Igor Ulitsky
@igorulitsky.bsky.social
Associate Professor, Weizmann Institute of Science. RNA biologist, interested in what (long) RNA molecules do and how. Father of 4.
Academic tweeps! How do your institutes implement support for scientists in the rapidly changing AI-era - i.e, who is training the students to use Claude Code, and making sure they don't wreckt the cluster? Does it work well? Tell here/DM + pls RT (heading a sub-committee...)
Transcription-dependent heterochromatin at the Xist promoter shapes the random choice of the inactive X chromosome https://www.biorxiv.org/content/10.64898/2026.07.22.737064v1
Woolfe et al, 2026. Decoding the mystery of ultra-conservation in developmental enhancers: a role for nucleosome positioning, DNA structure and transcription factor binding www.biorxiv.org/content/10.6... ▶️conserved non-coding elements ... favor nucleosome occupancy at their borders
Our paper out in Science today: The Metis defense system senses molecular byproducts released when a phage degrades the bacterial genome, and then prevents replication of the phage in the infected cell Congratulations @ostermanilya.bsky.social and co-authors!
Bacteria sense virus-induced genome degradation via methylated mononucleotides
Phages often degrade the genome of their bacterial host to individual nucleotides. Here we describe Metis, a bacterial defense system that directly senses phage-mediated host genome degradation. Metis...
science.org
Osterman Ilya@ostermanilya.bsky.social · 4w agoExcited to share that our Metis story is now published in Science! 🎉 Bacteria can sense phage-induced degradation of their genome and activate immunity. Many thanks to everyone who contributed to this work. 📄 www.science.org/doi/10.1126/... More details in my earlier thread 🧵⬇️
Insulin synthesis is sustained by Tent5 poly(A) polymerases https://www.biorxiv.org/content/10.64898/2026.07.04.736497v1
Excited to share that our Metis story is now published in Science! 🎉 Bacteria can sense phage-induced degradation of their genome and activate immunity. Many thanks to everyone who contributed to this work. 📄 www.science.org/doi/10.1126/... More details in my earlier thread 🧵⬇️
Bacteria sense virus-induced genome degradation via methylated mononucleotides
Phages often degrade the genome of their bacterial host to individual nucleotides. Here we describe Metis, a bacterial defense system that directly senses phage-mediated host genome degradation. Metis...
science.org
Osterman Ilya@ostermanilya.bsky.social · 9mo agoBacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides. Here’s the story of how we discovered the Metis defense system 👇 www.biorxiv.org/content/10.1...
Frank Grosveld has been a giant in the field of long-range gene regulation. Inspirational to me and I am sure for many others. Rest in peace.
Lluis Montoliu@lluismontoliu.bsky.social · last mo.Frank Grosveld, born in 1948, passed away last Friday. He was a colossal scientist in the transcriptional control of gene expression during development and helped us understand the complex regulation of beta-globin genes. His work will remain as a reference. May he rest in peace.
a small attempt to capture this enormous loss and what Greg meant and means to so many. www.cell.com/cell/fulltex...
Gregory J. Hannon (1964–2026)
Gregory J. Hannon passed away in April 2026 at the age of 61. A towering figure in modern molecular biology, Greg influenced remarkably diverse areas of science. His work reshaped our understanding of...
cell.com
Now out @natbiotech.nature.com ! Do lncRNAs commonly bind 1000s of genomic sites? Maybe they do, but the dozens of studies that report genomic binding maps of lncRNAs are deeply flawed, with probes binding suprious DNA sites rather than RNA-bound ones.
Igor Ulitsky@igorulitsky.bsky.social · 9mo agoA preprint‼️that's bound to ruffle some 🪶 "Widespread DNA off-targeting confounds studies of RNA chromatin occupancy" led by our Micah Goldrich and Louis Delhaye from Pieter Mestdagh in Ghent. TL;DR we show that many of lncRNA chromatin occupancy obtained are flawed www.biorxiv.org/content/10.1...
Sounds super interesting - hope we'll see more of these (lncRNAs linked by human genetics + mouse KOs to key phenotypes)! www.nature.com/articles/s41...
