bims-ginsta Biomed News
on Genome instability
Issue of 2025–11–16
28 papers selected by
Jinrong Hu, National University of Singapore
  1. Endothelial-zippering proceeds by sensing heartbeat-driven force through cadherin-6 during heart-vessel connection in zebrafish.
  2. Capturing trophectoderm-like stem cells enables step-wisely remodeling of placental development.
  3. Alternative start codon selection shapes mitochondrial function and rare human diseases.
  4. Reprogramming of H3K36me2 guides lineage-specific post-implantation de novo DNA methylation.
  5. SOX2 phosphorylation during mitosis limits genomic damage.
  6. TSLP links intestinal nutrient sensing with amplification of the ILC2-tuft cell circuit.
  7. Gene therapy CM-YAPon protects the mouse heart from myocardial infarction.
  8. Phase separation to buffer growth-mediated dilution in synthetic circuits.
  9. Uniform dynamics of cohesin-mediated loop extrusion in living human cells.
  10. Swimming motions evoke Piezo1-dependent Ca2+ events in vascular endothelial cells of larval zebrafish.
  11. Blocking nuclear receptor Nr4a3 unlocks the senescence barrier to promote direct cardiac reprogramming.
  12. Different repair pathways support intact or truncated insertions by R2 retrotransposon protein.
  13. A role for human senataxin in contending with pausing and backtracking during transcript elongation.
  14. Alterations in peroxisome-mitochondria interplay in skeletal muscle accelerate muscle dysfunction.
  15. Megabase-scale loss of heterozygosity provoked by CRISPR-Cas9 DNA double-strand breaks.
  16. Actomyosin contractility and a threshold of cadherin cell adhesion are required during tissue fusion.
  17. In situ structural mechanism of epothilone-B-induced CNS axon regeneration.
  18. iPEX enables micrometre-resolution deep spatial proteomics via tissue expansion.
  19. Nanoscale domains govern local diffusion and ageing within fused-in-sarcoma condensates.
  20. Adapting plasma membrane for mitotic cell rounding through Aurora A phosphorylation of numb.
  21. Pair-rule-like transcription patterns during neural tube closure in a proto-vertebrate.
  22. Erythroid precursors regulate local oxygen tension and repair outcomes in the bone marrow niche.
  23. Genetic and chromatin regulation of Pvt1 monoallelic expression.
  24. Signal control during tissue regeneration in adult animals.
  25. Branched actin networks mediate macrophage-dependent host-microbiota homeostasis.
  26. iGlucoSnFR2: A genetically encoded fluorescent sensor for measuring intracellular or extracellular glucose in vivo in mouse brain.
  27. Dynamic dosage changes in X-linked transposable elements during mammalian dosage compensation.
  28. KIF18A promotes chromosome congression in cooperation with CENP-E downstream of CENP-C.
  1. Dev Cell. 2025 Nov 11. pii: S1534-5807(25)00662-8. [Epub ahead of print]
    Endothelial-zippering proceeds by sensing heartbeat-driven force through cadherin-6 during heart-vessel connection in zebrafish.
    Moe Fukumoto, Haruko Watanabe-Takano, Hajime Fukui, Ayano Chiba, Keisuke Sako, Hiroyuki Nakajima, Naoki Mochizuki.
      The connection between the heart and great vessels established during embryogenesis is essential for circulation. However, how great veins adhere to the endocardium lining the inside lumen of the beating heart remains unknown. Here, using zebrafish, we demonstrate that the endocardium and great veins are sealed in a zipper-closing manner outside the beating heart. The gradual elongation of the endocardium, driven by convergent extension, organized this adhesion by pulling venous endothelial cells (ECs) along the anterior-posterior axis. Time-specific manipulation of the heart rate revealed that this endocardial elongation proceeds against heartbeat-driven force. From time-lapse imaging of adherens junctions, which would counterbalance mechanical forces, we found a specific contribution of cadherin-6 instead of cadherin-5 in sensing endocardium-specific mechanical force. This specificity was confirmed by the depletion of cadherin-6 that caused endocardium deformation. Altogether, we propose that cadherin-6-mediated EC-zippering updates the understanding of cadherin usage in dynamic morphogenesis.
    Keywords:  cadherin; common cardinal vein; convergent extension; endocardium; heartbeat; intercellular adhesion; zippering
    DOI:  https://doi.org/10.1016/j.devcel.2025.10.011
  2. Protein Cell. 2025 Nov 10. pii: pwaf098. [Epub ahead of print]
    Capturing trophectoderm-like stem cells enables step-wisely remodeling of placental development.
    Xinyi Jia, Bing Peng, Hongjin Zhao, Chunhui Wang, Aibin He, Wei Tao, Peng Du.
      The trophectoderm produced from totipotent blastomeres initiates trophoblast development, while placental deficiencies can cause pregnancy disorders. Yet, a culture system that fully recapitulates the entire placenta development is still lacking, greatly limiting related studies. Here, we captured mouse trophectoderm-like stem cells (TELSCs), which can give rise to all trophoblast lineages and be applied to generate trophoblast organoids. We achieved the induction and maintenance of TELSCs from totipotent blastomere-like stem cells or early embryos through a Hippo-YAP/Notch-to-TGFβ1 signaling switch. At the molecular level, TELSCs resemble E4.5 trophectoderm and are distinct from all previously known trophoblast-like stem cells. Functionally, TELSCs can generate all trophoblast lineages in both teratoma and chimera assays. We further applied TELSCs to generate trophoblast organoids containing various mature trophoblasts and a self-renewing extraembryonic ectoderm (ExE)-like progenitor population. Interestingly, we observed transiently formed rosette-like structures that rely on Itgb1, which are essential to induce ExE-like progenitors and to generate organoids eventually. Thus, the capture of TELSCs enables comprehensive insights into placental development.
