bims-ginsta Biomed News
on Genome instability
Issue of 2025–03–23
34 papers selected by
Jinrong Hu, National University of Singapore
  1. Self-organization of mouse embryonic stem cells into reproducible pre-gastrulation embryo models via CRISPRa programming.
  2. Nuclear and genome dynamics underlying DNA double-strand break repair.
  3. Dynamic cytoskeletal regulation of cell shape supports resilience of lymphatic endothelium.
  4. Growth of the maternal intestine during reproduction.
  5. Human skeletal development and regeneration are shaped by functional diversity of stem cells across skeletal sites.
  6. Transient silencing of hypermutation preserves B cell affinity during clonal bursting.
  7. Quantitative characterization of cell niches in spatially resolved omics data.
  8. A computational pipeline for spatial mechano-transcriptomics.
  9. The conserved Spd-2/CEP192 domain adopts a unique protein fold to promote centrosome scaffold assembly.
  10. Force transmission is a master regulator of mechanical cell competition.
  11. Epithelial polarization by the planar cell polarity complex is exclusively non-cell autonomous.
  12. A single-cell resolved genotype-phenotype map using genome-wide genetic and environmental perturbations.
  13. Mapping the transcriptional and epigenetic landscape of organotypic endothelial diversity in the developing and adult mouse.
  14. Chronic replication stress-mediated genomic instability disrupts placenta development in mice.
  15. Totipotency or plenipotency: rethinking stem cell bipotentiality.
  16. Drosophila ovarian stem cell niche ageing involves coordinated changes in transcription and alternative splicing.
  17. Identifying cross-lineage dependencies of cell-type-specific regulators in mouse gastruloids.
  18. VDAC2 loss elicits tumour destruction and inflammation for cancer therapy.
  19. Drivers of avian genomic change revealed by evolutionary rate decomposition.
  20. FoxO3 controls cardiomyocyte proliferation and heart regeneration by regulating Sfrp2 expression in postnatal mice.
  21. STIM1/2 maintain signaling competence at ER-PM contact sites during neutrophil spreading.
  22. DNA damage response regulator ATR licenses PINK1-mediated mitophagy.
  23. Membrane composition and curvature in SNX9-mediated actin polymerization.
  24. Turnover atlas of proteome and phosphoproteome across mouse tissues and brain regions.
  25. Interactions with multiple inner kinetochore proteins determine mitotic localization of FACT.
  26. Genome-wide transcriptional silencing and mRNA stabilization allow the coordinated expression of the meiotic program in mice.
  27. Mitochondrial quality control in cardiomyocytes: safeguarding the heart against disease and ageing.
  28. A CPC-shelterin-BTR axis regulates mitotic telomere deprotection.
  29. Base-pair resolution reveals clustered R-loops and DNA damage-susceptible R-loops.
  30. Transfer RNA acetylation regulates in vivo mammalian stress signaling.
  31. Marrying mechanics with spatial transcriptomics.
  32. Developmental mitochondrial complex I activity determines lifespan.
  33. Energy landscape analysis of the development of the chromosome structure across the cell cycle.
  34. The complete absence of cytoplasmic γ-actin results in no discernible phenotype in mice or primary fibroblasts.
  1. Cell Stem Cell. 2025 Mar 19. pii: S1934-5909(25)00083-9. [Epub ahead of print]
    Self-organization of mouse embryonic stem cells into reproducible pre-gastrulation embryo models via CRISPRa programming.
    Gerrald A Lodewijk, Sayaka Kozuki, Clara J Han, Benjamin R Topacio, Seungho Lee, Lily Nixon, Abolfazl Zargari, Gavin Knight, Randolph Ashton, Lei S Qi, S Ali Shariati.
      Embryonic stem cells (ESCs) can self-organize into structures with spatial and molecular similarities to natural embryos. During development, embryonic and extraembryonic cells differentiate through activation of endogenous regulatory elements while co-developing via cell-cell interactions. However, engineering regulatory elements to self-organize ESCs into embryo models remains underexplored. Here, we demonstrate that CRISPR activation (CRISPRa) of two regulatory elements near Gata6 and Cdx2 generates embryonic patterns resembling pre-gastrulation mouse embryos. Live single-cell imaging revealed that self-patterning occurs through orchestrated collective movement driven by cell-intrinsic fate induction. In 3D, CRISPRa-programmed embryo models (CPEMs) exhibit morphological and transcriptomic similarity to pre-gastrulation mouse embryos. CPEMs allow versatile perturbations, including dual Cdx2-Elf5 activation to enhance trophoblast differentiation and lineage-specific activation of laminin and matrix metalloproteinases, uncovering their roles in basement membrane remodeling and embryo model morphology. Our findings demonstrate that minimal intrinsic epigenome editing can self-organize ESCs into programmable pre-gastrulation embryo models with robust lineage-specific perturbation capabilities.
    Keywords:  CRISPRa; Collective Motion; embryo models; embryonic patterning; epigenome editing; synthetic biology
    DOI:  https://doi.org/10.1016/j.stem.2025.02.015
  2. Nat Rev Mol Cell Biol. 2025 Mar 17.
    Nuclear and genome dynamics underlying DNA double-strand break repair.
    Irene Chiolo, Matthias Altmeyer, Gaëlle Legube, Karim Mekhail.
      Changes in nuclear shape and in the spatial organization of chromosomes in the nucleus commonly occur in cancer, ageing and other clinical contexts that are characterized by increased DNA damage. However, the relationship between nuclear architecture, genome organization, chromosome stability and health remains poorly defined. Studies exploring the connections between the positioning and mobility of damaged DNA relative to various nuclear structures and genomic loci have revealed nuclear and cytoplasmic processes that affect chromosome stability. In this Review, we discuss the dynamic mechanisms that regulate nuclear and genome organization to promote DNA double-strand break (DSB) repair, genome stability and cell survival. Genome dynamics that support DSB repair rely on chromatin states, repair-protein condensates, nuclear or cytoplasmic microtubules and actin filaments, kinesin or myosin motor proteins, the nuclear envelope, various nuclear compartments, chromosome topology, chromatin loop extrusion and diverse signalling cues. These processes are commonly altered in cancer and during natural or premature ageing. Indeed, the reshaping of the genome in nuclear space during DSB repair points to new avenues for therapeutic interventions that may take advantage of new cancer cell vulnerabilities or aim to reverse age-associated defects.
    DOI:  https://doi.org/10.1038/s41580-025-00828-1
  3. Nature. 2025 Mar 19.
    Dynamic cytoskeletal regulation of cell shape supports resilience of lymphatic endothelium.
    Hans Schoofs, Nina Daubel, Sarah Schnabellehner, Max L B Grönloh, Sebastián Palacios Martínez, Aleksi Halme, Amanda M Marks, Marie Jeansson, Sara Barcos, Cord Brakebusch, Rui Benedito, Britta Engelhardt, Dietmar Vestweber, Konstantin Gaengel, Fabian Linsenmeier, Sebastian Schürmann, Pipsa Saharinen, Jaap D van Buul, Oliver Friedrich, Richard S Smith, Mateusz Majda, Taija Mäkinen.
