Alu repeat-containing RNAs spatially organize actively transcribed genomic regions around nuclear speckles Liu et al. identify nuclear speckle-enriched Alu repeat-containing RNAs that facilitate the organization of actively transcribed genes at speckles by binding Alu sequences and promoting speckle assembly. This spatial arrangement enhances efficient RNA processing and robust erythroid gene expression during erythropoiesis.

Online Now: Alu repeat-containing RNAs spatially organize actively transcribed genomic regions around nuclear speckles Online now:

Temporal degradation of PRC2 uncovers specific developmental dependencies www.biorxiv.org/content/10.64898/2026.04...

It's amazing that our CEO Oliver Bogler is representing the Night Science Institute at AACR. And can you see which issue of Nature he got a hold of?!
www.nature.com/articles/s41...
@oliverbogler.bsky.social @night-science-inst.bsky.social

There are Science papers and then there are *I just dropped and shattered my mug of coffee Usual Suspects style* Science papers www.science.org/doi/10.1126/...

🔥 A new episode of the Night Science Podcast just dropped! Prof. Lois Hetland, former chair of art education at MCA asks: what do artists and scientists truly share? We talk about the “studio habits of mind”: observe, reflect, envision, express engage & persist, stretch & explore, craft & connect.

The new episode of the Night Science Podcast is a must-listen! Art professor Lois Hetland wrote a classic
book about the “studio habits of mind” – observe, reflect, envision, express engage & persist, stretch & explore, craft & connect – and we explore how these relate to scientific process!

CRISPR–Cas-based live cell imaging of genome dynamics - Nature Reviews Genetics In this Review, Zhu et al. outline the various CRISPR-based tools recently built for dynamic DNA and RNA imaging, which have provided insights into various molecular mechanisms. The authors also discuss the important parameters to consider when using these tools, and how to approach the quantitative image analysis.

From cancer dysfunction to T cell exhaustion, the "live" 3D genome holds the answers.

Read our definitive reference in
@NaturePortfolio
: nature.com/articles/s41...

#CRISPR #Genomics #Biophysics #Stanford #3DGenomics #ScienceTwitter

(5/5)

There's a strange myth about science: that theory comes first, and that data cannot show anything new. But anyone who's ever done science knows the truth that there's a long conversation between data & hypotheses. Back & forth.. until the discovery. And if you think about it, it has to be this way!

Doing science requires us to speak 2 different languages: (1) Day science language is a highly precise language for designing & executing experiments; while (2) Night science language uses analogies & anthropomorphizes to give us intuitions about the unknowns we explore.
(Night Science recap, Day 4)

Expert's Dilemma: the more specialized you become, the less open you are to creative solutions from other fields. But the more you explore other fields, the more you risk losing credibility in your home field.
(Night Science recap, Day 3)

Every scientist is a bit of an artist
and every artist is a bit of a scientist

Our paper is now out in Science! Super excited to share our discovery that #mitochondria #pearling is the elusive mechanism driving the regular distribution and inheritance of #mtDNA nucleoids 🧬 [1/6]

APEX-seq maps transcriptome-wide subcellular RNA localization in living cells Nature Protocols - This Protocol describes the transcriptome-wide labeling of RNAs in a particular subcellular compartment using proximity biotinylation by localized APEX2 enzyme and subsequent...

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

Such a pleasure to spend the day with everyone at @fmiscience.bsky.social today.
Thx for having me.

Distinctive DNA sequence features define epigenetic longevity of inflammatory memory Tissues harbor memories of inflammation, which heighten sensitivity to diverse future assaults. Whether and how these adaptations are sustained through time and cell division remain poorly understood....

Our paper is out in @science.org describing how epithelial cells retain long-term inflammatory memory
www.science.org/doi/10.1126/...

My first PhD student‘s, Kavan Gor, paper on 5-color single-molecule imaging of co-transcriptional RNA folding is out in @science.org Advances!

