bims-ginsta 2025-10-12 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2025–10–12
twenty-two papers selected by
Jinrong Hu, National University of Singapore

Microtubule forces drive nuclear damage in LMNA cardiomyopathy.
Epidermal stem cells control periderm injury repair via matrix-driven specialization of intercellular junctions.
Comparative analysis of human and mouse ovaries across age.
Ddx61-enriched condensates refine heart regeneration programs.
Actomyosin forces trigger a conformational change in desmoplakin within desmosomes.
Spatial mapping of DNA synthesis reveals dynamics and geometry of human replication nanostructures.
CD4 T cells acquire Eomesodermin to modulate cellular senescence and aging.
Interfacial tension and growth both contribute to mechanical cell competition.
The biophysical mechanism of mitochondrial pearling.
Coupling and decoupling of the cell cycle from cell differentiation in development.
Distinct waves of ovarian follicles contribute to mouse oocyte production.
Calcium signaling is required for anterior patterning in the mouse embryo.
Generation of spatially patterned human neural tube-like structures using microfluidic gradient devices.
Endogenous p21 levels protect genomic stability by suppressing both excess and restrained nascent DNA syntheses.
Reporter CRISPR screens decipher cis-regulatory and trans-regulatory principles at the Xist locus.
Single-cell and spatial detection of senescent cells using DeepScence.
Fosl2 facilitates chromatin accessibility to determine developmental events during follicular maturation.
AMPKα2 signals amino acid insufficiency to inhibit protein synthesis.
An Orc6 tether mediates ORC binding-site switching during replication origin licensing.
mRNA initiation and termination are spatially coordinated.
Antagonistic stem cell fates under stress govern decisions between hair greying and melanoma.
Translational regulation in stress biology.

Nat Cardiovasc Res. 2025 Oct 10.

Microtubule forces drive nuclear damage in LMNA cardiomyopathy.

Daria Amiad Pavlov, Julie Heffler, Carmen Suay-Corredera, Mohammad Dehghany, Kaitlyn M Shen, Noam Zuela-Sopilniak, Rani Randell, Keita Uchida, Rajan Jain, Vivek Shenoy, Jan Lammerding, Benjamin Prosser.

Nuclear homeostasis requires balanced forces between the cytoskeleton and the nucleus. Mutations in LMNA, which encodes lamin A/C, weaken the nuclear lamina, leading to nuclear damage and muscle disease. Disrupting the linker of nucleoskeleton and cytoskeleton (LINC) complex, which connects the cytoskeleton to the nucleus, may ameliorate LMNA-associated cardiomyopathy, yet the cardioprotective mechanism remains unclear. Here we developed an assay to quantify the coupling between cardiomyocyte contraction and nuclear deformation and interrogate its dependence on the nuclear lamina and LINC complex. The LINC complex was mostly dispensable for transferring contractile strain to the nucleus, and its disruption did not rescue elevated nuclear strain in lamin A/C-deficient cardiomyocytes. Instead, LINC complex disruption eliminated the microtubule cage encircling the nucleus. Microtubule disruption prevented nuclear damage and preserved cardiac function in lamin A/C deficiency. Computational modeling revealed that microtubule forces create local stress concentrations that damage lamin A/C-deficient nuclei. These findings identify microtubule-dependent force transmission as a pathological driver and therapeutic target for LMNA cardiomyopathy.

DOI: https://doi.org/10.1038/s44161-025-00727-w
Nat Commun. 2025 Oct 10. 16(1): 8967

Epidermal stem cells control periderm injury repair via matrix-driven specialization of intercellular junctions.

Helen Mengze He, Liana C Boraas, Jon M Bell, Xiangyu Gong, Sophia L Iannaccone, Zhang Wen, Michael Mak, Marina Carlson, Kaelyn Sumigray, Stefania Nicoli.