      Lymphatic capillaries continuously take up interstitial fluid and adapt to resulting changes in vessel calibre1-3. The mechanisms by which the permeable monolayer of loosely connected lymphatic endothelial cells (LECs)4 maintains mechanical stability remain elusive. Here we identify dynamic cytoskeletal regulation of LEC shape, induced by isotropic stretch, as crucial for the integrity and function of dermal lymphatic capillaries. We found that the oak leaf-shaped LECs showed a spectrum of VE-cadherin-based junctional configurations at the lobular intercellular interface and a unique cytoskeletal organization, with microtubules at concave regions and F-actin at convex lobes. Multispectral and longitudinal intravital imaging of capillary LEC shape and actin revealed dynamic remodelling of cellular overlaps in vivo during homeostasis and in response to interstitial fluid volume increase. Akin to puzzle cells of the plant epidermis5,6, LEC shape was controlled by Rho GTPase CDC42-regulated cytoskeletal dynamics, enhancing monolayer stability. Moreover, cyclic isotropic stretch increased cellular overlaps and junction curvature in primary LECs. Our findings indicate that capillary LEC shape results from continuous remodelling of cellular overlaps that maintain vessel integrity while preserving permeable cell-cell contacts compatible with vessel expansion and fluid uptake. We propose a bellows-like fluid propulsion mechanism, in which fluid-induced lumen expansion and shrinkage of LEC overlaps are countered by actin-based lamellipodia-like overlap extension to aid vessel constriction.
    DOI:  https://doi.org/10.1038/s41586-025-08724-6
  4. Cell. 2025 Mar 14. pii: S0092-8674(25)00200-4. [Epub ahead of print]
    Growth of the maternal intestine during reproduction.
    Tomotsune Ameku, Anna Laddach, Hannah Beckwith, Alexandra Milona, Loranzie S Rogers, Cornelia Schwayer, Emma Nye, Iain R Tough, Jean-Louis Thoumas, Umesh Kumar Gautam, Yi-Fang Wang, Shreya Jha, Alvaro Castano-Medina, Christopher Amourda, Patric M Vaelli, Sira Gevers, Elaine E Irvine, Leah Meyer, Ivan Andrew, Ka Lok Choi, Bhavik Patel, Alice J Francis, Chris Studd, Laurence Game, George Young, Kevin G Murphy, Bryn Owen, Dominic J Withers, Maria Rodriguez-Colman, Helen M Cox, Prisca Liberali, Martin Schwarzer, François Leulier, Vassilis Pachnis, Nicholas W Bellono, Irene Miguel-Aliaga.
      The organs of many female animals are remodeled by reproduction. Using the mouse intestine, a striking and tractable model of organ resizing, we find that reproductive remodeling is anticipatory and distinct from diet- or microbiota-induced resizing. Reproductive remodeling involves partially irreversible elongation of the small intestine and fully reversible growth of its epithelial villi, associated with an expansion of isthmus progenitors and accelerated enterocyte migration. We identify induction of the SGLT3a transporter in a subset of enterocytes as an early reproductive hallmark. Electrophysiological and genetic interrogations indicate that SGLT3a does not sustain digestive functions or enterocyte health; rather, it detects protons and sodium to extrinsically support the expansion of adjacent Fgfbp1-positive isthmus progenitors, promoting villus growth. Our findings reveal unanticipated specificity to physiological organ remodeling. We suggest that organ- and state-specific growth programs could be leveraged to improve pregnancy outcomes or prevent maladaptive consequences of such growth.
    Keywords:  Fgfbp1; SGLT3a; adult organ remodeling; intestinal epithelium; isthmus progenitor; lactation; plasticity; pregnancy; reproduction; small intestine
    DOI:  https://doi.org/10.1016/j.cell.2025.02.015
  5. Cell Stem Cell. 2025 Mar 19. pii: S1934-5909(25)00081-5. [Epub ahead of print]
    Human skeletal development and regeneration are shaped by functional diversity of stem cells across skeletal sites.
    Thomas H Ambrosi, Sahar Taheri, Kun Chen, Rahul Sinha, Yuting Wang, Ethan J Hunt, L Henry Goodnough, Matthew P Murphy, Holly M Steininger, Malachia Y Hoover, Franco Felix, Kelly C Weldon, Lauren S Koepke, Jan Sokol, Daniel Dan Liu, Liming Zhao, Stephanie D Conley, Wan-Jin Lu, Maurizio Morri, Norma F Neff, Noelle L Van Rysselberghe, Erika E Wheeler, Yongheng Wang, J Kent Leach, Augustine Saiz, Aijun Wang, George P Yang, Stuart Goodman, Julius A Bishop, Michael J Gardner, Derrick C Wan, Irving L Weissman, Michael T Longaker, Debashis Sahoo, Charles K F Chan.
      The skeleton is one of the most structurally and compositionally diverse organ systems in the human body, depending on unique cellular dynamisms. Here, we integrate prospective isolation of human skeletal stem cells (hSSCs; CD45-CD235a-TIE2-CD31-CD146-PDPN+CD73+CD164+) from ten skeletal sites with functional assays and single-cell RNA sequencing (scRNA-seq) analysis to identify chondrogenic, osteogenic, stromal, and fibrogenic subtypes of hSSCs during development and their linkage to skeletal phenotypes. We map the distinct composition of hSSC subtypes across multiple skeletal sites and demonstrate their unique in vivo clonal dynamics. We find that age-related changes in bone formation and regeneration disorders stem from a pathological fibroblastic shift in the hSSC pool. Utilizing a Boolean algorithm, we uncover gene regulatory networks that dictate differences in the ability of hSSCs to generate specific skeletal tissues. Importantly, hSSC lineage dynamics are pharmacologically malleable, providing a new strategy to treat aberrant hSSC diversity central to aging and skeletal maladies.
    Keywords:  Boolean relationships; bone aging; fibrous dysplasia; fracture healing; gene regulatory networks; human skeletal stem cell; nonunion; skeletal development
    DOI:  https://doi.org/10.1016/j.stem.2025.02.013
  6. Nature. 2025 Mar 19.
    Transient silencing of hypermutation preserves B cell affinity during clonal bursting.
    Juhee Pae, Niklas Schwan, Bertrand Ottino-Loffler, William S DeWitt, Amar Garg, Juliana Bortolatto, Ashni A Vora, Jin-Jie Shen, Alvaro Hobbs, Tiago B R Castro, Luka Mesin, Frederick A Matsen, Michael Meyer-Hermann, Gabriel D Victora.
      In the course of antibody affinity maturation, germinal centre (GC) B cells mutate their immunoglobulin heavy- and light-chain genes in a process known as somatic hypermutation (SHM)1-4. Panels of mutant B cells with different binding affinities for antigens are then selected in a Darwinian manner, which leads to a progressive increase in affinity among the population5. As with any Darwinian process, rare gain-of-fitness mutations must be identified and common loss-of-fitness mutations avoided6. Progressive acquisition of mutations therefore poses a risk during large proliferative bursts7, when GC B cells undergo several cell cycles in the absence of affinity-based selection8-13. Using a combination of in vivo mouse experiments and mathematical modelling, here we show that GCs achieve this balance by strongly suppressing SHM during clonal-burst-type expansion, so that a large fraction of the progeny generated by these bursts does not deviate from their ancestral genotype. Intravital imaging and image-based cell sorting of a mouse strain carrying a reporter of cyclin-dependent kinase 2 (CDK2) activity showed that B cells that are actively undergoing proliferative bursts lack the transient CDK2low 'G0-like' phase of the cell cycle in which SHM takes place. We propose a model in which inertially cycling B cells mostly delay SHM until the G0-like phase that follows their final round of division in the GC dark zone, thus maintaining affinity as they clonally expand in the absence of selection.