An X-linked long non-coding RNA, PTCHD1-AS, and the core features of autism - Nature
PTCHD1-AS, which encodes a long non-coding RNA, is associated with the aetiology of autism spectrum disorder in humans through striatal molecular and circuit-level dysregulation.
nature.com
Amazing insight from David Brow @bmolchem.bsky.social on potential mechanisms of U6 snRNA dysfunction in retinitis pigmentosa! Plus a potential therapeutic strategy based on some classic nucleic acid biochemistry experiments and competing RNA structures. rnajournal.cshlp.org/content/earl...
Past studies suggest potential therapies for newly discovered retinitis pigmentosa mutations in U6 and U4 snRNAs
A monthly journal publishing high-quality, peer-reviewed research on all topics related to RNA and its metabolism in all organisms
rnajournal.cshlp.org
Hey, wouldja look at that! An incredible one man show from Pablo Bora, an amazing postdoc...we used Steven Floor's beautiful REMORA approach (fusing RNA base editors to RBPs, allowing RBP cargo to be identified by edits) to explore RBP-RNA binding in mouse embryos doi: doi.org/10.64898/202...
Probing RNA-protein interactions in the early mouse embryo
The union of two germ cells to form a zygote, and subsequent early embryo development, are marked by radical remodeling of virtually every major class of biomolecules as the specialized germline states give way to the rapid and active growth that marks early development. In recent years, advances in ultra-low input genome-wide methods have enabled systematic analyses of mRNA abundance, and of chromatin organization, throughout early development in a variety of model systems. Here, we extend these efforts to the study of RNA binding protein (RBP) function in early mouse embryos, adapting REMORA 1 -- based on fusing an RNA-editing enzyme to an RBP of interest -- for use in early embryos. We benchmark our approach for several well-studied RBPs, successfully recovering expected features of their RNA cargos, and assayed the RNA cargos for 17 RBPs of interest for early gene regulation. Analysis of changes in mRNA metabolism following knockdowns of the RBPs surveyed here allowed us to identify direct regulatory functions for a subset of RBPs in the early mammalian embryo, including an unanticipated role for the RNA export adaptor Alyref in control of 3 prime polyadenylation sites. Together, our data provide a proof of concept resource for systematically exploring RBP functions in mammalian embryogenesis. ### Competing Interest Statement The authors have declared no competing interest. Eunice Kennedy Shriver National Institute of Child Health and Human Development, https://ror.org/04byxyr05, NIHR01HD099816
doi.org
🆕 review with @jpunfried.bsky.social out in Nature SMB. Direct roles of lncRNAs in transcriptional activation. What do we understand about how lncRNAs lure Pol2 and set the stage for RNA production, and what do we still miss? www.nature.com/articles/s41...
Direct roles of long non-coding RNAs in transcription activation - Nature Structural & Molecular Biology
This Review discusses how long noncoding RNAs (lncRNAs) control transcription activation by RNA polymerase II, including how they are produced at active enhancers or chromatin-domain boundaries and ac...
nature.com
If you accept an invitation to review a manuscript and then decide not to do it, please be a decent person and notify the editor. Otherwise, you're part of the problem.
Can anyone recommend a tool for calling "transcribed regions" from chromatin/nascent RNA-seq data? (ideally, using annotated genes as a starting point)
Despite EVERYTHING, we're still on for our annual Nucleic Acids Therapeutics next week at the Weizmann! There are still places to register (for free!), link in the first comment. Looking forward to meeting friends, great science, deep discussions, and great food, as always :-)
I was in a coffee place and I don’t know who this person is who left their laptop to charge on a water fountain for over an hour unattended, but this person is the chillest person alive. I am sweating every time someone places something with liquid two meters away from my computer
I’m looking for an automated way to read others’s scientific data without giving credit or acknowledgement, and also claim full credit for insights from it. And I want it to have a fitting name OAI: say no more
OpenAI {bot}@openaibot.bsky.social · 4mo agoIntroducing GPT-Rosalind, our frontier reasoning model built to support research across biology, drug discovery, and translational medicine. Video: https://twitter.com/openai/status/2044861690911850863
I can certainly sympathize with the plight of the panelists, but this is a wrong decision. The idea of ERC is encouraging high-risk proposals. Saying "if a couple of panelists think its too crazy", you are banned for 2-3 years is the opposite message of discouraging bold ideas
Dr Ino Agrafioti@inoagrafioti.bsky.social · 4mo agoI don’t know if you saw the MASSIVE news announced by @erc.europa.eu today: from now on, if you get a B at step 1 you are eligible to apply at N+3(!!!) years. Say you got a B in STG2026 step 1, you thought you could apply in STG2028, but no: only in STG2029! erc.europa.eu/news-events/...
