New online! RBPscan measures protein–RNA interactions in living cells

📢 The Ghersi Lab is recruiting! We are looking for motivated students and postdoctoral fellows interested in stem cell biology, developmental hematopoiesis, and zebrafish genetics. Interested? Get in touch or share with your network! l1nq.com/d22fg4o

Finally out in @Cellcellpress! Proteins with long IDRs are prone to misfolding during protein synthesis. This is prevented by mRNA 3′UTRs that act as mRNA-based IDR chaperones. www.cell.com/cell/fulltex...

Exciting breakthrough technology from the lab, now live in @cellcellpress.bsky.social ! Instead of cutting the genome where proteins bind (e.g., Cut&Tag), D&D-seq scars the DNA with a deaminase, allowing single cell genome mapping of TFs and chromatin remodellers!

What is the role of #poison-exon in regulating splicing factors in stem cells and development? Check out new work from Nathan Leclair and Mattia Brugiolo and many others in my lab @jax.org #RNA #splicing www.biorxiv.org/content/10.6...

See our handy graphical abstract and article for free here: bit.ly/4vsl845

SAVE THE DATE for the 13th Canadian Developmental Biology Conference — March 7–10, 2027 — bringing together researchers, trainees, and innovators in developmental biology from across Canada and beyond.

For 40 years the 8-nt ‘Kozak Sequence’ was thought to mark sites of translation initiation. In a new study, we revise this model by identifying an ~80-nt sequence—the extended Translation Initiation Sequence (eTIS)— that guides ribosomes to correct start sites. 🧵 www.biorxiv.org/content/10.6...

If you want to know what 3′UTRs with long conserved sequence stretches do, check out our BioRxiv preprint doi.org/10.64898/202.... They form functional intermolecular 3′UTR-3′UTR interactions that enable co-folding of proteins to rapidly induce transcriptional programs.

New lab preprint lead by Ziqing, Siran and Ayse! doi.org/10.64898/202... In it they show that: 1) oskar mRNA clustering is driven by the synergistic action of osk concentration, the Staufen RBP and osk RNA palindrome.

The program for the 4th Canadian Zebrafish Research Conference is now available. 📅 May 15, 2026 📍 CHU Sainte-Justine, Montreal We are excited to highlight our three Postdoc Rising Stars and to have the privilege of welcoming three invited speakers. @izfs.bsky.social @zebrafishrock.bsky.social

A new paper from the lab shows that Nanos3 and Dead end1 can form a complex with eIF3d to activate RNA translation in primordial germ cells. link.springer.com/article/10.1...

Could the #ribosome be a selfish element? @mkrupovic.bsky.social & Eugene Koonin propose that the #evolution of life can viewed as a ribosomal takeover, where the ribosome evolved to consume most of the cell’s resources. 🧪 #OriginsOfLife

Excited to share our @natprot.nature.com paper on using RNA proximity labeling to map subcellular RNA transcriptomes. We’ve been working in this area for a while and wanted to create a resource paper to guide the uninitiated reader. rdcu.be/fblvI

🐟 Reminder! Registration is open for the 4th CZRC in Montréal (May 15, 2026). ⏰ Abstract deadline: April 17 Submit for talks, posters, travel awards & Postodoc Rising Stars! event.fourwaves.com/4czrc/pages @izfs.bsky.social @zfinmod.bsky.social @zebrafishrock.bsky.social

After 20 years, 58 generations and more than 30,000 cloning attempts, a team of researchers has hit the limit on the number of times a single mouse can be serially re-cloned go.nature.com/4sDtyET

The E3 ubiquitin ligase mechanism specifying target-directed microRNA degradation (TDMD) is now published! 🎉🍾 We, @bartellab.bsky.social and Schulman lab, describe how 2-RNA factors control protein degradation by recruiting an E3 ligase. @mpibiochem.bsky.social www.nature.com/articles/s41...

Very happy to see this out. 👏 @yinanwan.bsky.social Bogdan Bintu and team. Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis | free link Science www.science.org/eprint/5MHTM...

🐟 We are hiring a postdoc! Interested in RNA regulation, gene expression, and zebrafish embryogenesis? Join the Bazzini Lab at @stowersinstitute.bsky.social www.stowers.org/labs/bazzini... Please share! Details below 👇 #Postdoc #RNAbiology #zebrafish #devbio #Genomics

Please check out our latest #preprint to study #ACTIVELY TRANSLATING #tRNA populations and their dynamics upon #stress :) This was an wonderful collaborative effort between @novoalab.bsky.social @immagina.bsky.social and #Soares teams - thank you for making this possible!

With Eugene Koonin, we propose a concept of “the selfish ribosome”, under which evolution of life is viewed as a ribosomal takeover, where the ribosome evolved to consume most of the cell’s resources, while other cellular componentry ensures the propagation of the ribosome. arxiv.org/abs/2602.23268

I am delighted to report that this is now out! A giant congratulations and thank you to all the Bluesky-less coauthors: Hyeyeon Nam, Justin Deme, Soyeong Sim, Marco Boccitto and Susan Lea.

For those on the job market, University of Toronto 🇨🇦 is hiring a tenure-track Assistant Professor in Zebrafish Models of Genetic and Metabolic Pathologies 🐟 Yes, they want #zebrafish! 🔗 jobs.utoronto.ca/job/Toronto-...