    DOI:  https://doi.org/10.1038/s41586-025-08687-8
  7. Nat Genet. 2025 Mar 18.
    Quantitative characterization of cell niches in spatially resolved omics data.
    Sebastian Birk, Irene Bonafonte-Pardàs, Adib Miraki Feriz, Adam Boxall, Eneritz Agirre, Fani Memi, Anna Maguza, Anamika Yadav, Erick Armingol, Rong Fan, Gonçalo Castelo-Branco, Fabian J Theis, Omer Ali Bayraktar, Carlos Talavera-López, Mohammad Lotfollahi.
      Spatial omics enable the characterization of colocalized cell communities that coordinate specific functions within tissues. These communities, or niches, are shaped by interactions between neighboring cells, yet existing computational methods rarely leverage such interactions for their identification and characterization. To address this gap, here we introduce NicheCompass, a graph deep-learning method that models cellular communication to learn interpretable cell embeddings that encode signaling events, enabling the identification of niches and their underlying processes. Unlike existing methods, NicheCompass quantitatively characterizes niches based on communication pathways and consistently outperforms alternatives. We show its versatility by mapping tissue architecture during mouse embryonic development and delineating tumor niches in human cancers, including a spatial reference mapping application. Finally, we extend its capabilities to spatial multi-omics, demonstrate cross-technology integration with datasets from different sequencing platforms and construct a whole mouse brain spatial atlas comprising 8.4 million cells, highlighting NicheCompass' scalability. Overall, NicheCompass provides a scalable framework for identifying and analyzing niches through signaling events.
    DOI:  https://doi.org/10.1038/s41588-025-02120-6
  8. Nat Methods. 2025 Mar 17.
    A computational pipeline for spatial mechano-transcriptomics.
    Adrien Hallou, Ruiyang He, Benjamin D Simons, Bianca Dumitrascu.
      Advances in spatial profiling technologies are providing insights into how molecular programs are influenced by local signaling and environmental cues. However, cell fate specification and tissue patterning involve the interplay of biochemical and mechanical feedback. Here we develop a computational framework that enables the joint statistical analysis of transcriptional and mechanical signals in the context of spatial transcriptomics. To illustrate the application and utility of the approach, we use spatial transcriptomics data from the developing mouse embryo to infer the forces acting on individual cells, and use these results to identify mechanical, morphometric and gene expression signatures that are predictive of tissue compartment boundaries. In addition, we use geoadditive structural equation modeling to identify gene modules that predict the mechanical behavior of cells in an unbiased manner. This computational framework is easily generalized to other spatial profiling contexts, providing a generic scheme for exploring the interplay of biomolecular and mechanical cues in tissues.
    DOI:  https://doi.org/10.1038/s41592-025-02618-1
  9. Sci Adv. 2025 Mar 21. 11(12): eadr5744
    The conserved Spd-2/CEP192 domain adopts a unique protein fold to promote centrosome scaffold assembly.
    Liuyi Hu, Alan Wainman, Antonina Andreeva, Muladili Apizi, Ines Alvarez-Rodrigo, Siu-Shing Wong, Saroj Saurya, Devon Sheppard, Matthew Cottee, Steven Johnson, Susan M Lea, Jordan W Raff, Mark van Breugel, Zhe Feng.
      Centrosomes form when centrioles assemble pericentriolar material (PCM) around themselves. Spd-2/CEP192 proteins, defined by a conserved "Spd-2 domain" (SP2D) comprising two closely spaced AspM-Spd-2-Hydin (ASH) domains, play a critical role in centrosome assembly. Here, we show that the SP2D does not target Drosophila Spd-2 to centrosomes but rather promotes PCM scaffold assembly. Crystal structures of the human and honeybee SP2D reveal an unusual "extended cradle" structure mediated by a conserved interaction interface between the two ASH domains. Mutations predicted to perturb this interface, including a human mutation associated with male infertility and Mosaic Variegated Aneuploidy, disrupt PCM scaffold assembly in flies. The SP2D is monomeric in solution, but the Drosophila SP2D can form higher-order oligomers upon phosphorylation by PLK1 (Polo-like kinase 1). Crystal-packing interactions and AlphaFold predictions suggest how SP2Ds might self-assemble, and mutations associated with one such potential dimerization interface markedly perturb SP2D oligomerization in vitro and PCM scaffold assembly in vivo.
    DOI:  https://doi.org/10.1126/sciadv.adr5744
  10. Nat Mater. 2025 Mar 14.
    Force transmission is a master regulator of mechanical cell competition.
    Andreas Schoenit, Siavash Monfared, Lucas Anger, Carine Rosse, Varun Venkatesh, Lakshmi Balasubramaniam, Elisabetta Marangoni, Philippe Chavrier, René-Marc Mège, Amin Doostmohammadi, Benoit Ladoux.
      Cell competition is a tissue surveillance mechanism for eliminating unwanted cells, being indispensable in development, infection and tumourigenesis. Although studies have established the role of biochemical mechanisms in this process, due to challenges in measuring forces in these systems, how mechanical forces determine the competition outcome remains unclear. Here we report a form of cell competition that is regulated by differences in force transmission capabilities, selecting for cell types with stronger intercellular adhesion. Direct force measurements in ex vivo tissues and different cell lines reveal that there is an increased mechanical activity at the interface between two competing cell types, which can lead to large stress fluctuations resulting in upward forces and cell elimination. We show how a winning cell type endowed with a stronger intercellular adhesion exhibits higher resistance to elimination and benefiting from efficient force transmission to the neighbouring cells. This cell elimination mechanism could have broad implications for keeping the strong force transmission ability for maintaining tissue boundaries and cell invasion pathology.
    DOI:  https://doi.org/10.1038/s41563-025-02150-9
  11. Science. 2025 Mar 21. 387(6740): eads5704
    Epithelial polarization by the planar cell polarity complex is exclusively non-cell autonomous.
    Lena P Basta, Bradley W Joyce, Eszter Posfai, Danelle Devenport.
      For cells to polarize collectively along a tissue plane, asymmetrically localized planar cell polarity (PCP) complexes must form intercellular contacts between neighboring cells. Yet, it is unknown whether asymmetric segregation of PCP complexes requires cell-cell contact, or if cell autonomous, antagonistic interactions are sufficient for polarization. To test this, we generated mouse chimeras consisting of dual PCP-reporter cells mixed with unlabeled cells that cannot form PCP bridges. In the absence of intercellular interactions, PCP proteins failed to polarize cell autonomously. Rather, PCP-mediated contacts along single cell-cell interfaces were sufficient to sort PCP components to opposite sides of the junction, independent of junction orientation. Thus, intercellular binding of PCP complexes is the critical step that initiates sorting of opposing PCP complexes to generate asymmetry.
    DOI:  https://doi.org/10.1126/science.ads5704
  12. Nat Commun. 2025 Mar 18. 16(1): 2645
    A single-cell resolved genotype-phenotype map using genome-wide genetic and environmental perturbations.