    Keywords:  embryonic development; epigenetic; organoid; placenta; pregnancy; stem cell; totipotency; transcriptomic; trophectoderm; trophoblast
    DOI:  https://doi.org/10.1093/procel/pwaf098
  3. Mol Cell. 2025 Nov 07. pii: S1097-2765(25)00854-8. [Epub ahead of print]
    Alternative start codon selection shapes mitochondrial function and rare human diseases.
    Jimmy Ly, Matteo Di Bernardo, Yi Fei Tao, Ekaterina Khalizeva, Christopher J Giuliano, Sebastian Lourido, Mark D Fleming, Iain M Cheeseman.
      Rare genetic diseases collectively affect millions of individuals. A common target of many rare diseases is the mitochondria, intracellular organelles that originated through endosymbiosis. Eukaryotic cells require related proteins to function both within the mitochondria and in the host cell. By analyzing N-terminal protein isoforms generated through alternative start codon selection, we identify hundreds of differentially localized isoform pairs, including dual-localized isoforms that are essential for both mitochondrial and host cell function. Subsets of dual mitochondria-localized isoforms emerged during early eukaryotic evolution, coinciding with mitochondrial endosymbiosis. Importantly, we identify dozens of rare disease alleles that affect these alternative protein variants with unique molecular and clinical consequences. Alternative start codon selection can bypass pathogenic nonsense and frameshift mutations, thereby selectively eliminating specific isoforms, which we term isoform-selective alleles (ISAs). Together, our findings illuminate the evolutionary and pathological relevance of alternative translation, offering insights into the molecular basis of rare human diseases.
    Keywords:  TRNT1; alternative N-terminal isoforms; alternative translation; mitochondria; proteomic diversity; rare diseases; start codon selection; translation initiation
    DOI:  https://doi.org/10.1016/j.molcel.2025.10.013
  4. Nat Cell Biol. 2025 Nov 11.
    Reprogramming of H3K36me2 guides lineage-specific post-implantation de novo DNA methylation.
    Xukun Lu, Lijuan Wang, Bofeng Liu, Xiaoyu Hu, Zhengmao Wang, Ling Liu, Guang Yu, Lijun Dong, Feng Kong, Qiang Fan, Yu Zhang, Wei Xie.
      In mammals, DNA methylation is re-established after implantation following post-fertilization global erasure. Yet, the underlying mechanism remains elusive. Here we investigate H3K36me2 reprogramming in mouse early development and its role in post-implantation DNA methylation re-establishment. In oocytes, H3K36me2 accumulates in gene bodies upon transcription silencing and partially persists to the eight-cell stage. De novo H3K36me2 occurs at enhancers after zygotic genome activation, before spreading genome-wide after implantation, except on the inactive X chromosome. Mutation of the H3K36me2 methyltransferase NSD1 compromises global DNA methylation after implantation preferentially in extra-embryonic lineages and that at methylation-prone promoters, including those of germline-specific genes. However, DNA methylation establishment partially bypasses H3K36me2 through upregulated DNMT3B, a 'leaky' H3K36me2/3 reader. This contrasts with DNMT3A, which strictly requires H3K36me2/3 for DNA methylation through its PWWP domain. Finally, DNA methylation valleys escape de novo DNA methylation via PRC1/H2AK119ub1-mediated H3K36me2 exclusion. Thus, H3K36me2 reprogramming regulates lineage- and locus-specific post-implantation DNA methylation establishment.
    DOI:  https://doi.org/10.1038/s41556-025-01805-8
  5. Genes Dev. 2025 Nov 10.
    SOX2 phosphorylation during mitosis limits genomic damage.
    Charles A C Williams, Dounia Djeghloul, Nicolas Veland, Alhafidz Hamdan, Maria Kalantzaki, Erika Lo, Robert Illingworth, Alex Von Kriegsheim, Amanda G Fisher, Abdenour Soufi, Steven M Pollard.
      Pioneer transcription factors (TFs) such as SOX2 play critical roles in the control of stem cell identity and are dysregulated in many human cancers. For example, SOX2 regulates the self-renewal of neural stem cells (NSCs) and is typically highly expressed in glioblastoma stem cells (GSCs), where it is known to induce an immature NSC-like state. Here, we explored the regulation of SOX2 by phosphorylation during NSC division and identified an unexpected role for excessive SOX2 pioneer activity in driving mitotic damage. We found that SOX2 phosphorylation during mitosis is a key switch that prevents promiscuous chromatin binding across the genome. Without this regulatory control, excessive SOX2 in mitosis triggers chromatin opening, resulting in increased mitotic transit times and increased chromosomal damage. Therefore, elevated levels of SOX2 in cancers may have dual oncogenic roles: inducing stemness during interphase via its well-known transcriptional roles but simultaneously promoting chromosomal disruptions through unconstrained pioneer factor activity.
    Keywords:  DNA damage; SOX2; heterochromatin; mitosis; mitotic bookmarking; neural stem cell; phosphorylation; transcription
    DOI:  https://doi.org/10.1101/gad.352664.125
  6. Nat Immunol. 2025 Nov 12.
    TSLP links intestinal nutrient sensing with amplification of the ILC2-tuft cell circuit.
    Chang Liao, Elvira Mennillo, Michael G Kattah, Ming Ji, Zhi-En Wang, Daniel J Drucker, Hong-Erh Liang, Richard M Locksley.
      Group 2 innate lymphocytes (ILC2s) are prevalent in small intestine but their role during homeostasis is unclear. Here we show that thymic stromal lymphopoietin (TSLP)-a cytokine implicated in ILC2 activation-is expressed constitutively in subepithelial fibroblasts, including telocytes and crypt-associated trophocytes, which are specialized fibroblasts necessary to sustain epithelial identity. Feeding increases TSLP and induces ILC2 type 2 cytokines that are attenuated by deletion of TSLP in fibroblasts or TSLP receptor on ILC2s. Both mouse and human intestinal fibroblasts express receptors for glucagon-like peptide-2 (GLP-2)-an intestinotrophic growth factor released by enteroendocrine cells following food intake. GLP-2 promotes intestinal TSLP in mouse and human intestinal fibroblasts, and TSLP-dependent ILC2 activation and tuft cell hyperplasia in mice, thus linking nutrient detection with ILC2-mediated amplification of the tuft cell chemosensory circuit that promotes epithelial surveillance of ingested cargo.
