@dimitristypas.bsky.social
Senior editor @naturesmb.bsky.social. Views and opinions are personal.
This work presents a structural breakthrough and a conceptual advance, alongside the three relevant recent Nature papers, in our understanding of cytoplamic lattices (CPLs) in mammalian oocytes. CPLs appear to store degradative complexes and poised cytoskeletal complexes to quickly shape eggs.
Nature Structural & Molecular Biology@natsmb.nature.com · 4w agoNew online: Cytoplasmic lattices store developmentally poised degradative and cytoskeletal complexes in mammalian eggs
Excited to see James' Genome-wide Absolute Quantification of Looping paper out in @natsmb.nature.com : www.nature.com/articles/s41... This has been in collaboration with @lucagiorgetti.bsky.social @leonidmirny.bsky.social @zechnerlab.bsky.social labs. Brief thread below on some key updates
Anders Sejr Hansen@andersshansen.bsky.social · 2y agoExcited to share James Jusuf's preprint: By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%) We quantify mESC 36k loops: <loops> are generally rare (2.3%) www.biorxiv.org/content/10.1...
I am on paternity leave but I need to talk about this work by the @andersshansen.bsky.social lab that was published @natsmb.nature.com. The authors provide absolute quantification of chromatin loops across the genome. www.nature.com/articles/s41... Putting actual numbers in E-P, P-P and all loops!
Genome-wide absolute quantification of chromatin looping - Nature Structural & Molecular Biology
By calibrating Micro-C against live-imaging data in mouse embryonic stem cells, Jusuf et al. quantified 65,929 chromatin loops genome-wide, finding that most loops form pairwise interactions with an a...
nature.com
A group of great developers we know has made this entertaining and engaging game: store.steampowered.com/app/2437390/... It's now on playtest, so if you like challenging and fun playshooter games, give it a go!
Enginefall on Steam
Enginefall is a player-driven crafting shooter set on colossal, post-apocalyptic megatrains. Start in the tail alone or with friends as you scavenge, craft, and build your way to First Class. Seize be...
store.steampowered.com
Open Postdoc Position - Giant E3 ligases: mysterious mechanisms & non‑protein substrates. Interested? Join us to uncover how these molecular giants tag lipids, RNAs, sugars beyond proteins, on organelles and pathogens, to defend the cell. Details & Application here www.imp.ac.at/career/open-...
Happy to share our collaborative project with Stephane Marcand, on the protective role of Rap1 at telomeres. It turned out that our favorite protein, MRX, has the ability to measure telomere length, and activate response pathways when telomeres become too short. www.nature.com/articles/s41...
Our story on RNA recognition by Egl-BicD is now published! Also delighted to share the accompanying News & Views article by Florence Besse and Andres Ramos, which beautifully highlights the work. Paper: www.nature.com/articles/s41... News & Views: www.nature.com/articles/s41...
Structural basis for recognition of diverse localizing mRNAs by Egl–BicD - Nature Structural & Molecular Biology
Singh et al. combine cryo-electron microscopy and functional studies to reveal how a single protein complex selects diverse mRNAs for subcellular localization using a combination of shape, positional ...
nature.com
MRC Laboratory of Molecular Biology@mrclmb.ac.uk · 3mo agoThe hidden rules behind mRNA transport. A collaborative study between @simonbullock11.bsky.social & @carter-lab.bsky.social’s groups has found a structural code that explains how cells selectively transport mRNAs. Read more: mrclmb.ac.uk/news-events/... #LMBNews @cellbiol-mrclmb.bsky.social 🧪
So how do mRNAs get localised at specific areas of the cell if there are no unifying sequence or structural patterns? Work from the labs of @simonbullock11.bsky.social @carter-lab.bsky.social @natsmb.nature.com provides insightful answers to this longstanding question. www.nature.com/articles/s41...