    Mariona Nadal-Ribelles, Carme Solé, Anna Díez-Villanueva, Camille Stephan-Otto Attolini, Yaima Matas, Lars Steinmetz, Eulàlia de Nadal, Francesc Posas.
      Heterogeneity is inherent to living organisms and it determines cell fate and phenotypic variability. Despite its ubiquity, the underlying molecular mechanisms and the genetic basis linking genotype to-phenotype heterogeneity remain a central challenge. Here we construct a yeast knockout library with a clone and genotype RNA barcoding structure suitable for genome-scale analyses to generate a high-resolution single-cell yeast transcriptome atlas of 3500 mutants under control and stress conditions. We find that transcriptional heterogeneity reflects the coordinated expression of specific gene programs, generating a continuous of cell states that can be responsive to external insults. Cell state plasticity can be genetically modulated with mutants that act as state attractors and disruption of state homeostasis results in decreased adaptive fitness. Leveraging on intra-genetic variability, we establish that regulators of transcriptional heterogeneity are functionally diverse and influenced by the environment. Our multimodal perturbation-based single-cell Genotype-to-Transcriptome Atlas in yeast provides insights into organism-level responses.
    DOI:  https://doi.org/10.1038/s41467-025-57600-4
  13. Nat Cardiovasc Res. 2025 Mar 17.
    Mapping the transcriptional and epigenetic landscape of organotypic endothelial diversity in the developing and adult mouse.
    Manuel E Cantu Gutierrez, Matthew C Hill, Gabrielle E Largoza, William B Gillespie, James F Martin, Joshua D Wythe.
      The vascular endothelium features unique molecular and functional properties across different vessel types, such as between arteries, veins and capillaries, as well as between different organs, such as the leaky sinusoidal endothelium of the liver versus the impermeable vessels of the brain. However, the transcriptional networks governing endothelial organ specialization remain unclear. Here we profile the accessible chromatin and transcriptional landscapes of the endothelium from the mouse liver, lung, heart, kidney, brain and retina, across developmental time, to identify potential transcriptional regulators of endothelial heterogeneity. We then determine which of these putative regulators are conserved in human brain endothelial cells, and using single-cell transcriptomic profiling, we define which regulatory networks are active during brain maturation. Finally, we show that the putative transcriptional regulators identified by these three approaches molecularly and functionally reprogram naive endothelial cells. Thus, this resource can be used to identify potential transcriptional regulators controlling the establishment and maintenance of organ-specific endothelial specialization.
    DOI:  https://doi.org/10.1038/s44161-025-00618-0
  14. bioRxiv. 2025 Mar 04. pii: 2025.02.28.640689. [Epub ahead of print]
    Chronic replication stress-mediated genomic instability disrupts placenta development in mice.
    Mumingjiang Munisha, Rui Huang, John C Schimenti.
      Abnormal placentation drives many pregnancy-related pathologies and poor fetal outcomes, but the underlying molecular causes are understudied. Here, we show that persistent replication stress due to mutations in the MCM2-7 replicative helicase disrupts placentation and reduces embryo viability in mice. MCM-deficient embryos exhibited normal morphology but their placentae had a drastically diminished junctional zone (JZ). Whereas cell proliferation in the labyrinth zone (LZ) remained unaffected, JZ cell proliferation was reduced, independent of cell death during early development. Mouse trophoblast stem cells (TSCs) with high genomic instability failed to maintain stemness, suggesting that replication stress affects the initial trophoblast progenitor pool in a manner that preferentially impacts the developing JZ. Genetically increasing chromatin-bound MCM levels in the mutants rescued placental defects and embryo viability. Developing female mice deficient for FANCM, a protein involved in replication-associated DNA repair, also had placentae with a diminished JZ. These findings indicate that replication stress-induced genomic instability compromises embryo outcomes by impairing placentation.
    Keywords:  Embryogenesis; Genomic instability; MCM; Placenta development; Replication Stress
    DOI:  https://doi.org/10.1101/2025.02.28.640689
  15. Curr Opin Genet Dev. 2025 Mar 18. pii: S0959-437X(25)00034-6. [Epub ahead of print]92 102342
    Totipotency or plenipotency: rethinking stem cell bipotentiality.
    Duancheng Wen, Jianlong Wang.
      The term 'totipotency' has often been misapplied in stem cell research to describe cells with embryonic and extraembryonic bipotentiality, despite a lack of evidence that they can generate an entire organism from a single cell. Additionally, no specific term currently distinguishes bipotential stem cells from pluripotent cells, which contribute poorly to extraembryonic tissues. This review examines the developmental continuum from totipotency to pluripotency in early embryos and revisits the previously proposed concept of plenipotency in preimplantation development. We evaluate emerging stem cell models that exhibit bipotentiality but have lost the ability to autonomously initiate and sustain the sequential fate decisions necessary to develop into a complete organism. Unlike totipotent embryonic cells, which retain the information required to initiate fate decisions at the correct timing and cell numbers, these stem cells have lost that capacity. This loss of critical developmental information distinguishes totipotency from plenipotency, with bipotential stem cells aligning more closely with the latter. By distinguishing plenipotency from totipotency and pluripotency, we aim to refine terminology, enhance our understanding of early embryonic development, and address ethical considerations in human research.
    DOI:  https://doi.org/10.1016/j.gde.2025.102342
  16. Nat Commun. 2025 Mar 16. 16(1): 2596
    Drosophila ovarian stem cell niche ageing involves coordinated changes in transcription and alternative splicing.
    Dilamm Even-Ros, Judit Huertas-Romero, Miriam Marín-Menguiano, Gretel Nusspaumer, Miguel Borge, Manuel Irimia, Federico Zurita, Acaimo González-Reyes.
      Gene expression (GE) and alternative splicing (AS) contribute to the formation of new interaction networks with potentially significant cellular functions. Here, we investigate ageing in the Drosophila female germline stem cell (GSC) niche and describe functional changes in both GE and AS. The GSC niche comprises three types of support cells, whose ageing transcriptomes reveal differential GE and AS variations related to cell adhesion, cytoskeleton and neural signalling. Because each population show distinctive GE and AS changes, niche cell types possess unique ageing signatures. Depending on the cell population, groups of genes display changes in both GE and AS, revealing a coordinated regulation of transcription and splicing during niche ageing. One such gene is Fasciclin 2, a neural adhesion molecule that we find is essential for niche functioning. Furthermore, genes involved in AS undergo changes in GE and/or AS themselves, providing a mechanistic explanation for the coordination of these two processes during niche ageing. This is the case of the splicing factor Smu1, described here as a key element necessary for ovarian niche homeostasis.
    DOI:  https://doi.org/10.1038/s41467-025-57901-8
  17. Dev Cell. 2025 Mar 11. pii: S1534-5807(25)00118-2. [Epub ahead of print]
    Identifying cross-lineage dependencies of cell-type-specific regulators in mouse gastruloids.
    Luca Braccioli, Teun van den Brand, Noemi Alonso Saiz, Charis Fountas, Patrick H N Celie, Justina Kazokaitė-Adomaitienė, Elzo de Wit.
