This is now published in PNAS! And double-treat, we also made the cover :) www.pnas.org/doi/10.1073/...

Krishna Shrinivas@shrinivaslab.bsky.social · 11mo ago

Preprint! Inspired by condensates that form on specific DNA, we ask: can we design multicomponent fluids to form distinct condensates on diff. surfaces? i.e. perform classification by condensation ⚛️ 💻 exploiting phase transitions beyond compartmentalization! arxiv.org/abs/2509.08100 (1/2)

Congratulations to former grad student @heankel.bsky.social on being selected as a 2026 Jane Coffin Childs Fellow!

Jane Coffin Childs Fund for Medical Research@jcchildsfund.bsky.social · last mo.

We are thrilled to announce our 2026 Jane Coffin Childs Fellows! These thirty-two outstanding scientists are performing cutting-edge research to advance our understanding of human diseases such as cancer, neurodegeneration, autoimmunity, pathogenic infections, and more. 1/3

Congratulations to Heankel Lyons @heankel.bsky.social on being named a 2026 #JCCFellow! Lyons is a Wu Tsai Neuro Postdoc Scholar on the Brain Resilience Track. She studies how TDP-43—a protein linked to ALS—regulates gene expression in healthy motor neurons in Aaron Gitler's Lab.

Jane Coffin Childs Fund for Medical Research@jcchildsfund.bsky.social · last mo.

We are thrilled to announce our 2026 Jane Coffin Childs Fellows! These thirty-two outstanding scientists are performing cutting-edge research to advance our understanding of human diseases such as cancer, neurodegeneration, autoimmunity, pathogenic infections, and more. 1/3

Thank you 🙏🏼!! So grateful for this award from JCC to support my research on transcription dysregulation in ALS. And so lucky to join the JCC community! Thanks to my mentors Aaron Gitler (postdoc) and @bsabari.bsky.social (PhD). And Jim Shorter + Mike Rosen for supporting my application.

Jane Coffin Childs Fund for Medical Research@jcchildsfund.bsky.social · last mo.

We are thrilled to announce our 2026 Jane Coffin Childs Fellows! These thirty-two outstanding scientists are performing cutting-edge research to advance our understanding of human diseases such as cancer, neurodegeneration, autoimmunity, pathogenic infections, and more. 1/3

Excited to announce that our research group will be joining the St. Jude Children's Research Hospital Department of Chemical Biology & Therapeutics in September. 🥼 🧬 🧪 @stjuderesearch.bsky.social

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...

mRNA 3′ UTRs chaperone intrinsically disordered regions to control protein activity

Highly conserved mRNA 3′ UTRs act as co-translational chaperones for intrinsically disordered regions (IDRs), preventing inter-domain misfolding and enabling biogenesis of fully active proteins.

cell.com

Excited to share the first pre-print from our lab!! Check it out here! www.biorxiv.org/content/10.6... We found that many RNA-binding proteins canonically understood to regulate RNA processing can also function like transcription factors and cofactors to directly regulate transcription.

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

Jon Henninger@jhenninger.bsky.social · 2mo ago

Check out our new work in Cell Systems @cp-cellsystems.bsky.social! Much of the biochemistry in the cell is organized by biomolecular condensates, but what mechanisms control the distribution of a given condensate throughout the cell? And is this mesoscale organization important for function?

Proud milestone for our lab – Congrats to our first two graduate students, Lizz Maurais, PhD, and Justin Engel, PhD (@justeng95.bsky.social)! We also celebrated Lizz’s last day as she moves on to an exciting new adventure. Good luck Lizz!

🚨 New preprint: GATO-seq did it again! ELOF1 is the missing promoter-proximal factor that confers RNA Pol II resistance to TFIIF. Including ELOF1, DSIF, and NELF in GATO-seq reactions recapitulates promoter-proximal pausing in vitro at physiological conditions for the 1st time. tinyurl.com/ELOF1

⚡New preprint from the lab⚡: A key early checkpoint in gene expression is promoter proximal pausing of RNA polymerase II. For over 20 years, we as field have not been able to recreate pausing under realistic cellular conditions. @robertovn.bsky.social shows that ELOF1 is the missing piece.

Roberto Vázquez Núñez@robertovn.bsky.social · 2mo ago

🚨 New preprint: GATO-seq did it again! ELOF1 is the missing promoter-proximal factor that confers RNA Pol II resistance to TFIIF. Including ELOF1, DSIF, and NELF in GATO-seq reactions recapitulates promoter-proximal pausing in vitro at physiological conditions for the 1st time. tinyurl.com/ELOF1

Our work made the cover! (and my very first one!) Congrats to co-authors as well as Ramanna Shrinivas for cover art and @natcomputsci.nature.com for editing/cover design.

Nature Computational Science@natcomputsci.nature.com · 2mo ago

🚨Our May issue is now live, including a method to design dynamic unstructured proteins, a benchmark to evaluate spatial alignment methods for spatial transcriptomics, and much more! www.nature.com/natcomputsci... 📰Cover: www.nature.com/articles/s43...

Congratulations Dr. Mikayla Eppert!

Excited to share our latest paper! We found that large pieces of the human genome can transfer between cells upon direct contact, endowing recipient cells with heritable phenotypic changes. @cp-cell.bsky.social (1/7) www.cell.com/cell/fulltex...

New preprint alert! Together with Tetsuya Yamamoto at Hokkaido University, we propose a “polymer micelle” model of transcriptional bursting. www.biorxiv.org/content/10.6...

