, Perrimon doi: doi.org/10.1101/2025...

Independent research fellowships leading to tenured positions at the John Innes Centre. Repost = nice. Thank you very much!!!

Today I am so pleased to present our work on how chromatin remodelers affect mesoscale chromatin organization. www.science.org/doi/10.1126/...

Congratulations @jbuenrostro.bsky.social!!!

Genes are not On/Off switches. In a new preprint we show that HDAC3 is key to establish correct transcriptional dose in development. Gr8 work from N. Stamidis @ucph.bsky.social and collab. @jamiehackett.bsky.social @gregersenlab.bsky.social . Huge thx to all authors! www.biorxiv.org/content/10.1...

EEE meeting is BACK! Early Embryogenesis & Epigenetics conference in Berlin 02/2026. Checkout great program and over 12 slots for (not so) short talks for submitted abstracts!. Early registration now open - w.molgen.mpg.de/embryo2026

Asking BlueSky for help: For a review, I am trying to accurately credit the first paper that measured pairwise 3D distances between 2 pieces of DNA on the same chromosome (or cosmid). Is Trask 1989 the first? I know of earlier single-locus papers (1982). www.sciencedirect.com/science/arti...

Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up! www.biorxiv.org/content/10.1... A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)

1/ 🧵 I am excited to share a new preprint from our group: Single-cell Dam&T-seq during mouse corticogenesis reveals how genome–lamina interactions regulate long neuronal genes. doi.org/10.1101/2025... #Neurodevelopment #Epigenetics @hubrechtinstitute.bsky.social @oncodeinstitute.bsky.social

TDAC-seq is a method for targeted chromatin accessibility profiling that uses cytidine deaminases and long-read sequencing to resolve the effects of CRISPR edits on single chromatin fibers. www.nature.com/articles/s41...

Major overhaul on my personal website is now live! jlsteenwyk.com

This could be a neat method for species detection in #metagenomic datasets, but why on earth are we simulating PacBio and ONT error rates at >10%? 🫣🤔🫠 PacBio HiFi has had >99% accuracy since 2019. Very hard to interpret the results based on 90% accuracy. www.biorxiv.org/content/10.1...

New preprint with @gfudenberg.bsky.social We find the rate of cohesin loop extrusion in cells is set by NIPBL dosage and tunes many aspects of chromosome folding. This provides a molecular basis for NIPBL haploinsufficiency in humans. 🧵👇 www.biorxiv.org/content/10.1...

Thoughts on Illumina pip-seq in general and vs 10X?

Thrilled to share our latest work, just published in @nature.com ⬇ www.nature.com/articles/s41... We discovered that PARP inhibitors 💊 trigger histone eviction from the chromatin and this creates a hidden vulnerability in PARPi resistant tumors. 🧵 (1/8)

We are excited to share our new preprint demonstrating that nucleic acid interactions with SUZ12 constrain PRC2 activity, establishing a kinetic buffer essential for targeted gene silencing and revealing vulnerabilities in diffuse midline gliomas. www.biorxiv.org/content/10.1...

Our paper is now out in final form at Nature Genetics! For those who missed the preprint, we used large-scale Perturb-seq targeting transcription factors to push primary fibroblasts into diverse transcriptional states, including those observed in cell atlas studies.