He finds how RNA modification enzymes, antisense oligonucleotides and ribosomal proteins re-route nascent RNA folding.

See more details in EMBL post below!

ChromSMF preprint is out!🚀
tinyurl.com/ChromSMF

We often piece together chromatin regulation layer by layer from separate assays. But this can be limiting!

In @arnaudkr.bsky.social's lab, we developed a method to directly study multiple layers on the same DNA molecule! 🧬

What does this unlock? ⬇️

Kinetic proofreading as a mechanism for transcriptional specificity: www.biorxiv.org/content/10.6...
Very nice follow up to their review from last year genesdev.cshlp.org/content/39/1...
Non-equilibrium models may be key to understanding specificity in transcriptional regulation!

One of my very favorite papers from the lab! Shows that individual cells can learn by forming memories. Amazing work by Jess Li!

Unstructured transcription factor interactions enable emergent specificity How intrinsically disordered regions (IDRs) influence chromatin binding and nuclear organization of transcription factors (TFs) remains unclear. We employed proximity-assisted photoactivation (PAPA), ...

Unstructured transcription factor interactions enable emergent specificity | @science.org www.science.org/doi/10.1126/...

New preprint from our lab... We applied our hopping technology to relocate CTCF binding sites to thousands of alternative positions in the Sox2 locus: www.biorxiv.org/content/10.6...

🧵 CTCF is essential for embryonic development, but why has remained unclear. By combining gastruloids with a temporal degron system, we uncovered a surprising dual function — and it changes how we think about CTCF's role in development. 1/8 www.biorxiv.org/content/10.6...

Today we report single-cell APEX-seq (scAPEX-seq)—a method for unbiased mapping of subcellular transcriptomes at single-cell resolution. It reveals cell states invisible to standard scRNA-seq and identifies regulators of CAR T function that improve solid tumor killing.

tinyurl.com/32pf6b8p

AlphaFold database has entered the era of complexes. Together with NVIDIA, DeepMind and EBI, we use ColabFold, OpenFold and MMseqs2-GPU to predict ~31 million complexes (homo & hetro-dimers) resulting in 1.8 million high-quality predictions
📄 research.nvidia.com/labs/dbr/ass...
🌐 alphafold.ebi.ac.uk

Comic.[A gantry straddles the intersection of two tectonic plates, one under water and the other on a mountain. A tether connected to a winch on the gantry making a “click click click” sound is connected to the oceanic crust and is pulling it up, causing it to fold. Two people are standing on the fold next to the hook, looking down toward the space between the subducted crust where a shining object sits.] [caption] PSA: Please stay out of the Pacific Ocean today. Someone lost their wedding ring in a subduction zone and USGS is pulling the plate back up to retrieve it.

Subduction Retrieval

xkcd.com/3218/

Ever wondered how a eukaryotic transcription factor finds its specific DNA motif in the vast genome? In this preprint, we directly measured the dynamics of this search process in living cells, revealing a cooperative mechanism mediated by disordered regions. 1/10 doi.org/10.64898/202...

1/New preprint just dropped! 🔥🔥 We investigate how the genome is destroyed in apoptotic cells in a way that prevents DNA fragments from spreading beyond the dying cell 🧬⚰

Done here at @imbavienna.bsky.social & in the super @rcollepardo.bsky.social & Rosen labs:

www.biorxiv.org/content/10.6...

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.

Night Science comes to Denmark this week! I'm giving a (day science) talk on cellular learning on Monday at the Danish Cancer Institute in Copenhagen (1pm). And then on Tuesday we do a full day Night Science workshop there!
www.cancer.dk/danish-cance...

💫 We're hiring! The Computational Biology Facility is looking for a Computational Proteomics Scientist to collaborate on cutting-edge proteomics projects, develop new analytical approaches, and publish impactful research.
Apply by April 12 at: www.fmi.ch/education-ca...