      Correct gene expression levels are crucial for normal development. Advances in genomics enable the inference of gene regulatory programs active during development but cannot capture the complex multicellular interactions occurring during mammalian embryogenesis in utero. In vitro models of mammalian development, like gastruloids, can overcome this limitation. Using time-resolved single-cell chromatin accessibility analysis, we delineated the regulatory profile during mouse gastruloid development, identifying critical drivers of developmental transitions. Gastruloids develop from bipotent progenitor cells driven by the transcription factors (TFs) OCT4, SOX2, and TBXT, differentiating into the mesoderm (characterized by the mesogenin 1 [MSGN1]) and spinal cord (characterized by CDX2). ΔCDX gastruloids fail to form spinal cord, while Msgn1 ablation inhibits paraxial mesoderm and spinal cord development. Chimeric gastruloids with ΔMSGN1 and wild-type cells formed both tissues, indicating that inter-tissue communication is necessary for spinal cord formation. Our work has important implications for studying inter-tissue communication and gene regulatory programs in development.
    Keywords:  chromatin accessibility; gastruloid; inter-tissue communication; mesoderm; single-cell ATAC-seq; spinal cord; transcription factor
    DOI:  https://doi.org/10.1016/j.devcel.2025.02.013
  18. Nature. 2025 Mar 19.
    VDAC2 loss elicits tumour destruction and inflammation for cancer therapy.
    Sujing Yuan, Renqiang Sun, Hao Shi, Nicole M Chapman, Haoran Hu, Cliff Guy, Sherri Rankin, Anil Kc, Gustavo Palacios, Xiaoxi Meng, Xiang Sun, Peipei Zhou, Xiaoyang Yang, Stephen Gottschalk, Hongbo Chi.
      Tumour cells often evade immune pressure exerted by CD8+ T cells or immunotherapies through mechanisms that are largely unclear1,2. Here, using complementary in vivo and in vitro CRISPR-Cas9 genetic screens to target metabolic factors, we established voltage-dependent anion channel 2 (VDAC2) as an immune signal-dependent checkpoint that curtails interferon-γ (IFNγ)-mediated tumour destruction and inflammatory reprogramming of the tumour microenvironment. Targeting VDAC2 in tumour cells enabled IFNγ-induced cell death and cGAS-STING activation, and markedly improved anti-tumour effects and immunotherapeutic responses. Using a genome-scale genetic interaction screen, we identified BAK as the mediator of VDAC2-deficiency-induced effects. Mechanistically, IFNγ stimulation increased BIM, BID and BAK expression, with VDAC2 deficiency eliciting uncontrolled IFNγ-induced BAK activation and mitochondrial damage. Consequently, mitochondrial DNA was aberrantly released into the cytosol and triggered robust activation of cGAS-STING signalling and type I IFN response. Importantly, co-deletion of STING signalling components dampened the therapeutic effects of VDAC2 depletion in tumour cells, suggesting that targeting VDAC2 integrates CD8+ T cell- and IFNγ-mediated adaptive immunity with a tumour-intrinsic innate immune-like response. Together, our findings reveal VDAC2 as a dual-action target to overcome tumour immune evasion and establish the importance of coordinately destructing and inflaming tumours to enable efficacious cancer immunotherapy.
    DOI:  https://doi.org/10.1038/s41586-025-08732-6
  19. Nature. 2025 Mar 19.
    Drivers of avian genomic change revealed by evolutionary rate decomposition.
    David A Duchêne, Al-Aabid Chowdhury, Jingyi Yang, Maider Iglesias-Carrasco, Josefin Stiller, Shaohong Feng, Samir Bhatt, M Thomas P Gilbert, Guojie Zhang, Joseph A Tobias, Simon Y W Ho.
      Modern birds have diversified into a striking array of forms, behaviours and ecological roles. Analyses of molecular evolutionary rates can reveal the links between genomic and phenotypic change1-4, but disentangling the drivers of rate variation at the whole-genome scale has been difficult. Using comprehensive estimates of traits and evolutionary rates across a family-level phylogeny of birds5,6, we find that genome-wide mutation rates across lineages are predominantly explained by clutch size and generation length, whereas rate variation across genes is driven by the content of guanine and cytosine. Here, to find the subsets of genes and lineages that dominate evolutionary rate variation in birds, we estimated the influence of individual lineages on decomposed axes of gene-specific evolutionary rates. We find that most of the rate variation occurs along recent branches of the tree, associated with present-day families of birds. Additional tests on axes of rate variation show rapid changes in microchromosomes immediately after the Cretaceous-Palaeogene transition. These apparent pulses of evolution are consistent with major changes in the genetic machineries for meiosis, heart performance, and RNA splicing, surveillance and translation, and correlate with the ecological diversity reflected in increased tarsus length. Collectively, our analyses paint a nuanced picture of avian evolution, revealing that the ancestors of the most diverse lineages of birds underwent major genomic changes related to mutation, gene usage and niche expansion in the early Palaeogene period.
    DOI:  https://doi.org/10.1038/s41586-025-08777-7
  20. Nat Commun. 2025 Mar 14. 16(1): 2532
    FoxO3 controls cardiomyocyte proliferation and heart regeneration by regulating Sfrp2 expression in postnatal mice.
    Jing-Bo Xia, Kun Liu, Xiao-Lin Lin, Hong-Ji Li, Jin-Hua Lin, Li Li, Chi-Qian Liang, Yan Cao, Na Wen, Zhao-Fu Liao, Hui Zhao, Kyu-Sang Park, Guo-Hua Song, Ze-Bing Ye, Dong-Qing Cai, Zhen-Yu Ju, Xu-Feng Qi.
      The Forkhead box O3 (FoxO3) transcription factor is crucial to controlling heart growth in adulthood, but its exact role in cardiac repair and regeneration in postnatal mice remains unclear. Here, we show that FoxO3 deficiency promotes cardiomyocyte proliferation in postnatal mice and improves cardiac function in homeostatic adult mice. Moreover, FoxO3 deficiency accelerates heart regeneration following injury in postnatal mice at the regenerative and non-regenerative stages. We reveal that FoxO3 directly promotes the expression of secreted frizzled-related protein 2 (Sfrp2) and suppresses the activation of canonical Wnt/β-catenin signaling during heart regeneration. The increased activation of β-catenin in FoxO3-deficient cardiomyocytes can be blocked by Sfrp2 overexpression. In addition, Sfrp2 overexpression suppressed cardiomyocyte proliferation and heart regeneration in FoxO3-deficient mice. These findings suggest that FoxO3 negatively controls cardiomyocyte proliferation and heart regeneration in postnatal mice at least in part by promoting Sfrp2 expression, which leading to the inactivation of canonical Wnt/β-catenin signaling.
    DOI:  https://doi.org/10.1038/s41467-025-57962-9
  21. J Cell Biol. 2025 May 05. pii: e202406053. [Epub ahead of print]224(5):
    STIM1/2 maintain signaling competence at ER-PM contact sites during neutrophil spreading.
    Camille Rabesahala de Meritens, Amado Carreras-Sureda, Nicolas Rosa, Robert Pick, Christoph Scheiermann, Nicolas Demaurex.