Structural basis for recognition of diverse localizing mRNAs by Egl–BicD - Nature Structural & Molecular Biology
Singh et al. combine cryo-electron microscopy and functional studies to reveal how a single protein complex selects diverse mRNAs for subcellular localization using a combination of shape, positional ...
nature.com
www.nature.com/articles/s41... An insighful study, leveraging MINFLUX to study chromatin dynamics by the @andersshansen.bsky.social lab @natsmb.nature.com . I am left wondering what if how we model chromatin with polymer simualtions needs rethinking, but surely many interesting findings here.
Integrated MINFLUX tracking reveals two distinct chromatin dynamics classes across cell types - Nature Structural & Molecular Biology
Chromatin dynamics govern search times between DNA elements. Using integrated MINFLUX imaging, Mazzocca, Narducci, Grosse-Holz and colleagues track chromatin dynamics over seven orders of magnitude in...
nature.com
back to back with related study from Jan-Michael Peters' group PDS5 proteins control genome architecture by limiting the lifetime of cohesin-NIPBL complexes www.cell.com/molecular-ce...
PDS5 proteins control genome architecture by limiting the lifetime of cohesin-NIPBL complexes
PDS5 proteins regulate genome organization by halting cohesin-mediated loop extrusion. Wutz et al. show that PDS5 promotes NIPBL dissociation from cohesin, enabling CTCF boundary formation and proper ...
cell.com
📖 The final version of our paper is out in press Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption authors.elsevier.com/a/1m%7EU03vV... or www.cell.com/molecular-ce...
Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption
Shah, Tortora, et al. show that cells can dial the rate of cohesin loop extrusion by balancing the relative dosage of NIPBL and PDS5. Their models provide a quantitative mechanistic basis for the gene...
cell.com
Elphege Nora Lab at UCSF@elphegenoralab.bsky.social · 12mo agoNew preprint with @gfudenberg.bsky.social We find the rate of cohesin loop extrusion in cells is set by NIPBL dosage and tunes many aspects of chromosome folding. This provides a molecular basis for NIPBL haploinsufficiency in humans. 🧵👇 www.biorxiv.org/content/10.1...
Quantitative biology community: QBMM is back! Line up is just stellar and many abstract selected talks. Apply! 👇
Mike Dorrity@mwdorr.bsky.social · 5mo agoThe time has come for another round of QBMM - we have a fantastic lineup of speakers in genomics, systems biology, and modeling cell dynamics. Check it out! Co-orgs @elowitzlab.bsky.social @tinekelenstra.bsky.social @trayon.bsky.social @savitski-lab.bsky.social and I look forward to seeing you
✉️ Research Briefing by @mamartirenom.bsky.social and I on our recent study, where we employ a new method, METALoci, to explore the 3D regulatory landscape of sex determination. 👏Thanks to @mcgambetta.bsky.social & @dimitristypas.bsky.social for their insights. 👉 Full manuscript: rdcu.be/e5sm2
Nature Structural & Molecular Biology@natsmb.nature.com · 5mo agoICYMI: New online: Charting the 3D regulatory landscape of sex determination with geostatistics
The @natsmb.nature.com March issue is out! Though always interested in proteostasis, in 2026 we have published and will continue to do so relevant content. Our editorial www.nature.com/articles/s41... recaps why the processes and mechanisms of proteostasis continue to interest us.
No stasis in proteostasis - Nature Structural & Molecular Biology
In this issue of Nature Structural & Molecular Biology, we focus on all things protein homeostasis, highlighting a variety of processes, from protein quality control in translation to autophagy.
nature.com
A well-worth-your-time Comment by Dr. Edith Heard, of @crick.ac.uk, and Dr. Gitte Neubauer, one of the founders of Cellzome, now at GSK, is out @natsmb.nature.com. They provide valuable insight into what makes a successful partnership between academia and industry. www.nature.com/articles/s41...