Epidermal stem cells interact with the extracellular matrix (ECM) to regulate their differentiation and maintain skin architecture. Here, we demonstrate a role for basal epidermal stem cells (BECs)-ECM interaction in regulating adhesion molecules expressed by the periderm-the superficial epidermal cells (SECs) of the embryonic bilayered skin. Using the developing zebrafish fin fold, we identify BECs form distinct regions of collagen- versus laminin- enriched basement membranes through integrin-mediated adhesions. Mechanistically, collagen-associated BECs form desmosomes and adherens junctions (AJs) with SECs while laminin-associated BECs display reduced desmosomes but sustain AJs and actomyosin expression with SECs. Notably, we show both in vivo and in a bilayered human keratinocyte model, that laminin, compared to collagen, is sufficient to repress desmosome formation while sustaining AJs specifically at the interlayer cell contacts. In vivo, laminin deficiency enhances desmosome expression across layers and impairs the wound-healing capacity of SECs. This defect was partially rescued by genetic reduction of the desmosome protein Desmoplakin-1a, highlighting the role of ECM-dependent junctional specialization in mediating differences in SEC injury response. Overall, our findings identify that stem cells, through their matrix, establish specialized junctions in the overlying stratified epithelium, which contribute to skin healing properties.

DOI: https://doi.org/10.1038/s41467-025-64040-7
Science. 2025 Oct 09.

Comparative analysis of human and mouse ovaries across age.

Eliza A Gaylord, Mariko H Foecke, Ryan M Samuel, Bikem Soygur, Angela M Detweiler, Tara I McIntyre, Leah C Dorman, Michael Borja, Amy E Laird, Ritwicq Arjyal, Juan Du, James M Gardner, Norma Neff, Faranak Fattahi, Diana J Laird.

The mouse is a tractable model for human ovarian biology, however its utility is limited by incomplete understanding of how transcription and signaling differ interspecifically and with age. We compared ovaries between species using three-dimensional imaging, single-cell transcriptomics, and functional studies. In mice, we mapped declining follicle numbers and oocyte competence during aging; in human ovaries, we identified cortical follicle pockets and decreases in density. Oocytes had species-specific gene expression patterns during growth that converged toward maturity. Age-related transcriptional changes were greater in oocytes than granulosa cells across species, although mature oocytes change more in humans. We identified ovarian sympathetic nerves and glia; axon density increased in aged ovaries and, when ablated in mice, perturbed folliculogenesis. This comparative atlas defines shared and species-specific hallmarks of ovarian biology.

DOI: https://doi.org/10.1126/science.adx0659
Nat Commun. 2025 Oct 09. 16(1): 8992

Ddx61-enriched condensates refine heart regeneration programs.

Mira I Pronobis, Sophia DeLuca, Siyun Lee, Lucas Garcia, Jianhong Ou, Nenad Bursac, Kenneth D Poss.

Gene regulatory mechanisms that underlie tissue regeneration have been largely studied at the level of transcription. Here, proximity labeling methods identify increased presence of the RNA helicase and P-body marker Ddx61 in adult zebrafish cardiomyocytes induced to divide by injury or mitogens. Ddx61 molecules form complex condensates in cardiomyocytes during cardiogenic settings in zebrafish, developing mice, and cultured human cells. ddx61 mutations disrupt cardiomyocyte proliferation and heart regeneration indices in adult zebrafish, and DDX6 knockdown reduces proliferation of cultured human cardiomyocytes. During heart regeneration, Ddx61 associates with and is required to restrain expression of mRNA encoding Chordin, a secreted BMP inhibitor that impedes regeneration if present at high levels. Our experiments indicate that mRNA sorting by context-dependent condensates can impact tissue regenerative capacity.

DOI: https://doi.org/10.1038/s41467-025-64026-5
Nat Commun. 2025 Oct 10. 16(1): 9052

Actomyosin forces trigger a conformational change in desmoplakin within desmosomes.

Yinchen Dong, Ahmed Elgerbi, Bin Xie, Yerin Han, Adam V Kwiatkowski, John S Choy, Sanjeevi Sivasankar.

Desmosomes are essential cell-cell adhesion organelles that enable tension-prone tissues, like the skin and heart, to withstand mechanical stress. Desmosomal anomalies are associated with numerous epidermal disorders, cardiomyopathies, and cancer. Despite their critical importance, how desmosomes sense and respond to mechanical stimuli is not understood. Here, we combine super-resolution imaging in epithelial cells and primary cardiomyocytes, FRET-based tension sensors, atomistic computer simulations, and biochemical assays to demonstrate that actomyosin forces induce a conformational change in desmoplakin, a key cytoplasmic desmosomal protein. We show that in human breast cancer MCF7 cells, keratin-19 couples F-actin filaments to desmosomes and regulates the level of actomyosin forces integrated into the desmosomal complex. We demonstrate that actomyosin contractility reorients keratin intermediate filaments and directs force to desmoplakin along the keratin network, plausibly converting the N-terminal plakin domain from a folded to an extended conformation. We also show that desmoplakin undergoes a similar actomyosin force-dependent conformational change in primary cardiomyocytes, with the extent of the change affected by myofibril orientation. Our findings establish that desmoplakin is mechanosensitive and its structural states reflect the level of forces transmitted through the actin network across cell types.