      Neutrophils are highly motile leukocytes that migrate inside tissues to destroy invading pathogens. Ca2+ signals coordinate leukocytes migration, but whether Ca2+ fluxes mediated by Stim proteins at ER-PM contact sites regulate neutrophil actin-based motility is unclear. Here, we show that myeloid-specific Stim1/2 ablation decreases basal cytosolic Ca2+ levels and prevents adhesion-induced Ca2+ elevations in mouse neutrophils, reducing actin fiber formation and impairing spreading. Unexpectedly, more ER-PM contact sites were detected on the actin-poor adhesive membranes of Stim1/2-deficient neutrophils, which had reduced inositol-1,4,5-trisphosphate receptor (IP3R) immunoreactivity on confocal and immunogold micrographs despite preserved IP3R levels on western blots. Remarkably, Stim1/2-deficient neutrophils regained signaling and spreading competence in Ca2+-rich solutions and were recruited more effectively in mouse inflamed cremaster muscles in vivo. Our findings indicate that Stim1/2 preserve IP3R functionality in neutrophils, generating adhesion-dependent Ca2+ signals that control actin dynamics during neutrophil spreading. Stim proteins thus maintain IP3R signaling competence at adhesive membranes, enabling Ca2+-dependent actin remodeling during spreading in mouse neutrophils.
    DOI:  https://doi.org/10.1083/jcb.202406053
  22. Nucleic Acids Res. 2025 Feb 27. pii: gkaf178. [Epub ahead of print]53(5):
    DNA damage response regulator ATR licenses PINK1-mediated mitophagy.
    Christian Marx, Xiaobing Qing, Yamin Gong, Joanna Kirkpatrick, Kanstantsin Siniuk, Galina V Beznoussenko, Gururaj Rao Kidiyoor, Murat Kirtay, Katrin Buder, Philipp Koch, Martin Westermann, Christopher Bruhn, Eric J Brown, Xingzhi Xu, Marco Foiani, Zhao-Qi Wang.
      Defective DNA damage response (DDR) and mitochondrial dysfunction are a major etiology of tissue impairment and aging. Mitochondrial autophagy (mitophagy) is a mitochondrial quality control (MQC) mechanism to selectively eliminate dysfunctional mitochondria. ATR (ataxia-telangiectasia and Rad3-related) is a key DDR regulator playing a pivotal role in DNA replication stress response and genomic stability. Paradoxically, the human Seckel syndrome caused by ATR mutations exhibits premature aging and neuropathies, suggesting a role of ATR in nonreplicating tissues. Here, we report a previously unknown yet direct role of ATR at mitochondria. We find that ATR and PINK1 (PTEN-induced kinase 1) dock at the mitochondrial translocase TOM/TIM complex, where ATR interacts directly with and thereby stabilizes PINK1. ATR deletion silences mitophagy initiation thereby altering oxidative phosphorylation functionality resulting in reactive oxygen species overproduction that attack cytosolic macromolecules, in both cells and brain tissues, prior to nuclear DNA. This study discloses ATR as an integrated component of the PINK1-mediated MQC program to ensure mitochondrial fitness. Together with its DDR function, ATR safeguards mitochondrial and genomic integrity under physiological and genotoxic conditions.
    DOI:  https://doi.org/10.1093/nar/gkaf178
  23. Mol Biol Cell. 2025 Mar 19. mbcE24090419
    Membrane composition and curvature in SNX9-mediated actin polymerization.
    Pankti Vaishnav, Hanae Shimo Kondo, Jonathan R Gadsby, Thomas C A Blake, Ulrich Dobramysl, Julia Mason, Joseph Atherton, Jennifer L Gallop.
      Sorting nexin 9 (SNX9) is a membrane-binding scaffold protein that contributes to viral uptake and inflammation and is associated with worse outcomes in several cancers. It is involved in endocytosis of epidermal growth factor receptors, β1-integrin and membrane type 1 matrix metalloprotease, and formation of mitochondrial-derived vesicles. The SNX9 Bin-Amphiphysin-Rvs (BAR) - Phox homology (PX) domains bind phosphoinositide lipids and the Src homology 3 (SH3) domain interacts with dynamin and N-Wiskott Aldrich syndrome protein (N-WASP) to stimulate Arp2/3 complex-mediated actin polymerization. Here we use biolayer interferometry, cell-free reconstitution and superresolution microscopy to analyse the specificity and activities of SNX9 at membranes. We find that more SNX9 can bind liposomes containing phosphatidylinositol (4,5)-bisphosphate (PI(4,5)P2) and phosphatidylinositol (3)-phosphate (PI(3)P) compared to phosphatidylinositol (3,4)-bisphosphate (PI(3,4)P2), despite similar affinities. Actin assembly requires the network of both PX-BAR and SH3 interactions. 3D direct stochastic optical reconstruction microscopy on filopodia-like reconstitutions shows that SNX9 and related protein Transducer of Cdc42-dependent actin assembly-1 (TOCA-1) can form both flat and ∼0.5 µm curved assemblies at actin incorporation sites. Finally, using cryo-electron tomography we show that SNX9 builds both branched and bundled actin networks demonstrating its potential for multifunctional roles in actin remodelling. [Media: see text] [Media: see text] [Media: see text].
    DOI:  https://doi.org/10.1091/mbc.E24-09-0419
  24. Cell. 2025 Mar 14. pii: S0092-8674(25)00209-0. [Epub ahead of print]
    Turnover atlas of proteome and phosphoproteome across mouse tissues and brain regions.
    Wenxue Li, Abhijit Dasgupta, Ka Yang, Shisheng Wang, Nisha Hemandhar-Kumar, Surendhar R Chepyala, Jay M Yarbro, Zhenyi Hu, Barbora Salovska, Eugenio F Fornasiero, Junmin Peng, Yansheng Liu.
      Understanding how proteins in different mammalian tissues are regulated is central to biology. Protein abundance, turnover, and post-translational modifications such as phosphorylation are key factors that determine tissue-specific proteome properties. However, these properties are challenging to study across tissues and remain poorly understood. Here, we present Turnover-PPT, a comprehensive resource mapping the abundance and lifetime of 11,000 proteins and 40,000 phosphosites in eight mouse tissues and various brain regions using advanced proteomics and stable isotope labeling. We reveal tissue-specific short- and long-lived proteins, strong correlations between interacting protein lifetimes, and distinct impacts of phosphorylation on protein turnover. Notably, we discover a remarkable pattern of turnover changes for peroxisome proteins in specific tissues and that phosphorylation regulates the stability of neurodegeneration-related proteins, such as Tau and α-synuclein. Thus, Turnover-PPT provides fundamental insights into protein stability, tissue dynamic proteotypes, and functional protein phosphorylation and is accessible via an interactive web-based portal at https://yslproteomics.shinyapps.io/tissuePPT.
    Keywords:  DIA-MS; TMT; brain regions; mouse tissues; protein lifetime; protein phosphorylation; protein turnover; proteomics; pulse SILAC
    DOI:  https://doi.org/10.1016/j.cell.2025.02.021
  25. J Cell Biol. 2025 May 05. pii: e202412042. [Epub ahead of print]224(5):
    Interactions with multiple inner kinetochore proteins determine mitotic localization of FACT.
    Julia Schweighofer, Bhagyashree Mulay, Ingrid Hoffmann, Doro Vogt, Marion E Pesenti, Andrea Musacchio.