Factors for a successful partnership between academia and industry - Nature Structural & Molecular Biology
The partnership between a leading European research institute, the European Molecular Biology Laboratory (EMBL), and a pharmaceutical company, GSK, has set an example of how to build a successful acad...
nature.com
Tempted to add Metal gifs; that's how cool METALoci sounds! In their recent article @natsmb.nature.com, @dariloops.bsky.social @mamartirenom.bsky.social @jrotwitguez.bsky.social @imotagom.bsky.social and colleagues shed light on sex-determining 3D regulatory hubs. www.nature.com/articles/s41...
Chromatin spatial analysis by METALoci unveils sex-determining 3D regulatory hubs - Nature Structural & Molecular Biology
METALoci, a new three-dimensional genome computational tool, reveals a major rewiring of regulatory interactions during sex determination. By combining this method with transgenic models, the authors ...
nature.com
March kickstarted @natsmb.nature.com focus on Proteostasis. Throughout the year we will be publishing state-of-the-art Reviews and Perspectives. What a better way to start than excellent Review by Michael Rapé and colleagues on the mitochondrial stress response. www.nature.com/articles/s41...
Function and regulation of the mitochondrial stress response - Nature Structural & Molecular Biology
In this review, the authors discuss and contextualize the cellular responses launched after mitochondrial stress and note the importance of the emerging understanding in applying this new knowledge in...
nature.com
Late to the party, but I wanted to highlight a recent @natsmb.nature.com paper by the Hajkova and Vaquerizas labs, which notably advances our understanding of how chromatin organisations regulates gametogenesis. Very enjoyable and insightful work! www.nature.com/articles/s41...
Global reorganization of genome architecture at the transition to gametogenesis - Nature Structural & Molecular Biology
Huang, Rigau and colleagues observe major changes in how DNA is organized in early germ cells before they start developing into sperm or eggs. These results show that germline removes structural ‘memo...
nature.com
An insightful piece worth reading and pondering about by @pedrobeltrao.bsky.social on our pages @natsmb.nature.com on AlphaGenome, www.nature.com/articles/s41...
The AlphaGenome deep learning model predicts effects of non-coding variants - Nature Structural & Molecular Biology
Google’s DeepMind presents AlphaGenome, the largest multimodal DNA sequence model for non-coding regions so far. It advances the state of the art in almost all prediction tasks and offers a new unifie...
nature.com
These scientists and medical experts are taking to social media to counter climate denialism, vaccine scepticism and wellness pseudoscience go.nature.com/4rUFb9C
The science influencers going viral on TikTok to fight misinformation
Scientists and medical experts are countering climate denialism, vaccine scepticism and wellness pseudoscience on social media.
go.nature.com
New online: Interplay between cohesin and RNA polymerase II in regulating chromatin interactions and gene transcription
Interplay between cohesin and RNA polymerase II in regulating chromatin interactions and gene transcription
Nature Structural & Molecular Biology, Published online: 13 January 2026; doi:10.1038/s41594-025-01708-0Kim, Wang, Clow and colleagues show that long-range chromatin loops bringing distal enhancers or super-enhancers together with promoters are cohesin dependent and cell type specific, whereas most short-range and promoter-centric transcriptional loops are cohesin independent and constitutive.
dlvr.it
A striking mechanism in how histone supply is regulated out @natsmb.nature.com which is definitely worth reading, www.nature.com/articles/s41...
Cell-cycle-dependent repression of histone gene transcription by histone H4 - Nature Structural & Molecular Biology
Ahmad et al. show that soluble histone H4 binds at histone genes and acts as a repressor of their expression. These findings suggest that histone H4 is a sensor of ongoing DNA replication. Ongoing chr...
nature.com
Exciting new paper out! @allanaschooley.bsky.social and Sergey Venev led this project that let to the discovery of two chromosome folding programs: one inherited via mitotic chromosomes and one mitotic inherited through the cytoplasm! www.nature.com/articles/s41...
Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm - Nature Cell Biology
Schooley et al. find that mitotically bookmarked loci drive a transient chromosome folding state during G1 entry that is subsequently modulated by factors inherited through the cytoplasm.
nature.com
Happy to see our HT-PELSA paper now published in @natsmb.nature.com 🎊 Big thanks for the constructive review process! 📖Read the manuscript here (www.nature.com/articles/s41...) & check the thread for additional information ⬇️
High-throughput peptide-centric local stability assay extends protein–ligand identification to membrane proteins, tissues and bacteria - Nature Structural & Molecular Biology
Li et al. further develop a high-throughput peptide-centric local stability assay that speeds up sample preparation 100-fold and extends protein–ligand identification to membrane proteins, tissues and...
nature.com
Savitski Lab@savitski-lab.bsky.social · last yr.Want to know how the ligands interact with proteins beyond model cell lines, e.g., in tissues or bacteria? Interested in membrane targets? Check out our High-Throughput PELSA method which allows you do all these cool screenings for dozens of ligands within two hours! www.biorxiv.org/content/10.1...
I'd be remiss not to highlight this study www.nature.com/articles/s41... from the lab of @kevincorbett.bsky.social now out @natsmb.nature.com Always striking to see how inventive bacteria are and what an unorthodox ubiquitylation-like mechanism this may be (probably oxyester dependent).
Mechanistic basis for protein conjugation in a diverged bacterial ubiquitination pathway - Nature Structural & Molecular Biology
Ye et al. define the structure and mechanisms of a bacterial pathway that performs ubiquitination-like protein conjugation, revealing new insights into the evolution and biological roles of ubiquitina...
nature.com
Very glad to see this work www.nature.com/articles/s41... by the @savitski-lab.bsky.social out @natsmb.nature.com High hopes that HT-PELSA will be a very useful tool to study protein-ligand interactions.
High-throughput peptide-centric local stability assay extends protein–ligand identification to membrane proteins, tissues and bacteria - Nature Structural & Molecular Biology
Li et al. further develop a high-throughput peptide-centric local stability assay that speeds up sample preparation 100-fold and extends protein–ligand identification to membrane proteins, tissues and...
nature.com
Very happy that this insightful story by @andersshansen.bsky.social is out @natsmb.nature.com, www.nature.com/articles/s41.... A nice press release explaining the progress also from the home institute @mitdeptofbe.bsky.social here: news.mit.edu/2025/surpris...
Dynamics of microcompartment formation at the mitosis-to-G1 transition - Nature Structural & Molecular Biology
Goel et al. produce high-resolution three-dimensional genome structure mapping from mitosis to G1 phase to show unseen interactions between enhancers and promoters in prometaphase. Polymer modeling in...
nature.com
The @natsmb.nature.com Returning Home series is now complete, www.nature.com/nsmb/article... with the final piece by Hugo Sepulveda on his return to Chile published. It has been a joy to work on this series and, if our readers appreciate these pieces, I hope that it may continue or evolve!
World View | Nature Structural & Molecular Biology
Browse the archive of articles on Nature Structural & Molecular Biology
nature.com
We @natsmb.nature.com aim to provide a stage for our readers. That includes voicing their experiences and perspectives. We hope this makes us a more attuned and representative outlet for our communities. We launched new content to do so and explain why in our editorial www.nature.com/articles/s41...
Voices of NSMB - Nature Structural & Molecular Biology
We are delighted to introduce additional content types at Nature Structural & Molecular Biology, which allow us to offer more discussion of societal and scientific issues, better represent the uni...
nature.com
here is the correct link: ista.ac.at/en/job/tenur...
Tenure-based Research Staff Scientist Position in Computational Structural Biology
ISTA (www.ista.ac.at) is seeking a highly skilled Staff Scientist in Computational Structural Biology to support and advance the Institute’s structural biology research through the development and imp...
ista.ac.at