Have you ever wondered how cells in developing embryos manage to squeeze through tiny spaces? And how do they cope with mechanical stresses imposed by surrounding tissues? Check out our paper, now out @natcellbio.nature.com : www.nature.com/articles/s41...

In vivo DNA damage protection during cell migration across confining embryonic tissue environments - Nature Cell Biology

Häkkinen et al. show that zebrafish neural crest cells encounter increased tissue-scale confinement along the body axis. Despite nuclear deformation, migrating neural crest cells experience neither nu...

nature.com

Article: RAPseq enables large-scale identification of RBP–RNA interactions and reveals essentials of post-transcriptional gene regulation #research supported by Knut and Alice Wallenberg Foundation @claudiakutter.bsky.social #science #genetics tinyurl.com/ymrd8zxr

RAPseq enables large-scale identification of RBP–RNA interactions and reveals essentials of post-transcriptional gene regulation

Abstract. Over the past decade, thousands of putative human RNA-binding proteins (RBPs) have been identified, increasing the need for methods that define t

tinyurl.com

How do cells sense tissue damage - and help their neighbors withstand it? Our new paper on the redox-sensitive 5-oxoETE lipid pathway shines light on this question. A huge THANK-YOU to all the colleagues and funding bodies that made this work possible! www.nature.com/articles/s41...

5-oxoETE links redox control of epithelial damage detection and resilience - Nature

The DHRS7–OXER1 pathway links oxidative stress to immunity and tissue resilience by modulating 5-oxoETE via NADP+–NADPH, activating OXER1 to recruit antimicrobial cells and induce NUDIX enzymes t...

nature.com

#RNA Framework 2.9.8 is out! Check the full CHANGELOG: github.com/dincarnato/R.... Get the latest version at: github.com/dincarnato/R... This release features a major renovation of the engine. A few highlights in a short thread (1/n).

RNAFramework/CHANGELOG.md at master · dincarnato/RNAFramework

RNA structure probing and post-transcriptional modifications mapping high-throughput data analysis - dincarnato/RNAFramework

github.com

Our latest study about how stratified myosin motors at the plasma membrane drive distinct nanoscale clusters that organize into segregated mesoscale active emulsions is out in Science Advances! Read on to find out more| Science Advances www.science.org/doi/10.1126/...

📢🧬Join us on Wednesday, Oct 7th for the next #FragileNucleosome seminar to hear exciting chromatin stories from Moonmoon and Paul! If you still haven't registered for our series: us06web.zoom.us/webinar/regi...

Excited to share two recent collaborative works from the lab related to cell surface RNA binding proteins (csRBPs) in cancer.

😮 Whole- #transcriptome -scale isoform-resolved spatial imaging of single #cells in tissues: Cell www.cell.com/cell/fulltex...

Whole-transcriptome-scale isoform-resolved spatial imaging of single cells in tissues

RT&T-AMP-MERFISH enables whole-transcriptome-scale, isoform-resolved spatial imaging of single cells in intact tissues and reveals how gene programs and transcript isoform usage vary across cell types...

cell.com

Photolabile oligonucleotides with topological light gradients enable spatially resolved single-cell transcriptomics and epigenomics - @ucsantabarbara.bsky.social www.nature.com/articles/s41...

Photolabile oligonucleotides with topological light gradients enable spatially resolved single-cell transcriptomics and epigenomics - Nature Biotechnology

A photolabile oligonucleotide system enables spatially resolved single-cell measurements to show how the epigenome regulates gene expression.

nature.com

Arp2/3 iso-complexes strike again! Axonal actin ring assembly and maintenance involves different iso-complexes that change expression during neuronal maturation 🎉 Great collaboration with Ana Rita Costa & Monica Sousa @ i3S in Porto www.i3s.up.pt/research-gro... www.science.org/doi/10.1126/...

Distinct Arp2/3 isocomplexes drive axonal actin ring assembly and integrity

The actin-related protein 2/3 (Arp2/3) complex is a central nucleator of branched actin filaments, essential for numerous cellular processes. Using superresolution imaging, we demonstrate that Arp2/3 ...

science.org

Zeng et al, 2026. Transcription factors read a second regulatory code in chromatin www.biorxiv.org/content/10.6... "our findings establish that TFs interpret two complementary layers of genomic information: the primary DNA sequence and a second code written into the nucleosome architecture"

Maladaptive trained immunity as a hematopoietic stem cell driver of inflammaging www.nature.com/articles/s43...

Maladaptive trained immunity as a hematopoietic stem cell driver of inflammaging - Nature Aging

A new study reveals that aging hematopoietic stem cells trigger a form of innate immune memory, known as trained immunity, that fuels the chronic low-grade inflammation that underlies age-related phys...

nature.com

See you on Wednesday!

FragileNucleosome@fnucleosome.bsky.social · 3w ago

📢🧬join us on Wednesday, Sept 23rd for the next #FNucleosome seminar to hear exciting chromatin/transcription stories from Oscar Campos and @giacomodonatijd.bsky.social! Register here: us06web.zoom.us/webinar/regi...

Interesting article on how different strains of the same species use different strategies to adapt to the intestinal environment. Additionally: extremely nice visual presentation and lovely color palette!

