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The EMBO Journal
@embojournal.org
Non-for-profit publication of research in molecular, cell & organismal biology - as part of @embopress.org
Fast-fair-transparent / Open Access / Open Science
Pinned
Final issue 24/25!
Comment: Measuring mitochondrial membrane potential
Highlights: Tau/TDP-43 double-trouble; immunoactive complement C3 fragment
Review: antifungal immunity signaling

Cover: liver capture of bacteria by CRP; Chen et al
link.springer.com/journal/4431...
Hong Cheng and collaborators show how alternative polyadenylation can facilitate muscle differentiation and regeneration: 3’UTR shortening of differentiation-gene mRNAs alleviates their repression by myomiR muscle-specific miRNAs
link.springer.com/article/10.1...
3′UTR shortening alleviates miRNA repression of mRNAs critical for muscle stem cell differentiation - The EMBO Journal
Alternative polyadenylation (APA) modulates gene expression by altering 3′ untranslated region (3′UTR) length. Although 3′UTR lengthening typically accompanies cell differentiation, we unexpectedly ob...
link.springer.com
December 22, 2025 at 12:13 PM
Basonuclin-2 promotes fracture repair through NuRD-dependent chromatin remodeling in periosteal stem cells
Weiguo Zou, Lijun Wang and colleagues
link.springer.com/article/10.1...
Basonuclin-2 promotes fracture repair through NuRD-dependent chromatin remodeling in periosteal stem cells - The EMBO Journal
Bone fracture healing remains a significant challenge in orthopedics, as injury-responsive skeletal stem cell (SSC) populations and the regulatory mechanisms governing SSC activation during nonunion fracture repair remain poorly delineated. This study identifies zinc finger transcription factor basonuclin-2 (BNC2) as a skeletal fracture repair control factor in periosteal stem cells. BNC2 marks quiescent periosteal cells during homeostasis and is significantly upregulated upon injury in mice, driving endochondral ossification post-fracture via clonal expansion. Moreover, knockout of Bnc2 in Prx1-cre+ cells (not Ocn-cre+ osteoblasts or LepR-creER+ BMSCs) resulted in impaired fracture healing, suppressing SSC proliferation. Mechanistically, ATAC-seq revealed that BNC2 deletion reduced chromatin accessibility at promoter regions of proliferation genes, hindering transcriptional activation. Additionally, BNC2 regulates histone H3 acetylation by interacting with the NuRD complex. Pharmacologically inhibition of HDAC1/2 activity partially ameliorated the fracture repair defects observed in Prx1-cre; Bnc2f/f mice. Collectively, we identified BNC2+ cells as a rapidly expanding periosteal cell population inducing endochondral ossification niches during repair, providing potential therapeutic strategies for nonunion fractures.
link.springer.com
December 22, 2025 at 12:12 PM
Reposted by The EMBO Journal
The Dana-Farber Cancer Institute’s multimillion-dollar settlement has been applauded by science integrity sleuths. https://scim.ag/4j3S65W
Misconduct sleuth wins $2.63 million from major cancer institute in $15 million settlement
Data detectives see validation in deal with U.S. government that penalizes Dana-Farber Cancer Institute for misrepresenting data in NIH grant applications
www.science.org
December 17, 2025 at 10:38 PM
Reposted by The EMBO Journal
link.springer.com/article/10.1...