    DOI:  https://doi.org/10.1038/s41590-025-02328-y
  7. Nat Cardiovasc Res. 2025 Nov 13.
    Gene therapy CM-YAPon protects the mouse heart from myocardial infarction.
    Fansen Meng, Jeffrey D Steimle, Elizabeth Straight, Rich G Li, Yuka Morikawa, Zohaib Iqbal, Bing Xie, Jun Wang, Wyatt G Paltzer, Yi Zhao, Chang-Ru Tsai, Lin Liu, Maggie Lim, Rita A Schack, Daniel Ramirez, Katherine Carlson, Vaibhav Deshmukh, Jason M Karch, Robia G Pautler, Xiao Li, James F Martin.
      Myocardial infarction (MI) affects millions of people worldwide, causing irreversible injury to the heart and impairing cardiac function1. In both mouse and pig MI models, activating YAP in cardiomyocytes (CMs) stimulates regenerative repair2,3. Here we develop an adeno-associated virus 9-based therapy, termed CM-YAPon, which enables transient expression of an active YAP variant (YAP5SA) in CMs after exposure to the small molecule LMI070. A single LMI070 dose in mice triggers YAP5SA expression, CM cell cycle reentry and reprogramming of the cardiac microenvironment. YAP5SA induction after MI rapidly improves cardiac function while pre-MI induction confers cardioprotection and reduces cell death across multiple cardiac cell types. These findings reveal the therapeutic potential of reversible gene activation for ischemic heart disease.
    DOI:  https://doi.org/10.1038/s44161-025-00744-9
  8. Cell. 2025 Nov 07. pii: S0092-8674(25)01182-1. [Epub ahead of print]
    Phase separation to buffer growth-mediated dilution in synthetic circuits.
    Rong Zhang, Wangfei Yang, Rixin Zhang, Amanda Godar, Sadikshya Rijal, Abdelrahaman Youssef, David R Nielsen, Wenwei Zheng, Xiao-Jun Tian.
      Fluctuations in host cell growth pose a critical challenge for maintaining reliable function in synthetic gene circuits. Growth-mediated dilution causes a global reduction in circuit component concentrations, which can significantly destabilize circuit behavior. However, effective strategies to counteract this problem remain lacking. Here, we present a phase-separation-based strategy to directly mitigate dilution effects. By fusing transcription factors (TFs) to intrinsically disordered regions (IDRs), we drive the formation of transcriptional condensates that concentrate TFs at their target promoters. These condensates buffer against prolonged rapid dilution of TF concentration and preserve bistable memory in self-activation circuits across variable growth conditions. We further show that this approach improves production efficiency in a cinnamic acid biosynthesis pathway. Together, our results establish liquid-liquid phase separation as an emerging design principle for constructing resilient synthetic circuits that maintain robust performance under dynamic growth conditions.
    Keywords:  buffering capacity; circuit memory retention; circuit robustness; condensate-promoter co-localization; gene circuit stability; spatial control of gene expression; synthetic biology; synthetic condensate; synthetic gene circuit
    DOI:  https://doi.org/10.1016/j.cell.2025.10.017
  9. Nat Genet. 2025 Nov 14.
    Uniform dynamics of cohesin-mediated loop extrusion in living human cells.
    Thomas Sabaté, Benoît Lelandais, Marie-Cécile Robert, Michael Szalay, Jean-Yves Tinevez, Edouard Bertrand, Christophe Zimmer.
      Most animal genomes are partitioned into topologically associating domains (TADs), created by cohesin-mediated loop extrusion and defined by convergently oriented CCCTC-binding factor (CTCF) sites. The dynamics of loop extrusion and its regulation remain poorly characterized in vivo. Here we tracked the motion of TAD anchors in living human cells to visualize and quantify cohesin-dependent loop extrusion across multiple endogenous genomic regions. We show that TADs are dynamic structures whose anchors are brought in proximity about once per hour and for 6-19 min (~16% of the time). Moreover, TADs are continuously extruded by multiple cohesin complexes. Remarkably, despite strong differences in Hi-C patterns across chromatin regions, their dynamics is consistent with the same density, residence time and speed of cohesin. Our results suggest that TAD dynamics is primarily governed by the location and affinity of CTCF sites, enabling genome-wide predictive models of cohesin-dependent chromatin interactions.
    DOI:  https://doi.org/10.1038/s41588-025-02406-9
  10. Curr Biol. 2025 Nov 13. pii: S0960-9822(25)01400-9. [Epub ahead of print]
    Swimming motions evoke Piezo1-dependent Ca2+ events in vascular endothelial cells of larval zebrafish.
    Bill Z Jia, Xin Tang, Marlies P Rossmann, Leonard I Zon, Florian Engert, Adam E Cohen.
      Calcium signaling in the vascular endothelium regulates vascular growth,1,2 immune responses,3 and tone.4 Endothelial cells (ECs) are mechanosensitive,5,6,7 and flow-driven shear stress is widely assumed to be the main trigger for EC Ca2+ responses in vivo.8,9,10 Vascular ECs experience a range of distinct mechanical forces in vivo.1,2,6,7 These include shear stress from blood flow, radial stretch from blood pressure, circumferential stretch from smooth-muscle-mediated vasodilation, and, in some parts of the animal, axial stretch from skeletal-muscle-mediated body motion6,11 In principle, these different modes of stimulation could activate distinct signaling pathways and cellular responses.12,13,14 Mechanical perturbation experiments on cultured cells or explants typically impose stresses that differ in magnitude and direction from the forces encountered in vivo,5,15,16 and thus they cannot readily be used to assign biochemical responses to specific sources of mechanical stress in vivo. Here, we show that, in larval zebrafish, the dominant trigger for vascular endothelial Ca2+ events comes from body motion, not heartbeat-driven blood flow. Through a series of pharmacological and mechanical perturbations, we showed that body motion is necessary and sufficient to induce endothelial Ca2+ events, while neither neural activity nor blood circulation is necessary or sufficient. CRISPR-Cas9 knockout and temporally restricted photomorpholino knockdown identified Piezo1 as necessary for the rapid, mechanically evoked EC Ca2+ events.10,17 Our results demonstrate that swimming-induced tissue motion is an important driver of endothelial Ca2+ dynamics in larval zebrafish.
