Dmitry Kretov

Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis Gene expression patterns underlie development, but their systematic detection in whole embryos has remained elusive. We introduce a whole-embryo imaging platform using multiplexed error-robust fluores...

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

Nuclear import of malaria RNA rewires splicing in host immune cells Abou Karam et al. identify a cell communication mechanism used by the malaria parasite Plasmodium falciparum. The parasite delivers its mRNAs into monocytes and imports them into their protected nucle...

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...

Thank you, Stefania!

🚨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...

Bridging technical innovation and computational advances in studies of RNA–protein assemblies Nature Reviews Genetics, Published online: 16 February 2026; doi:10.1038/s41576-026-00931-9Empirical and artificial intelligence-based approaches are redefining how RNA-dependent protein assemblies are mapped, modelled and targeted, revealing their dynamic roles in health and disease and outlining closed-loop strategies for predictive functional RNA and ribonucleoprotein design.

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

Decoding RNA–protein interactions using high-throughput methods RNA-binding proteins (RBPs) constitute a diverse class of proteins essential for every stage of the gene expression process. Many RBPs are also linked to human diseases and pathologies. Understandi...

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

Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation Transcriptional adaptation (TA) is a genetic robustness mechanism through which mutant messenger RNA (mRNA) decay induces sequence-dependent up-regulation of so-called adapting genes. How cytoplasmica...

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

A small polymerase ribozyme that can synthesize itself and its complementary strand The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

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

Now out in @cp-molcell.bsky.social !

🧵 8/
Special thanks to the members of my newly established lab at @crchudequebec.bsky.social whose efforts were instrumental in bringing this project to completion.

🧵 7/ This project wouldn’t have been possible without many amazing people. A huge thank you to Daniel Cifuentes for the constant support and to all lab members who contributed along the way.

🧵 6/ If you’re interested in learning more about the method, here’s the free access link to the full paper: authors.elsevier.com/c/1mZlb3vVUP.... We hope RBPscan becomes a valuable tool for the RNA community

🧵 5/ RBPscan also provides positional information about where RBPs bind along RNA. As a showcase, we mapped Pumilio binding sites on lncRNA NORAD, recovering known sites and identifying several new ones.

🧵 4/ By titrating RBP expression levels, RBPscan can generate binding curves, allowing us to quantitatively describe RNA–protein associations in vivo.

🧵 3/ With RBPscan, we can perform de novo motif discovery using fully randomized RNA libraries.
In this study, we profiled the binding specificities of 12 RNA-binding proteins in zebrafish embryos, and show that RBPscan also works in HEK293 cells and yeast.

🧵 2/ Building on RNA base-editing approaches such as TRIBE, we developed RBPscan, which combines massively parallel reporter assays and an RNA-editing–based sensor that "records" information about RBP–RNA interactions in vivo.

RBPscan: A quantitative in vivo tool for profiling RNA-binding protein interactions Kretov et al. introduce RBPscan, an RNA-editing-based platform that measures how RNA-binding proteins engage their targets in living cells. This approach quantifies the binding strength of protein-RNA...

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

Signaling to make human ribosomes: Connections between the cytoplasm and the nucleolus Lawrence et al. examine how ribosome production in the eukaryotic nucleolus is coordinated by cytoplasmic processes to maintain appropriate ribosome numbers. The authors highlight regulatory inputs from cytoplasmic signaling, mitosis, and cytoplasmic organelles that converge on nucleolar function, and they discuss how disruption of these pathways contributes to human disease.

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