The transaminase-ω-amidase pathway senses oxidative stress to control glutamine metabolism and α-ketoglutarate levels in endothelial cells
The transaminase-ω-amidase pathway senses oxidative stress to control glutamine metabolism and α-ketoglutarate levels in endothelial cells - The EMBO Journal
Oxidative stress is a major driver of cardiovascular disease; however, the fast changes in cellular metabolism caused by short-lived reactive oxygen species (ROS) remain ill-defined. Here, we characte...
link.springer.com
December 18, 2025 at 8:57 AM
Tumor-secreted clusterin promotes cachectic fat wasting via disrupting circadian gene expression and adipogenesis
Yan Liu, Liming Chen et al
link.springer.com/article/10.1...
Tumor-secreted clusterin promotes cachectic fat wasting via disrupting circadian gene expression and adipogenesis - The EMBO Journal
Fat mass loss is a severe complication in cancer-associated cachexia, but its underlying mechanisms remain unclear. This study identifies the tumor-secreted chaperone clusterin (CLU) as a driver of wh...
link.springer.com
December 17, 2025 at 5:06 PM
The transaminase-ω-amidase pathway senses oxidative stress to control glutamine metabolism and α-ketoglutarate levels in endothelial cells
Ralf Brandes, Flavia Rezende and coworkers
link.springer.com/article/10.1...
The transaminase-ω-amidase pathway senses oxidative stress to control glutamine metabolism and α-ketoglutarate levels in endothelial cells - The EMBO Journal
Oxidative stress is a major driver of cardiovascular disease; however, the fast changes in cellular metabolism caused by short-lived reactive oxygen species (ROS) remain ill-defined. Here, we characte...
link.springer.com
December 17, 2025 at 5:01 PM
Widespread mono- and oligoadenylation direct small noncoding RNA maturation versus degradation fates
Jens Lykke-Andersen and colleagues
link.springer.com/article/10.1...
Widespread mono- and oligoadenylation direct small noncoding RNA maturation versus degradation fates - The EMBO Journal
Small noncoding RNAs (sncRNAs) are subject to 3’-end trimming and tailing activities that impact maturation versus degradation decisions during biogenesis. To investigate the dynamics of human sncRNA ...
link.springer.com
December 15, 2025 at 1:21 PM
Reposted by The EMBO Journal
Thanks, Chris! And yep, all going brilliantly - 270 delegates and fantastic talks and posters. Great to see so much support for fundamental discovery science and membrane biology here! Thanks @jcellsci.bsky.social, @embojournal.org and @bscb-official.bsky.social for support!
Haven’t posted for a while but @jezcarlton.bsky.social opening up the annual UK membrane trafficking meeting #UKMT seems like an appropriate reason to post!

Great line up - as ever - with organisers Jez and Chris Stefan introducing a poster session too 🤓
December 15, 2025 at 12:39 PM
A mechanism for controlling mRNA localization to neuronal projections:
Daniel Dominguez, Matthew Taliaferro @jmtali.bsky.social and collaborators implicated ALS-linked TDP-43 as inhibitor of mRNA accumulation in neurites, possibly by promoting their decay
link.springer.com/article/10.1...
TDP-43 directly inhibits mRNA accumulation in neurites through modulation of mRNA stability - The EMBO Journal
The subcellular localization of many mRNAs to neuronal projections allows neurons to efficiently and rapidly react to spatially restricted external cues. However, for most of these RNAs, the mechanism...
link.springer.com
December 15, 2025 at 1:00 PM
Final issue 24/25!
Comment: Measuring mitochondrial membrane potential
Highlights: Tau/TDP-43 double-trouble; immunoactive complement C3 fragment
Review: antifungal immunity signaling

Cover: liver capture of bacteria by CRP; Chen et al
link.springer.com/journal/4431...
December 15, 2025 at 9:44 AM
Weekend reading needed?
Aygul Subkhangulova & Marina Mikhaylova review Golgi apparatus adaptations to neuronal shape and functions
link.springer.com/article/10.1...
The Golgi apparatus: adaptations to neuronal shape and functions - The EMBO Journal
The Golgi apparatus is the central hub of secretory and endosomal pathways in a eukaryotic cell. Despite having a conserved basic organization, the Golgi varies greatly in structure and operation mode...
link.springer.com
December 12, 2025 at 11:56 AM
New methods article:
David Fay et al integrate endogenous TurboID labeling and data-independent acquisition mass-spectrometry for in vivo proximity labeling
link.springer.com/article/10.1...
Integrating endogenous TurboID and data-independent acquisition mass spectrometry for in vivo proximity labeling - The EMBO Journal
Proximity labeling has emerged as a powerful approach for identifying protein–protein interaction networks within living systems, particularly those involving weak or transient associations. Here, we ...
link.springer.com
December 12, 2025 at 10:50 AM
Somatic hypermutation patterns are shaped by both motif position and sequence grammar
Rushad Pavri and coworkers
link.springer.com/article/10.1...
Somatic hypermutation patterns are shaped by both motif position and sequence grammar - The EMBO Journal
Somatic hypermutation (SHM) in variable regions of immunoglobulin genes by activation-induced deaminase (AID) is essential for the maturation of protective antibodies against pathogen and vaccine anti...
link.springer.com
December 12, 2025 at 9:39 AM
Reposted by The EMBO Journal
Sign up now for the EMBO | The Company of Biologists Workshop "Interfacing biophysical and molecular mechanisms of animal #homeostasis and repair" in #Haining, China, 6–10 April 2026.