    Keywords:  behavior; blood flow; body motion; calcium; ion channels; mechanotransduction
    DOI:  https://doi.org/10.1016/j.cub.2025.10.053
  11. Sci Adv. 2025 Nov 14. 11(46): eadz4847
    Blocking nuclear receptor Nr4a3 unlocks the senescence barrier to promote direct cardiac reprogramming.
    Mengxin Liu, Zhangyi Yu, Zechun He, Zhigao Zhou, Jie Liu, Lanbing Liu, Xin Wu, Jun Li, Yuanru Huang, Lilin Xiang, Xiangjie Kong, Zhibing Lu, Li Wang.
      Direct reprogramming of fibroblasts into induced cardiomyocytes (iCMs) offers a regenerative strategy for heart repair, but efficiency declines in adult and aged cells. Transcriptomic and epigenetic profiling identified cellular senescence as a major barrier limiting cardiac fibroblast (CF) plasticity and cardiogenic conversion. Postneonatal fibroblasts exhibited impaired activation of cardiac gene programs and persistent expression of fibrotic and inflammatory signatures. A loss-of-function screen identified Nr4a3 as a central repressor. Nr4a3 overexpression promoted senescence and suppressed iCM induction, whereas knockdown enhanced reprogramming in murine and human senescent CFs. Mechanistically, Nr4a3 depletion remodeled the chromatin landscape from a fibrotic and inflammatory state to a regenerative cardiac program. Blocking downstream Cxcl14 restored reprogramming in refractory fibroblasts. In vivo, Nr4a3 knockdown improved heart function following myocardial infarction. These findings established cellular senescence as a major barrier to cardiac reprogramming and identified Nr4a3 and its effectors as potential targets to enhance heart regeneration.
    DOI:  https://doi.org/10.1126/sciadv.adz4847
  12. Science. 2025 Nov 13. eadz3121
    Different repair pathways support intact or truncated insertions by R2 retrotransposon protein.
    Jeremy J R McIntyre, Connor A Horton, Kathleen Collins.
      Non-LTR retrotransposon proteins copy their RNA template into a genome via coordinated nicking and reverse transcriptase activities of target-primed reverse transcription. Mechanisms by which the first-strand cDNA becomes stably inserted duplex, including requirements for junction formation at the cDNA 3' end and second-strand synthesis, are unknown. We screened for cellular factors that influence site-specific transgene synthesis into the human genome by an R2 retrotransposon protein. We discover that insertion lengths and junction signatures differ based on alternative repair processes involving ATR-dependent Polymerase θ end-joining, 53BP1-directed Shieldin/CST-Polα-primase fill-in synthesis, or limited strand annealing dependent on CtIP-MRN. These insights shed light on how genome-primed cDNA synthesis by a non-LTR retrotransposon protein can support stable new gene insertion, with major implications for native retrotransposon mobility and genome engineering.
    DOI:  https://doi.org/10.1126/science.adz3121
  13. Mol Cell. 2025 Nov 12. pii: S1097-2765(25)00860-3. [Epub ahead of print]
    A role for human senataxin in contending with pausing and backtracking during transcript elongation.
    Zhong Han, Shiqing Fu, Jens Vilstrup Johansen, David Lopez Martinez, Jiangman Lou, Thierry Boissière, Dandan He, Daniel Blears, Anouk M Olthof, A Barbara Dirac-Svejstrup, Jesper Q Svejstrup.
      Senataxin (SETX) regulates RNA polymerase II (RNAPII) transcription and helps maintain genome stability, at least partly by suppressing R-loops. However, despite its importance in human disease, the precise function of SETX has remained unclear. Employing the degradation tag system for acute protein depletion, we demonstrate that SETX loss perturbs RNAPII elongation but does not markedly influence transcription termination at the end of genes. Through in vitro reconstitution of elongation, we show that SETX uses ATP-dependent RNA translocation to drive RNAPII forward across challenging DNA sequences, reminiscent of how bacterial ribosomes help mitigate RNAP pausing. In vivo, SETX depletion accordingly results in increased RNAPII pausing or backtracking, particularly during early elongation, with a corresponding, time-dependent local increase in R-loop formation. Together, these findings redefine our understanding of SETX's role in transcription and provide a mechanistic framework for interpreting R-loops and the causes of neurological disorders associated with SETX mutation.
    Keywords:  DNA-RNA hybrid; DSIF; PAF1C; R-loop; RNA polymerase II; SETX; SPT5; SPT6; Sen1; TFIIS; biochemical reconstitution; genome-wide analysis; senataxin; transcript elongation; transcription termination
    DOI:  https://doi.org/10.1016/j.molcel.2025.10.019
  14. Nat Commun. 2025 Nov 10. 16(1): 9868
    Alterations in peroxisome-mitochondria interplay in skeletal muscle accelerate muscle dysfunction.
    Marco Scalabrin, Eloisa Turco, Ilaria Davigo, Riccardo Filadi, Leonardo Nogara, Gaia Gherardi, Lucia Barazzuol, Andrea Armani, Giulia Trani, Samuele Negro, Anais Franco-Romero, Yorrick Jaspers, Elisa Baschiera, Rossella De Cegli, Eugenio Del Prete, Tito Cali, Bert Blaauw, Leonardo Salviati, Michela Rigoni, Cristina Mammucari, Sylvie Caspar-Bauguil, Cedric Moro, Paola Pizzo, Marco Sandri, Stephan Kemp, Vanina Romanello.