🎉Proud to present our latest paper, out now in Nature Communications: www.nature.com/articles/s41... RNA Binding Proteins (RBPs) are often full of intrinsically disordered regions (IDRs), but what these regions do during RNA recognition is often unclear. 1/10 #RNA #IDR #RBP

Looks like Plasmodium delivers an anti-splicing RNA bomb to the nucleus of its host's WBC --oof! Nuclear import of malaria RNA rewires splicing in host immune cells: Cell Reports www.cell.com/cell-reports...

🚨Just join us🚨 This is a fantastic meeting with great science and better people, can't miss it!! 🦓🐟+🧑‍🔬+🇨🇦

🧵 Thread: What happens when transcription isn’t properly shut off during mitosis? Our new preprint explores just that 👇 www.biorxiv.org/content/10.6...

New online! Bridging technical innovation and computational advances in studies of RNA–protein assemblies

Happy to share the first review article from our lab! We discuss the landscape of available high-throughput approaches for profiling RNA–protein interactions in vitro and in vivo. We hope it will be useful when designing your next experiment. www.tandfonline.com/doi/full/10.... #RNAsky

@science.org Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation | Science www.science.org/doi/10.1126/...

How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller? Excited to share our latest work in @science.org on a new small polymerase. 1/n

1/3 New bioRxiv preprint from the lab: “Minute-scale coupling of chromatin marks and transcriptional bursts”. Led by Xiohui Gao & Chaebeen Ko. bioRxiv : www.biorxiv.org/cgi/content/...

Thank you @cp-molcell.bsky.social for publishing our work

I am thrilled to share our paper introducing RBPscan, a novel approach to profile RNA–protein interactions in living cells. Free access link at the end ⬇️ 🧵 1/ www.cell.com/molecular-ce...

Does the noncoding genome actually carry more genetic information than coding seqs? Motivated by this question we mutated every bp in the 10kb MYC locus. Results are even more exciting: Decoding the MYC locus reveals a druggable ultraconserved RNA element www.biorxiv.org/content/10.6...

Programmable artificial RNA condensates in mammalian cells https://www.biorxiv.org/content/10.64898/2026.01.28.702393v1

Online Now: Signaling to make human ribosomes: Connections between the cytoplasm and the nucleolus Online now:

I’m happy to share the main result of my PhD, which you can find on bioRxiv www.biorxiv.org/content/10.6.... If you are interested in learning about a new way to perform DNA-PAINT multiplexing, which we call Combi-PAINT, or if you are interested in the study of mRNA conformation, keep reading! 1/10

Out now in @science.org Endogenous retroviruses synthesize heterologous chimeric RNAs to reinforce human early embryo development | Science www.science.org/doi/10.1126/...

Happy New Year all. I know it's been a draining and difficult year for science in general, but wanted to share some good news: our intrabody paper has now been published in Science Advances with lots of additional data. www.science.org/doi/10.1126/...

What's larger, a protein or its templating mRNA ? > The mRNA is much larger. ⬛ 𝐀 𝐬𝐞𝐧𝐬𝐞 𝐨𝐟 𝐬𝐜𝐚𝐥𝐞 -- 𝐪𝐮𝐚𝐧𝐭𝐢𝐭𝐚𝐭𝐢𝐯𝐞 𝐢𝐧𝐭𝐮𝐢𝐭𝐢𝐨𝐧 & 𝐜𝐨𝐧𝐬𝐭𝐫𝐚𝐢𝐧𝐭𝐬 -- 𝐢𝐬 𝐚 𝐩𝐨𝐰𝐞𝐫𝐟𝐮𝐥 𝐞𝐧𝐚𝐛𝐥𝐞𝐫 𝐨𝐟 𝐫𝐞𝐬𝐞𝐚𝐫𝐜𝐡. The figure shows myoglobin protein drawn to scale next to its mRNA template. The coding sequence of an mRNA ...

Amazing: TimeVaults! www.science.org/doi/10.1126/...

Starting the New Year with exciting news! A major paper started during my postdoc and finished in my own lab has just been accepted. More details soon.

Greetings! I decided to make a YouTube video of my AlphaFold workshop that I've given a few times in the past year. Caveats aside, people seem to find this useful for thinking about how to model protein interactions and how to interpret various AF outputs 1/2 www.youtube.com/watch?v=u63o...

Happy to share two BioRxiv manuscripts from our lab. One on genetic Argonaute interaction and unexpected non-correlation between small RNAs and their targets: doi.org/10.64898/202... The second on IDR processing and IDR-mediated Argonaute loading control: doi.org/10.64898/202... Merry Xmas😊

Helix: a structure-aware deep learning model for accurate prediction of A-to-I RNA editing by endogenous ADARs https://www.biorxiv.org/content/10.64898/2025.12.18.695251v1

My "News & views" was published today @natmethods.nature.com Thanks @ritastrack.bsky.social for the invitation to write it and Allison Doerr for the editing after Rita left... www.nature.com/articles/s41...

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

After a huge amount of work w/ @alex-stark.bsky.social's group, a new version of our Ledidi preprint is now out! In an era of AI-designed proteins, the next leap will be controlling when, where, and how much of these proteins are expressed in living cells. www.biorxiv.org/content/10.1...