Thrilled to share that I’ll be starting my lab as an Assistant Professor and Endowed Scholar in the UT Southwestern Molecular Biology Dept this Fall! 🥳 We’ll study #peroxisomes #mitochondria #metabolism via the lens of neonatology 👶🏻, a very exciting frontier in medicine! #neotwitter

Happy 30th birthday to this paper published March 22, 1996, one of the studies that moved chromatin biology from correlation toward mechanism. Brownell et al. linked a transcription-associated Tetrahymena HAT to yeast Gcn5p, providing a biochemical link for chromatin modification to gene activation.

Our most recent work on the “function and evolution” of #nuclear-speckles is now online at Cell @cp-cell.bsky.social doi.org/10.1016/j.ce... Read the thread👇 for the highlights of our findings.

The function of nuclear speckles is revealed! This is an incredibly important paper with absolutely beautiful data! Wow! www.cell.com/cell/fulltex...

Nuclear speckles enable processing of RNA from GC-rich isochores

Nuclear speckles are key subnuclear structures that regulate gene expression in GC-rich regions. This work shows that the evolution and expansion of core speckle proteins were crucial for the increase...

cell.com

Pleased to share the final version of this behemoth of a paper, now finally published. I guess I can retire now? www.nature.com/articles/s41... More functional data, many thousands of words removed, and a few other updates from last year's preprint.

Sequence and chemical specificity define the functional landscape of intrinsically disordered regions - Nature Cell Biology

Langstein-Skora, Schmid, Huth et al. propose that intrinsically disordered region functionality can be driven by the interplay between linear binding motifs and contextual chemical characteristics suc...

nature.com

Alex Holehouse@alexholehouse.bsky.social · 2y ago

We’re pleased to share our substantially updated (more below on that…) version of our manuscript exploring the relationship between conservation in sequence/function for intrinsically disordered regions (IDRs) www.biorxiv.org/content/10.1...

3️⃣4️⃣ Robert G. Roeder collecting sea urchings, the organism in which eukaryotic RNA Pols I, II and III were discovered (source : youtu.be/efNtZyXSHC4?...)

🧪🧬New preprint We present cryo-EM structures of reconstituted CTCF–nucleosome complexes, showing CTCF dimerization drives nucleosome oligomerization into defined higher-order assemblies. Disrupting CTCF–CTCF interfaces in mESCs reduces looping and impairs differentiation. tinyurl.com/CTCF-nucleos...

I am excited to share a new review @cp-molcell.bsky.social written in collaboration with @tanjamittag.bsky.social , Mikayla Eppert, and Ambuja Navalkar where we review the current evidence for and against the role of density transitions in regulating transcription www.cell.com/molecular-ce...

Now published in @science.org www.science.org/doi/10.1126/...

Live-cell single-molecule dynamics of eukaryotic RNA polymerase machineries

Eukaryotic gene expression is orchestrated by RNA polymerases (RNAPI, II, and III) and associated factors, yet their real-time dynamics remain obscure. Using single-molecule tracking in living yeast, ...

science.org

Alexis Verger 🧬🧫🧪@alexis-verger.cpesr.fr · 8mo ago

This preprint dates from July 2024, but I just stumbled upon it. Single-molecule tracking in living yeast to assess the physiological kinetics of over 50 representative proteins encompassing all three RNAP machineries. www.biorxiv.org/content/10.1...

New preprint from the lab! We identify the ZnF protein Mulberry as a condensation-dependent structural regulator of genome topology that organizes “multi-way regulatory hubs” in early Drosophila embryos. www.biorxiv.org/content/10.6...

IDPSeminas is back again TOMORROW! Talks from Lucia Strader (@luciastrader.bsky.social) and Heather Meyer! Sign up at idpseminars.com. Talks start at 1 pm EST / 7 PM CET!! Come learn about transcriptional adaptation and IDRs as environmental sensors and accuators!

I am recruiting postdoctoral fellows to develop new research directions in the lab. We study transcriptional regulation through biomolecular condensates in development and disease, with an emphasis on first-principles and mechanistic discovery. Please repost or share with colleagues.

Activator-promoter compatibility in mammals - Hcfc1 is a key and intrinsically CGI-promoter-specific co-activator that cannot activate non-CGI promoters. Lead by @nemcko.bsky.social & Kevin Sabath in collab. with @plaschkalab.bsky.social @impvienna.bsky.social www.biorxiv.org/content/10.6... (1/2)

Activator-promoter compatibility in mammals: a CpG-Island-specific co-activator directly bridges transcription factors to TFIID

Transcription from CpG island (CGI) promoters controls the expression of two-thirds of mammalian genes, yet despite their prevalence, it remains unknown whether CGI-specific co-activators with intrins...

biorxiv.org

Do transcriptional activators work on any promoter? Our data says no. 🙅‍♂️ Despite driving ~2/3 of mammalian genes, CpG island (CGI) promoters have remained a puzzle. We identified >50 activators that are exclusively compatible with this promoter class. 🧬

🎉Publication alert🎉 Congratulations to @lemkelab.bsky.social, @wittmann-lab.bsky.social, Girard Lab & their teams on their new Nature Communications publication. This work showcases the active cross-disciplinary dialogue that lies at the heart of our network. www.nature.com/articles/s41...

Differential conformational expansion of NUP98-HOXA9 oncoprotein from nanosized assemblies to macrophases - Nature Communications

Some transcription factors can organize into different structural states, from small nanoscale clusters to macrophases. Here authors show that NHA9 undergoes differential conformational expansion acro...

nature.com