      Skeletal muscles, which constitute 40-50% of body mass, regulate whole-body energy expenditure and glucose and lipid metabolism. Peroxisomes are dynamic organelles that play a crucial role in lipid metabolism and clearance of reactive oxygen species, however their role in skeletal muscle remains poorly understood. To clarify this issue, we generated a muscle-specific transgenic mouse line with peroxisome import deficiency through the deletion of peroxisomal biogenesis factor 5 (Pex5). Here, we show that Pex5 inhibition results in impaired lipid metabolism, reduced muscle force and exercise performance. Moreover, mitochondrial structure, content, and function are also altered, accelerating the onset of age-related structural defects, neuromuscular junction degeneration, and muscle atrophy. Consistent with these observations, we observe a decline in peroxisomal content in the muscles of control mice undergoing natural aging. Altogether, our findings show the importance of preserving peroxisomal function and their interplay with mitochondria to maintain muscle health during aging.
    DOI:  https://doi.org/10.1038/s41467-025-64833-w
  15. Mol Cell. 2025 Nov 07. pii: S1097-2765(25)00856-1. [Epub ahead of print]
    Megabase-scale loss of heterozygosity provoked by CRISPR-Cas9 DNA double-strand breaks.
    Samantha B Regan, Darpan Medhi, Yuanlin Xu, Travis B White, Yi-Zhen Jiang, Jung Eun Kim, Shih-Chun Wang, Qichen Deng, Su Jia, Dulguun Baasan, Jon P Connelly, Ti-Cheng Chang, Shondra M Pruett-Miller, Maria Jasin.
      Harnessing DNA double-strand breaks (DSBs) is a powerful approach for gene editing, but it may provoke loss of heterozygosity (LOH), a common feature of tumor genomes. To interrogate this risk, we developed a flow cytometry-based system (Flo-LOH), detecting LOH in ∼5% of mouse embryonic and human epithelial cells following a DSB. Inhibition of both non-homologous end joining (NHEJ) and microhomology-mediated end joining (MMEJ) massively increases LOH, although the dependence on individual pathways differs in the two cell types. Multiple mechanisms lead to LOH, including chromosome truncations with de novo telomere addition and whole chromosome loss. LOH spans megabases distal from the DSB but also frequently tens of megabases centromere-proximal, which can arise from breakage-fusion-bridge events. Unlike DSBs, Cas9 nicks and adenine base editing did not noticeably impact LOH. The capacity for large-scale LOH must therefore be considered when using DSB-based gene editing, especially in conjunction with end-joining inhibition.
    Keywords:  BLM; CRISPR-Cas9; DNA double-strand break; HDR; MMEJ; breakage-fusion-bridge cycle; genomic instability; inter-homolog homologous recombination; loss of heterozygosity; nickase
    DOI:  https://doi.org/10.1016/j.molcel.2025.10.015
  16. J Cell Biol. 2026 Jan 05. pii: e202503070. [Epub ahead of print]225(1):
    Actomyosin contractility and a threshold of cadherin cell adhesion are required during tissue fusion.
    Camilla S Teng, Sarah W Curtis, Grace C Brewer, Elizabeth J Leslie-Clarkson, Jeffrey O Bush.
      Tissue fusion is integral to mammalian morphogenesis, and its failure is a significant cause of structural anomalies, yet the underlying cellular mechanisms are incompletely understood. We examine cellular drivers of upper lip fusion in the mammalian embryo by establishing a live-imaging modality, revealing specific enrichment of F-actin that propagates in multicellular cables anchored at the fusion site. Actomyosin contractility drives lip fusion, and its pharmacological or genetic attenuation results in failed fusion and cleft lip. Generating a series of mice deficient in specific p120-catenin molecular functions, we reveal that p120-catenin binding to RhoA and Kaiso is dispensable during mammalian development, while stabilization of cadherins is crucial. Through generating an allelic series of new compound P-cadherin/E-cadherin mouse mutations disrupting combined cadherin levels, we unveil an elevated cadherin cell adhesion threshold requirement specific to upper lip fusion. Finally, we identify CDH3 variants in individuals with cleft lip, supporting the relevance of this mechanism in human tissue fusion.
    DOI:  https://doi.org/10.1083/jcb.202503070
  17. Nature. 2025 Nov 12.
    In situ structural mechanism of epothilone-B-induced CNS axon regeneration.
    Satish Bodakuntla, Kenichiro Taira, Yurika Yamada, Pelayo Alvarez-Brecht, A King Cada, Nirakar Basnet, Rui Zhang, Antonio Martinez-Sanchez, Christian Biertümpfel, Naoko Mizuno.
      Axons in the adult central nervous system (CNS) do not regenerate following injury, in contrast to neurons in the peripheral nervous system and neuronal growth during embryonic development. The molecular mechanisms that prevent regeneration of neurons in the CNS remain largely unknown1,2. Here, to address the intracellular response to injury, we developed an in situ cryo-electron tomography and cryo-electron microscopy platform to mimic axonal damage and present the structural mechanism underlying thalamic axon regeneration induced by the drug epothilone B. We observed that stabilized microtubules extend beyond the injury site, generating membrane tension and driving membrane expansion. Cryo-electron microscopy reveals the in situ structure of microtubules at 3.19 Å resolution, which engage epothilone B within the microtubule lattice at the regenerating front. During repair, tubulin clusters are delivered and incorporated into polymerizing microtubules at the regenerating site. These microtubule shoots serve as scaffolds for various types of vesicles and endoplasmic reticulum, facilitating the supply of materials necessary for axon repair until membrane tension normalizes. We demonstrate the unexpected ability of neuronal cells to adjust to strain induced by epothilone B, which creates homeostatic imbalances and activates axons to regeneration mode.