      The FAcilitates Chromatin Transcription (FACT) complex is a dimeric histone chaperone that operates on chromatin during transcription and replication. FACT also interacts with a specialized centromeric nucleosome containing the histone H3 variant centromere protein A (CENP-A) and with CENP-TW, two subunits of the constitutive centromere-associated network (CCAN), a 16-protein complex associated with CENP-A. The significance of these interactions remains elusive. Here, we show that FACT has multiple additional binding sites on CCAN. The interaction with CCAN is strongly stimulated by casein kinase II phosphorylation of FACT. Mitotic localization of FACT to kinetochores is strictly dependent on specific CCAN subcomplexes. Conversely, CENP-TW requires FACT for stable localization. Unexpectedly, we also find that DNA readily displaces FACT from CCAN, supporting the speculation that FACT becomes recruited through a pool of CCAN that is not stably integrated into chromatin. Collectively, our results point to a potential role of FACT in chaperoning CCAN during transcription or in the stabilization of CCAN at the centromere during the cell cycle.
    DOI:  https://doi.org/10.1083/jcb.202412042
  26. Nucleic Acids Res. 2025 Feb 27. pii: gkaf146. [Epub ahead of print]53(5):
    Genome-wide transcriptional silencing and mRNA stabilization allow the coordinated expression of the meiotic program in mice.
    Laura Bellutti, Edith Chan Sock Peng, Victoria Cluzet, Marie-Justine Guerquin, Antoine Rolland, Sébastien Messiaen, Elena Llano, Ihsan Dereli, Emmanuelle Martini, Attila Tóth, Alberto M Pendás, Frederic Chalmel, Gabriel Livera.
      The transcriptional dynamic of mammalian cells when these transit from the ubiquitous mitotic to a meiotic-specific program is key to understand this switch central to sexual reproduction. By quantifying active RNA polymerase II and nascent transcripts using single cell dataset and ethynyl-uridine pool-down with sorted cells from synchronized testes, we detailed the transcriptional activity of murine male germ cells. When spermatogonia differentiate, transcription slows down, reaching minimal activity at meiotic entry and resumes during pachytene stage. This event, we termed EMLT (for early meiotic low transcription), is distinct from the silencing of sex chromosomes as it is independent of Setdb1, though it is accompanied by the same chromatin mark, H3K9me3. EMLT is delayed in Stra8KO but occurs in mutants altering meiotic chromosome structure or double-strand break formation or repair. By comparing transcript abundance and nascent transcription we unveil a massive event of messenger RNA stabilization that parallels EMLT. Altogether our data indicate that meiosis is initiated with a nearly silent genome, and we propose that the stabilization of transcripts at that time facilitates the meiotic entry by synchronizing the expression of several meiotic subprograms.
    DOI:  https://doi.org/10.1093/nar/gkaf146
  27. Nat Rev Cardiol. 2025 Mar 20.
    Mitochondrial quality control in cardiomyocytes: safeguarding the heart against disease and ageing.
    Rishith Ravindran, Åsa B Gustafsson.
      Mitochondria are multifunctional organelles that are important for many different cellular processes, including energy production and biosynthesis of fatty acids, haem and iron-sulfur clusters. Mitochondrial dysfunction leads to a disruption in these processes, the generation of excessive reactive oxygen species, and the activation of inflammatory and cell death pathways. The consequences of mitochondrial dysfunction are particularly harmful in energy-demanding organs such as the heart. Loss of terminally differentiated cardiomyocytes leads to cardiac remodelling and a reduced ability to sustain contraction. Therefore, cardiomyocytes rely on multilayered mitochondrial quality control mechanisms to maintain a healthy population of mitochondria. Mitochondrial chaperones protect against protein misfolding and aggregation, and resident proteases eliminate damaged proteins through proteolysis. Irreparably damaged mitochondria can also be degraded through mitochondrial autophagy (mitophagy) or ejected from cells inside vesicles. The accumulation of dysfunctional mitochondria in cardiomyocytes is a hallmark of ageing and cardiovascular disease. This accumulation is driven by impaired mitochondrial quality control mechanisms and contributes to the development of heart failure. Therefore, there is a strong interest in developing therapies that directly target mitochondrial quality control in cardiomyocytes. In this Review, we discuss the current knowledge of the mechanisms involved in regulating mitochondrial quality in cardiomyocytes, how these pathways are altered with age and in disease, and the therapeutic potential of targeting mitochondrial quality control pathways in cardiovascular disease.
    DOI:  https://doi.org/10.1038/s41569-025-01142-1
  28. Nat Commun. 2025 Mar 17. 16(1): 2277
    A CPC-shelterin-BTR axis regulates mitotic telomere deprotection.
    Diana Romero-Zamora, Samuel Rogers, Ronnie Ren Jie Low, Scott G Page, Blake J E Lane, Shunya Kosaka, Andrew B Robinson, Lucy French, Noa Lamm, Fuyuki Ishikawa, Makoto T Hayashi, Anthony J Cesare.
      Telomeres prevent ATM activation by sequestering chromosome termini within telomere loops (t-loops). Mitotic arrest promotes telomere linearity and a localized ATM-dependent telomere DNA damage response (DDR) through an unknown mechanism. Using unbiased interactomics, biochemical screening, molecular biology, and super-resolution imaging, we found that mitotic arrest-dependent (MAD) telomere deprotection requires the combined activities of the Chromosome passenger complex (CPC) on shelterin, and the BLM-TOP3A-RMI1/2 (BTR) complex on t-loops. During mitotic arrest, the CPC component Aurora Kinase B (AURKB) phosphorylated both the TRF1 hinge and TRF2 basic domains. Phosphorylation of the TRF1 hinge domain enhances CPC and TRF1 interaction through the CPC Survivin subunit. Meanwhile, phosphorylation of the TRF2 basic domain promotes telomere linearity, activates a telomere DDR dependent on BTR-mediated double Holliday junction dissolution, and leads to mitotic death. We identify that the TRF2 basic domain functions in mitosis-specific telomere protection and reveal a regulatory role for TRF1 in controlling a physiological ATM-dependent telomere DDR. The data demonstrate that MAD telomere deprotection is a sophisticated active mechanism that exposes telomere ends to signal mitotic stress.
    DOI:  https://doi.org/10.1038/s41467-025-57456-8
  29. Mol Cell. 2025 Mar 18. pii: S1097-2765(25)00150-9. [Epub ahead of print]
    Base-pair resolution reveals clustered R-loops and DNA damage-susceptible R-loops.
    Yaoyi Li, Yingliang Sheng, Chao Di, Hongjie Yao.
      R-loops are pervasive triplex nucleic acid structures across diverse organisms, yet their biological functions remain incompletely understood. Here, we develop R-loop identification assisted by nucleases and sequencing (RIAN-seq), a nuclease-assisted, antibody-free sequencing technology, to map R-loops at base-pair resolution. By digesting single-stranded RNA (ssRNA), single-stranded DNA (ssDNA), and double-stranded DNA (dsDNA) with nuclease P1, T5 exonuclease, and lambda exonuclease while preserving RNA:DNA hybrids, RIAN-seq achieves unprecedented precision in identifying the position and size of R-loops, detecting an order of magnitude more R-loops than existing methods. Approximately 50% of RNA:DNA hybrids span between 60 and 130 bp, with many forming previously undetectable clusters. Clustered R-loops at promoters recruit zinc-finger proteins VEZF1 and SP5, enhancing transcription in a number-dependent manner and resisting transcriptional perturbation. Conversely, R-loops featuring the Y(C/T)M(A/C)CAG motif at both ends contribute to DNA damage, a phenomenon conserved from yeast to mammalian cells. Our findings reveal a dual role for R-loops: clustered R-loops promote gene expression, while YMCAG-associated R-loops compromise genome stability.