Super excited that our two companion papers on saturation genome editing (SGE) of RNU4-2 and discovery of a novel recessive neurodevelopmental disorder (NDD) were published yesterday 🥳 SGE experiment: www.nature.com/articles/s41... Recessive NDD characterisation: www.nature.com/articles/s41... 🧵
Saturation editing of RNU4-2 reveals distinct dominant and recessive disorders - Nature
Saturation genome editing of RNU4-2 identifies the functional and clinical impact of variants across the entire gene and delineates variants that cause a new recessive neurodevelopmental disorder distinct from ReNU syndrome.
nature.com
We are excited to share our new paper in Molecular Cell uncovering how the viral lncRNA RNA2.7 reshapes host cell biology! sciencedirect.com/science/authShare/S1097276526001565/20260324T143400Z/1?md5=16c84051c2f253c4665427f837a529d3&dgcid=author A thread 🧵
As a kid, watching Walker, Texas Ranger taught me that many problems in life can be solved by a well-timed roundhouse kick, a lesson that has served me well in academia
The Washington Post@washingtonpost.com · 5mo agoBreaking news: Chuck Norris, the actor and martial artist who played the lead in “Walker, Texas Ranger” has died at age 86.
Timely reminder that a few years ago we named the Norris1 lncRNA, which remains quite enigmatic, but, fittingly for Chuck, is expressed primarily in the testis pmc.ncbi.nlm.nih.gov/articles/PMC...
Regulation of neuroregeneration by long noncoding RNAs
In mammals, neurons in the peripheral nervous system (PNS) have regenerative capacity following injury, but it is generally absent in the central nervous system (CNS). This difference is attributed, at least in part, to the intrinsic ability of PNS ...
pmc.ncbi.nlm.nih.gov
Human DHX29 detects nonoptimal codon usage to regulate mRNA stability | @science.org www.science.org/doi/10.1126/...
Human DHX29 detects nonoptimal codon usage to regulate mRNA stability
Synonymous codon usage controls global gene expression in both prokaryotic and eukaryotic species. Nonoptimal codons are known to induce mRNA decay; however, the underlying molecular mechanism remains...
science.org
There has never been a better time to study functional and mechanistic biology at the organismal (!) level than now in the age of AlphaFold and CRISPR.
Science Magazine@science.org · 5mo agoAn analysis of published papers on eight widely studied “model” organisms suggests work on them is fading, but not everyone is worried. https://scim.ag/3PaOvIs
"This observation supports the error hypothesis and suggests that metazoan transcript diversity is largely deleterious." Love this since it matches my priors :-) dx.plos.org/10.1371/jour...
Transcript diversity reflects deleterious RNA processing errors shaped by population size in metazoans
Alternative transcription initiation, splicing and polyadenylation generate extensive transcript diversity in eukaryotes, but its evolutionary significance has been disputed. This study analyses 166 t...
dx.plos.org
This line of business would make tons of $$$ in Israel this week
Gen Wojcik@genandgenes.bsky.social · 5mo agoThinking of starting a new party business in which I bring around a soundproof booth with padded walls so people can take turns going in and screaming. Just screaming and thrashing and getting it out. Available for your next kids birthday party, holiday shindig, or book club meeting.
Out today: We discovered new viral proteins that target immune signaling molecules, solely based on their AlphaFold-predicted shapes www.science.org/doi/10.1126/... Congrats Nitzan Tal and coauthors! Thank you Kranzusch lab for the fun collaboration! Linking below previous thread on our findings
Structural modeling reveals phage proteins that manipulate bacterial immune signaling
Immune systems in animals, plants, and bacteria often rely on intracellular nucleotide signaling, which viruses can block by sequestering or degrading these signals. We identified structural and bioph...
science.org
Nitzan Tal@nitzantal.bsky.social · last yr.📢Preprint out! Excited to share my final work from the @soreklab.bsky.social! We mined phage dark matter using structural features shared by anti-defense proteins (viral tools that help phages bypass bacterial immunity) to guide discovery. Found 3 new families targeting immune signaling!
Don’t worry. Soon, everyone here will be an expert on air wars in the Middle East.
TFW you generously accepted review invitations thinking you'd have two ~18 hr flights TLV<->Cancun this week for reviewing, then war breaks out, but you still need to review these papers/grants