    DOI:  https://doi.org/10.1038/s41586-025-09654-z
  18. Nature. 2025 Nov 12.
    iPEX enables micrometre-resolution deep spatial proteomics via tissue expansion.
    Fengxiang Wang, Cuiji Sun, Tianshu William Wu, Yuting Fu, Yujing Fan, Shuchang Zhao, Kaiyin Huang, Zijian Pan, Yang Lu, Jingrong Regina Han, Shikai Jia, Lizhou Zeng, Sheng Zhang, Ting Chen, Shaowei An, Shuang Susie Meng, Xun Guo, Weizhe Li, Heyuan Lian, Xiaoting Sun, Jin Hu, Chuanzhen Yang, Shan Feng, Pengfei Li, Liyuan Du, Xiaodong Liu, Kiryl D Piatkevich, Yilong Zou.
      The number of spatial omics technologies being developed is increasing1. However, a missing tool is one that can locate proteins in tissues in an untargeted manner at high spatial resolution and coverage. Here we present in situ imaging proteomics via expansion (iPEX), which integrates isotropic tissue magnification2 with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging. iPEX provides scalable spatial resolution down to the micrometre scale and substantially increases the sensitivity of protein identification by 10-100-fold. Using the retina as a model, iPEX enabled the construction of spatial proteomic maps with high precision, the visualization of single-cell layers and extrasomatic structures and the identification of colocalized proteins. iPEX was readily applied to diverse tissues, including brain, intestine, liver and organoids, detecting 600-1,500 proteins at 1-5-µm effective pixel size. The application of iPEX to depict spatial proteomic maps in brains of mice with 5xFAD Alzheimer's disease revealed an early-onset mitochondrial aberrancy. Notably, in young mice, the peroxisomal acetyl-CoA acyltransferase ACAA1A-of which the N392S mutant is a monogenic risk factor in Alzheimer's disease3-was downregulated. ACAA1 depletion blocked the biosynthesis of long-chain polyunsaturated fatty acids, including docosahexaenoic acid, in multiple cellular contexts. These lipidome alterations were restored in cells overexpressing wild-type ACAA1 but not ACAA1(N392S), which suggests that the dysregulation of long-chain polyunsaturated fatty acids has an early role in neurodegeneration. Together, these results demonstrate that iPEX facilitates untargeted spatial proteomics at micrometre resolution for diverse applications.
    DOI:  https://doi.org/10.1038/s41586-025-09734-0
  19. Nat Nanotechnol. 2025 Nov 14.
    Nanoscale domains govern local diffusion and ageing within fused-in-sarcoma condensates.
    Guoming Gao, Emily R Sumrall, Nils G Walter.
      Biomolecular condensates regulate cellular physiology by sequestering and processing RNAs and proteins, yet how these processes are locally tuned within condensates remains unclear. Moreover, in neurodegenerative diseases such as amyotrophic lateral sclerosis, condensates undergo liquid-to-solid phase transitions, but capturing early intermediates in this process has been challenging. Here we present a surface multi-tethering approach to achieve intra-condensate single-molecule tracking of fluorescently labelled RNA and protein molecules within liquid-like condensates. Using RNA-binding protein fused-in-sarcoma as a model for condensates implicated in amyotrophic lateral sclerosis, we discover that RNA and protein diffusion is confined within distinct nanometre-scale domains, or nanodomains, which exhibit unique connectivity and chemical environments. The properties of these nanodomains are tunable by guest molecules. As condensates age, nanodomains reposition, facilitating fused-in-sarcoma fibrilization at the condensate surface, a process further enhanced by anti-amyotrophic lateral sclerosis drugs. Our findings demonstrate that nanodomain formation governs condensate function by modulating the residence time and spatial organization of constituent biomolecules, providing previously unattainable insights into condensate ageing and mechanisms underlying disease.
    DOI:  https://doi.org/10.1038/s41565-025-02077-x
  20. J Cell Biol. 2025 Dec 01. pii: e202412005. [Epub ahead of print]224(12):
    Adapting plasma membrane for mitotic cell rounding through Aurora A phosphorylation of numb.
    Yanyan Li, Ke Liu, Xian Lin, Zhihao Ding, Haiyan Sun, Xiangyun Liao, Binghua Cheng, Wenli Shi, Junde Xu, Jiaming Liang, Zeyu Zhou, Wenjie Zhou, Hui Tian, Long Meng, Guangyong Chen, Ximing Shao, Hongchang Li.
      Cell rounding during mitosis necessitates adaptive remodeling of plasma membrane and cortical cytoskeleton. However, the underlying mechanisms remain poorly elucidated. Here, we have identified Numb phosphorylation as a pivotal mechanism in the membrane-cytoskeleton remodeling associated with mitotic cell rounding. Upon mitotic entry, Aurora A phosphorylates Numb, leading to the dissociation of Numb from plasma membrane. This is crucial for proper plasma membrane retraction, since overexpression of a non-phosphorylatable mutant or a constitutively membrane-bound variant of Numb dramatically disrupts mitotic plasma membrane retraction. Mechanistically, releasing Numb from the plasma membrane enhances the myosin I-mediated membrane-to-cortex adhesion, thereby facilitating the plasma membrane retraction accompanied with cytoskeletal withdrawal. Further analysis showed that compromised plasma membrane retraction confines mitotic cell rounding and consequently leads to spindle orientation defects. Thus, our study elucidates a phosphorylation-mediated mechanism underlying plasma membrane retraction and underscores the functional importance of this process in the context of mitotic cell rounding.
    DOI:  https://doi.org/10.1083/jcb.202412005
  21. Development. 2025 Nov 11. pii: dev.205064. [Epub ahead of print]
    Pair-rule-like transcription patterns during neural tube closure in a proto-vertebrate.
    Gabrielle Östlund-Sholars, Laurence A Lemaire, Michael S Levine.