Deadline: 20 December 2025

https://meetings.embo.org/event/26-homeostasis
#EMBOBiophysicalRepair #EMBOevents 🧪
December 10, 2025 at 6:49 AM
Evolutionary adaptation of bacterial proteomes:
Keigo Fujiwara, Shinobu Chiba et al show that RAPP-like sequences are widely selected against in microbial proteins, while somtimes employed as a ribosome-stalling mechanism in arrest peptides with diverse functions
link.springer.com/article/10.1...
Evolutionary adaptation of bacterial proteomes to translation-impeding sequences - The EMBO Journal
Microbial translation arrest peptides monitor intracellular environments and feedback-regulate downstream gene expression. Previous studies have identified a class of bacterial arrest peptides with C-...
link.springer.com
December 10, 2025 at 8:01 AM
The m6A reader IGF2BP3 cooperates with YBX2 to regulate histone-to-protamine replacement during mouse spermiogenesis
Mei Wang and coworkers
link.springer.com/article/10.1...
December 10, 2025 at 7:59 AM
ERAD without N-glycosylation?
Yeast screen by Leticia Lemus, Veit Goder et al reveals a novel O-mannosyltransferase complex acting on misfolded secretory substrates that lack N-glycans
link.springer.com/article/10.1...
December 5, 2025 at 1:53 PM
Reposted by The EMBO Journal
New paper out!

How can we force HIV genomes out of their capsid shells and what can we learn about HIV biology doing so?

Hint: capsid inhibitors actively re-route nuclear HIV complexes, and expose genomes via intriguing structural effects!
open access:
link.springer.com/article/10.1...
read below
Lenacapavir-induced capsid damage uncovers HIV-1 genomes emanating from nuclear speckles - The EMBO Journal
Following cell entry, HIV-1 capsids enter the nucleus by passage through nuclear pores and reach nuclear speckles with subsequent uncoating of the reverse-transcribed genome and its integration into s...
link.springer.com
December 4, 2025 at 1:58 PM
In ISSUE 23
Highligh: IL-26 - no guts, no glory
Review: initiating autophagy by selective receptors
Method: 3D-SPARK for spatial mapping of DNA synthesis
Resource: senotypes across aging human and mouse tissues
Cover: Sachin Kotak et al @spindlebehavior.bsky.social
link.springer.com/journal/4431...
December 4, 2025 at 7:43 AM
Reposted by The EMBO Journal
Come join us in beautiful Roscoff for this Conference Jacques Monod on Developmental regulation: from molecular to ecological niches
May 18-22, 2026 Roscoff, France
Abstract deadline: January 31, 2026
Apply here: cjm.sb-roscoff.fr/en
December 3, 2025 at 8:00 AM
and here's the link to the article:
www.embopress.org/doi/full/10....
👍 Nice work from Sandra Khau and colleagues from CEPR INSERM Lab (Team “ Pathophysiology of lung infections") in @embojournal.org. They propose a didactic review summarizing the cytosolic receptors and the signaling pathways involved in antifungal innate immunity.
December 3, 2025 at 9:14 AM
Reposted by The EMBO Journal
Wow, researchers from our #SFB1129 are implicated in the Science 2024 Breakthrough of the Year, because they showed that HIV-capsids are flexible and go through nuclear pores. The latest paper on Lenacapavir-induced capsid damage just came out in @embojournal.org

link.springer.com/article/10.1...
December 3, 2025 at 7:53 AM
Lysosomal localization impacts their function in neurons:
Jie Luo and coworkers identify ER-linked AREL1 ubiquitin ligase as regulator of lysosome positioning and acidification via V-ATPase ubiquitination
www.embopress.org/doi/full/10....
December 2, 2025 at 2:17 PM
Lenacapavir-induced capsid damage uncovers HIV-1 genomes emanating from nuclear speckles
By exposing integration-competent genomes, Müller, Kräusslich et al find that reverse transcription can be completed in closed viral capsids without directly inducing uncoating
www.embopress.org/doi/full/10....
December 2, 2025 at 10:47 AM
ALYREF condensation stabilizes m5C-modified PARP10 mRNA and promotes PI3K-AKT signaling in ovarian cancer
www.embopress.org/doi/full/10....
December 2, 2025 at 9:20 AM