    Keywords:  DNA damage; R-loop; RIAN-seq; YMCAG-associated R-loops; base-pair resolution; clustered R-loops; gene regulation
    DOI:  https://doi.org/10.1016/j.molcel.2025.02.019
  30. Sci Adv. 2025 Mar 21. 11(12): eads2923
    Transfer RNA acetylation regulates in vivo mammalian stress signaling.
    Supuni Thalalla Gamage, Roxane Khoogar, Shereen Howpay Manage, Judey T DaRos, McKenna C Crawford, Joe Georgeson, Bogdan V Polevoda, Chelsea Sanders, Kendall A Lee, Kellie D Nance, Vinithra Iyer, Anatoly Kustanovich, Minervo Perez, Chu T Thu, Sam R Nance, Ruhul Amin, Christine N Miller, Ronald J Holewinski, Sudipto Das, Thomas J Meyer, Vishal Koparde, Acong Yang, Parthav Jailwala, Joe T Nguyen, Thorkell Andresson, Kent Hunter, Shuo Gu, Beverly A Mock, Elijah F Edmondson, Simone Difilippantonio, Raj Chari, Schraga Schwartz, Mitchell R O'Connell, Colin Chih-Chien Wu, Jordan L Meier.
      Transfer RNA (tRNA) modifications are crucial for protein synthesis, but their position-specific physiological roles remain poorly understood. Here, we investigate the impact of N4-acetylcytidine (ac4C), a highly conserved tRNA modification catalyzed by the essential acetyltransferase Nat10. By targeting Thumpd1, a nonessential adapter protein required for Nat10-catalyzed tRNA acetylation, we determine that loss of tRNA acetylation leads to reduced levels of tRNALeu, increased ribosome stalling, and activation of eIF2α phosphorylation. Thumpd1 knockout mice exhibit growth defects and sterility. Concurrent knockout of Thumpd1 and the stress-sensing kinase Gcn2 causes penetrant postnatal lethality in mice, indicating a critical genetic interaction. Our findings demonstrate that a modification restricted to a single position within type II cytosolic tRNAs can regulate ribosome-mediated stress signaling in mammalian organisms, with implications for our understanding of translational control and therapeutic interventions.
    DOI:  https://doi.org/10.1126/sciadv.ads2923
  31. Nat Methods. 2025 Mar 19.
    Marrying mechanics with spatial transcriptomics.
    Alexandre Francou, Woonyung Hur, Anna-Katerina Hadjantonakis.
      
    DOI:  https://doi.org/10.1038/s41592-024-02491-4
  32. EMBO Rep. 2025 Mar 17.
    Developmental mitochondrial complex I activity determines lifespan.
    Rhoda Stefanatos, Fiona Robertson, Beatriz Castejon-Vega, Yizhou Yu, Alejandro Huerta Uribe, Kevin Myers, Tetsushi Kataura, Viktor I Korolchuk, Oliver D K Maddocks, L Miguel Martins, Alberto Sanz.
      Aberrant mitochondrial function has been associated with an increasingly large number of human disease states. Observations from in vivo models where mitochondrial function is altered suggest that maladaptations to mitochondrial dysfunction may underpin disease pathology. We hypothesized that the severity of this maladaptation could be shaped by the plasticity of the system when mitochondrial dysfunction manifests. To investigate this, we have used inducible fly models of mitochondrial complex I (CI) dysfunction to reduce mitochondrial function at two stages of the fly lifecycle, from early development and adult eclosion. Here, we show that in early life (developmental) mitochondrial dysfunction results in severe reductions in survival and stress resistance in adulthood, while flies where mitochondrial function is perturbed from adulthood, are long-lived and stress resistant despite having up to a 75% reduction in CI activity. After excluding developmental defects as a cause, we went on to molecularly characterize these two populations of mitochondrially compromised flies, short- and long-lived. We find that our short-lived flies have unique transcriptomic, proteomic and metabolomic responses, which overlap significantly in discrete models of CI dysfunction. Our data demonstrate that early mitochondrial dysfunction via CI depletion elicits a maladaptive response, which severely reduces survival, while CI depletion from adulthood is insufficient to reduce survival and stress resistance.
    Keywords:  Ageing; Complex I; Drosophila; Mitochondria; Mitochondrial Disease
    DOI:  https://doi.org/10.1038/s44319-025-00416-6
  33. Proc Natl Acad Sci U S A. 2025 Mar 25. 122(12): e2425225122
    Energy landscape analysis of the development of the chromosome structure across the cell cycle.
    Vinícius G Contessoto, Antonio B Oliveira, Sumitabha Brahmachari, Peter G Wolynes, Michele Di Pierro, José N Onuchic.
      During mitosis, there are significant structural changes in chromosomes. We used a maximum entropy approach to invert experimental Hi-C data to generate effective energy landscapes for chromosomal structures at different stages during the cell cycle. Modeled mitotic structures show a hierarchical organization of helices of helices. High-periodicity loops span hundreds of kilobases or less, while the other low-periodicity ones are larger in genomic separation, spanning several megabases. The structural ensembles reveal a progressive decrease in compartmentalization from interphase to mitosis, accompanied by the appearance of a second diagonal in prometaphase, indicating an organized array of loops. While there is a local tendency to form chiral helices, overall, no preferential left-handed or right-handed chirality appears to develop on the time scale of the cell cycle. Chromatin thus appears to be a liquid crystal containing numerous defects that anneal rather slowly.
    Keywords:  chromatin dynamics; energy landscape; mitotic chromosome
    DOI:  https://doi.org/10.1073/pnas.2425225122
  34. FEBS J. 2025 Mar 20.
    The complete absence of cytoplasmic γ-actin results in no discernible phenotype in mice or primary fibroblasts.
    Lauren J Sundby, Katelin M Hawbaker, Jacob Powers, William M Southern, Erynn E Johnson, Xiaobai Patrinostro, Benjamin J Perrin, James M Ervasti.
      Mice and primary fibroblasts derived from mouse embryos completely lacking cytoplasmic β-actin, because the Actb gene was engineered to instead express γ-actin protein, have previously been found to be virtually devoid of phenotype. Here, we report the characterization of mice and mouse embryonic fibroblasts homozygous for an Actg1 allele edited to translate β-actin instead of γ-actin (Actg1-coding beta; Actg1c-b/c-b), which resulted in mice and fibroblasts that are devoid of γ-actin. We demonstrate that these Actg1c-b/c-b mice present with no measurable phenotype in survival, body mass, activity, muscle contractility, or auditory function. Primary fibroblasts derived from Actg1c-b/c-b mouse embryos were still proliferative, with several measured parameters of cell motility not different from wild type. From these and previous data, we conclude that β- and γ-actin proteins are redundant in primary embryonic fibroblasts and during normal mouse development.
    Keywords:  Actg1; actin; stereocilia; γ‐actin
    DOI:  https://doi.org/10.1111/febs.70075
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