      Neural tube closure (NTC) is a conserved morphogenetic process in chordates in which the neural plate folds and fuses to form a closed neural tube. While the mechanical forces and signaling pathways governing NTC have been characterized in vertebrates, the transcriptional programs coordinating these behaviors remain less understood. Here, we identify a transcriptional circuit involving Lmx1, Cdkn1b, and Msx that regulates dorsal midline dynamics during NTC in the tunicate Ciona. High-resolution HCR in situ hybridization reveals that Lmx1 expression is dynamically enriched at the zippering point and advances in a posterior-to-anterior transcription wave, while Msx is downregulated in the same region, marking a transition from early neural patterning to morphogenesis. As closure progresses, Lmx1 and Cdkn1b exhibit complementary, alternating expression at the dorsal midline, resembling a pair-rule-like pattern. Misexpression experiments show that Lmx1 promotes proliferation and autoregulates, whereas Cdkn1b limits proliferation and impedes closure. Single-cell RNA-seq datasets reveal transcriptionally distinct dorsal neural populations enriched for Lmx1 or Cdkn1b. This transcriptional switch coordinates proliferation and fusion during NTC, suggesting a general strategy for regulating epithelial remodeling in animal embryos.
    Keywords:  Cell-cycle; Ciona; Gene regulation; Lmx1; Neurulation; Patterning
    DOI:  https://doi.org/10.1242/dev.205064
  22. Proc Natl Acad Sci U S A. 2025 Nov 18. 122(46): e2522548122
    Erythroid precursors regulate local oxygen tension and repair outcomes in the bone marrow niche.
    Annemarie Lang, Joseph M Collins, Madhura P Nijsure, Simin Belali, Mohd Parvez Khan, Yasaman Moharrer, Ernestina Schipani, Yvette Y Yien, Yi Fan, Michael Gelinsky, Sergei A Vinogradov, Cameron Koch, Joel D Boerckel.
      Oxygen tension dynamically regulates stem cell fate and tissue regeneration, yet how local oxygen availability is controlled within the bone marrow niche remains poorly understood. While bone marrow injury, such as by bone fracture, disrupts marrow vasculature, the consequences for local oxygen tension remain unclear. Here, we show in mice that while the tissue oxygen tension in bone marrow is low (25 mmHg, ~4% O2), intracellular oxygenation is heterogeneous, and erythroid cells are high in oxygen. Bone fracture elevates oxygen tension in the injured bone marrow (>55 mmHg, ~8%), which persists for over a week postinjury. This oxygen elevation results not from angiogenesis, but rather from localized expansion of erythroid precursor cells in the injured bone marrow. Injury-activated erythroid precursors synthesize hemoglobin and concentrate oxygen at the injury site; however, blocking transferrin receptor 1 (CD71)-mediated iron uptake impairs hemoglobin synthesis, reduces local oxygen levels, and enhances bone regeneration through increased angiogenesis and osteogenesis. Together, these findings identify erythroid precursors as active regulators of local oxygen availability in the bone marrow niche, which may be targetable to enhance tissue regeneration.
    Keywords:  bone marrow injury; erythropoiesis; oxygen microenvironment
    DOI:  https://doi.org/10.1073/pnas.2522548122
  23. Cell Rep. 2025 Nov 11. pii: S2211-1247(25)01325-7. [Epub ahead of print]44(11): 116554
    Genetic and chromatin regulation of Pvt1 monoallelic expression.
    Christy Luong, Mason Chen, Julia A Belk, Katerina Kraft, Anne-Valerie Gendrel, Edith Heard, Joanna Wysocka, Howard Y Chang.
      While most genes are equivalently expressed on both alleles, genes with random monoallelic expression (RME) stably maintain expression from only one allele, but the mechanisms and consequences of RME remain unclear. We performed allele-specific RNA sequencing (RNA-seq) on ∼100 F1 hybrid neural progenitor cell (NPC) clonal lines to reveal the extent of autosomal RME (aRME). Of the 287 aRME genes, Pvt1, an oncogenic long non-coding RNA, is an aRME with a genetic bias. In the absence of genetic differences, Pvt1 undergoes balanced aRME. Pvt1 monoallelic expression is maintained by allele-specific active and repressive histone modifications, opposed to DNA methylation. Additionally, we provide a two-step mechanism for the initiation of aRME and demonstrate that Pvt1 monoallelic expression results in a growth phenotype due to the interplay with Myc. These findings provide insight into how genetic differences can skew a stochastic process, resulting in monoallelic expression with a phenotypic consequence in early development.
    Keywords:  CP: genomics; MYC; Pvt1; allele-specific expression; chromatin state; enhancer-promter interaction; epigenetic; gene regulation; genetic; histone modifications; long non-coding RNA; monoallelic expression
    DOI:  https://doi.org/10.1016/j.celrep.2025.116554
  24. Nat Rev Mol Cell Biol. 2025 Nov 11.
    Signal control during tissue regeneration in adult animals.
    Sushant Bangru, Rocky Diegmiller, Stefano Di Talia, Kenneth D Poss.
      Tissue regeneration has historically been the subject of intense scientific scrutiny, from basic biology to applications in regenerative medicine. Use of model organisms and cutting-edge technologies have uncovered various mechanisms of regeneration, but understanding how signals are regulated spatiotemporally to renew lost structures at scale remains a challenge. Recent insights into chromatin structure and enhancer regulation, immune-tissue crosstalk, bioelectric and metabolic cues and quantitative modelling are broadening and reshaping our understanding of how tissues repair and renew. The evolution of cutting-edge tools for in vivo profiling and tracking of single cells is providing unprecedented dynamic views of regeneration across scales. Here, we synthesize the current knowledge of signal control in regeneration, with emphasis on conceptual advances, technical innovations and future directions for a more quantitative understanding of regenerative biology.