Nature Microbiology@natmicrobiol.nature.com · 3w ago

Out Now! In vivo CRISPRi screens reveal Escherichia coli functional adaptations in the mouse gut #MicroSky

How do epithelial cells make a lumen as they polarize? We have some exciting new answers to this long standing question. Check out our new paper in which we show that lumen initiation is driven by large vacuoles that deliver a pre-assembled apical cortex to the AMIS: www.nature.com/articles/s41...

Bulk delivery of a preassembled apical surface initiates epithelial lumen formation - Nature Communications

Epithelial lumen formation is fundamental to organ development, yet how apical surfaces first emerge remains unclear. Ghosh, Martin, and Chen et al., show that lumen initiation is driven via bulk deli...

nature.com

Everything you wanted to know about single-molecule epigenomics but were too afraid to ask! Wonderful to co-write (h/t ENORMOUS lift by @arnaudkr.bsky.social) this primer on our nascent field. Also, a 💯 example of wonderful colleagues building something *together*, not in competition =)

A practical guide to studying genome function using single-molecule genomics

Nature Reviews Molecular Cell Biology - Single-molecule genomics methods are used to study the activity of regulatory factors on individual DNA molecules genome-wide, thereby enabling...

nature.com

Cngratulations to @JoanaESaraiva and Sandra from the lab on their new review @embojournal.org we discussed few points about the coordination of cell state transitions in #embryos and #regeneration Also welcome @joanaesaraiva.bsky.social to BlueSky! link.springer.com/article/10.1...

www.biorxiv.org/content/10.6... Mechanochemical cues control the coupling of metabolic and migratory patterns in cancer

🧬🔬 Why are enhancers transcribed and how does that impact gene regulation? I’m really excited to share our new paper in @science.org showing that noncoding RNAs control the timing of gene activation in embryos. With Mike Levine #ScienceResearch @columbiamed.bsky.social A few highlights below... 🧵👇

Noncoding transcription controls the developmental dynamics of long-range gene regulation

The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely ...

science.org

🔬 New publication, now out in #ScienceImmunology led by Mathieu Deygas in Pablo Vargas team, shows that Adaptive motility enables neutrophils to rapidly navigate confined capillaries 📰 To read the article: tinyurl.com/52vxuhmp

Incredibly happy to share the first publication from our lab, now published in Nature Cell Biology! 🎉 How do cells coordinate RNA processing with nuclear organization and the cell cycle? www.nature.com/articles/s41...

It was great working with students Kun and Ryan and @hannahlong.bsky.social, combing the literature to try and find examples of bona fide disease-causing variants in non-coding elements - promoters, enhancers and silencers. www.nature.com/articles/s41...

Mechanisms underlying disease-causing variants in promoters and enhancers - Nature Genetics

This Review discusses how rare-disease-causing variants in the noncoding genome impact gene regulation, why these examples are so few and how new approaches could accelerate discovery of noncoding var...

nature.com

@lsprahl.bsky.social and Ronald Canlla in the lab just published a detailed study on remote-controlled epithelial budding morphogenesis. We can direct budding, tubule elongation, and perhaps branching in human kidney organoids via a light-activated RET receptor. www.biorxiv.org/content/10.6...

Very happy to share my postdoc paper is out now in @natcellbio.nature.com titled "Tissue flow acts as a guidance cue for immune cell polarization and directional migration". If you love imaging and immune cells, this is for you! #microscopymonday www.nature.com/articles/s41... A 🧵: 1/n

☕ @anhhle2702.bsky.social @mayorlab.bsky.social & co show that in Xenopus embryos, local ectodermal tissue flows provide a directional cue that polarizes and guides embryonic myeloid cells migration via cell-on-cell interactions. www.nature.com/articles/s41...

Tissue flow acts as a guidance cue for immune cell polarization and directional migration - Nature Cell Biology

Le et al. show that in Xenopus embryos, local ectodermal tissue flows provide a directional cue that polarizes and guides embryonic myeloid cells migration via cell-on-cell interactions.

nature.com

Dynamic control of cell state transitions during tissue morphogenesis Elias Barriga et al @eliasbarrigalab.bsky.social review how gene expression, chromatin modifications & microenvironmental biophysical factors contribute to robust coordination of morphogenesis link.springer.com/article/10.1...

Extrinsic factors can create a local tissue environment that encourages restoration @science.org www.science.org/doi/10.1126/... www.science.org/doi/10.1126/... @canaztekin.bsky.social www.science.org/doi/10.1126/... @storerlab.bsky.social @scicambridge.bsky.social @kevinchalut.bsky.social

Online today 👉 Dermal papillary #fibroblasts promote persistent granulation tissue formation in #JunctionalEpidermolysisBullosa ➡️ doi.org/10.1038/s44321-026-00475-9 By M. Khan, M. Caley, E. Rognoni & collaborators at @qmul.bsky.social Read also www.qmul.ac.uk/news/latest-...

🚨New preprint alert 🚨 "Pancreatic cancer cells breach endothelial barriers through protrusion-driven invasion or endothelial retraction" www.biorxiv.org/content/10.6...

wait, wait, what ????? protein-coding chimeric mRNAs 🤯 www.nature.com/articles/s41...

Functional chimeric mRNAs encode proteins in mammalian immunity - Nature

Inflammation induces interchromosomal DNA interactions that bring parent genes into close proximity, facilitating the formation of chimeric mRNAs that encode physiologically relevant, functional prote...

nature.com