    DOI:  https://doi.org/10.1038/s41580-025-00917-1
  25. Science. 2025 Nov 13. 390(6774): 728-734
    Branched actin networks mediate macrophage-dependent host-microbiota homeostasis.
    Luiz Ricardo C Vasconcellos, Shaina Chor Mei Huang, Alejandro Suarez-Bonnet, Simon Priestnall, Probir Chakravarty, Sunita Varsani-Brown, Matthew L Winder, Kathleen Shah, Naoko Kogata, Brigitta Stockinger, Michael Way.
      Branched actin networks formed by the Arp2/3 complex are essential for immune system function. Patients with loss-of-function mutations in the ARPC5 subunit of the Arp2/3 complex develop inflammation and immunodeficiency after birth, leading to early mortality. The basis for these phenotypes remains obscure. We found that loss of ARPC5, but not the ARPC5L isoform, in the mouse hematopoietic system caused early-onset intestinal inflammation after weaning. This condition was initiated by microbiota breaching the ileal mucosa and led to systemic inflammation. ARPC5-deficient macrophages and neutrophils infiltrated the ileum but failed to restrict microbial invasion. Specifically, macrophages that lack ARPC5 struggled to phagocytose and kill intracellular bacteria. Our results highlight the indispensable role of ARPC5-containing, but not ARPC5L-containing, Arp2/3 complexes in mononuclear phagocyte function and host-microbiota homeostasis.
    DOI:  https://doi.org/10.1126/science.adr9571
  26. Sci Adv. 2025 Nov 14. 11(46): eadz3889
    iGlucoSnFR2: A genetically encoded fluorescent sensor for measuring intracellular or extracellular glucose in vivo in mouse brain.
    Jonathan S Marvin, Philipp Mächler, Chengbo Meng, Tayfun Ates, Ronak H Patel, Raghabendra Adhikari, Monika A Makurath, Zaneta Ku, Daniel Feliciano, Deniz Atasoy, Guohong Cui, David Kleinfeld, Timothy A Brown.
      Continuous glucose monitors have proven invaluable for monitoring blood glucose levels for diabetics, but they are of limited use for observing glucose dynamics at the cellular (or subcellular) level. We have developed a second generation, genetically encoded intensity-based glucose sensing fluorescent reporter (iGlucoSnFR2). We show that when it is targeted to the cytosol, it reports intracellular glucose consumption and gluconeogenesis in cell culture, along with efflux from the endoplasmic reticulum. It outperforms the original iGlucoSnFR in vivo when observed by fiber photometry in mouse brain and reports transient increase in glucose concentration when stimulated by noradrenaline or electrical stimulation. Last, we demonstrate that membrane localized iGlucoSnFR2 can be calibrated in vivo to indicate absolute changes in extracellular glucose concentration in awake mice. We anticipate iGlucoSnFR2 facilitating previously unobservable measurements of glucose dynamics with high spatial and temporal resolution in living mammals and other experimental organisms.
    DOI:  https://doi.org/10.1126/sciadv.adz3889
  27. Nat Commun. 2025 Nov 11. 16(1): 9918
    Dynamic dosage changes in X-linked transposable elements during mammalian dosage compensation.
    Chunyao Wei, Barry Kesner, Uri Weissbein, Peera Wasserzug-Pash, Priyojit Das, Jeannie T Lee.
      In mammals, X-linked dosage compensation involves X-chromosome inactivation to balance X chromosome dosage between males and females, and hyperactivation of the remaining X-chromosome (Xa-hyperactivation) to achieve X-autosome balance in both sexes. Studies of both processes have largely focused on coding genes and have not accounted for transposable elements which comprise 50% of the X-chromosome with numerous epigenetic functions. Here we develop a new bioinformatic pipeline tailored to repetitive elements with capability for allelic discrimination. We then apply the pipeline to our recent So-Smart-Seq analysis of single embryos to comprehensively interrogate whether X-linked transposable elements are subject to either X-chromosome inactivation or Xa-hyperactivation. We observe significant differences in repeat silencing in parentally driven "imprinted" versus zygotically driven "random" X-chromosome inactivation. Chromosomal positioning, genetic background and evolutionary age impact their silencing. In contrast, transposable elements do not undergo Xa-hyperactivation. Evolutionary and functional implications are discussed.
    DOI:  https://doi.org/10.1038/s41467-025-64865-2
  28. Cell Rep. 2025 Nov 10. pii: S2211-1247(25)01286-0. [Epub ahead of print] 116515
    KIF18A promotes chromosome congression in cooperation with CENP-E downstream of CENP-C.
    Jiahang Miao, Masatoshi Hara, Kuan-Chung Su, Heather R Keys, Weixia Kong, Yusuke Takenoshita, Iain M Cheeseman, Tatsuo Fukagawa.
      Chromosome congression is a key process that acts to align chromosomes at the spindle equator via kinetochore-microtubule interactions, with defects in chromosome alignment leading to chromosomal instability. However, defining the mechanisms that underlie chromosome congression is limited due to the multiple factors that act in parallel to regulate chromosome movement. Here, we conducted a genome-wide Cas9-based functional genetics screen using a hypomorphic CENP-C mutant that affects its kinetochore interactions. Our analysis identified KIF18A, whose knockout resulted in synthetic lethality with the CENP-C mutant. Further analysis revealed that the synthetic defect was due to a reduction in CENP-E function in the CENP-C mutant. Our work suggests that KIF18A promotes chromosome alignment in cooperation with CENP-E downstream of CENP-C during early prometaphase. Thus, our analysis enables us to dissect parallel molecular mechanisms for chromosome congression and identify sensitivities and biomarkers that might guide anti-KIF18A chemotherapeutics.
    Keywords:  CENP-C; CENP-E; CP: Molecular biology; KIF18A; KMN network; kinetochore
    DOI:  https://doi.org/10.1016/j.celrep.2025.116515
This page is being maintained by Thomas Krichel. It was last updated on 2025‒12‒20 at 5:34.