DOI: https://doi.org/10.1038/s41467-025-64124-4
EMBO J. 2025 Oct 07.

Spatial mapping of DNA synthesis reveals dynamics and geometry of human replication nanostructures.

Michael Hawgood, Bruno Urién, Ana Agostinho, Praghadhesh Thiagarajan, Giovanni Giglio, Yiqiu Yang, Xue Zhang, Gemma Quijada, Matilde Fonseca, Jiri Bartek, Hans Blom, Bennie Lemmens.

  DNA replication is essential to life and ensures the accurate transmission of genetic information, which is significantly disturbed during cancer development and chemotherapy. While DNA replication is tightly controlled in time and space, methods to visualise and quantify replication dynamics within 3D human cells are lacking. Here, we introduce 3D-Spatial Assay for Replication Kinetics (3D-SPARK), an approach enabling nanoscale analysis of DNA synthesis dynamics in situ. 3D-SPARK integrates optimised nucleotide analogue pulse labelling with super-resolution microscopy to detect, classify, and quantify replication nanostructures in single cells. By combining immunofluorescence techniques with click chemistry-based nascent DNA labelling and transfection of fluorescent nucleotide derivatives, we map multi-colour DNA synthesis events in relation to established replication proteins, local RNA-protein condensates or large subnuclear domains. We demonstrate quantitative changes in size, relative abundance and spatial arrangement of nanoscale DNA synthesis events upon chemotherapeutic treatment, CDC6 oncogene expression and loss of chromatin organiser RIF1. The flexibility, precision and modular design of 3D-SPARK helps bridging the gap between spatial cell biology, genomics, and 2D fibre-based replication studies in health and disease.

Keywords:  DNA Replication Dynamics; Genome Architecture; Nanoscale Imaging; Nascent DNA Labelling; Super-Resolution Microscopy

DOI:  https://doi.org/10.1038/s44318-025-00574-2
Nat Aging. 2025 Oct 07.

CD4 T cells acquire Eomesodermin to modulate cellular senescence and aging.

Yehezqel Elyahu, Ilana Feygin, Ekaterina Eremenko, Noa Pinkas, Alon Zemer, Amit Shicht, Omer Berner, Roni Avigdory-Meiri, Anna Nemirovsky, Keren Reshef, Lior Roitman, Valery Krizhanovsky, Alon Monsonego.

Aging is characterized by the progressive deterioration of tissue structure and function, leading to increased vulnerability to diseases. Senescent cells (SCs) accumulate with age, but how the immune system regulates their burden is unclear. Here we show that CD4 T cells differentiate into Eomesodermin (Eomes)+CCL5+ T lymphocytes (CD4-Eomes) in a SC-rich environment and that a reduction in the SC load, achieved using senolytic drugs, was sufficient to halt this differentiation. We further demonstrate that eliminating CD4-Eomes cells at advanced age by selectively deleting the Eomes transcription factor in CD4 T cells results in increased accumulation of SCs, profound physical deterioration and a decreased lifespan. In liver cirrhosis, a model of localized chronic inflammation, CD4-Eomes cell elimination increased fibrosis, SC load and worsened the disease. Collectively, our findings demonstrate the fundamental role of CD4-Eomes cells in modulating tissue senescence, with implications for age-related diseases and longevity.

DOI: https://doi.org/10.1038/s43587-025-00953-8
Curr Biol. 2025 Oct 09. pii: S0960-9822(25)01210-2. [Epub ahead of print]

Interfacial tension and growth both contribute to mechanical cell competition.

Léo Valon, Alexis Matamoro-Vidal, Alexis Villars, Romain Levayer.

  Tissue plasticity and homeostasis rely on the interplay between cell behavior and mechanical inputs.1 Mechanical stress also contributes to the evolution of pathologies, notably by accelerating pretumoral cell expansion through mechanical cell competition (MCC).2,3,4,5 MCC is a conserved process in which one cell population is preferentially eliminated when mixed with another cell population due to its higher sensitivity to mechanical stress.2,3,5,6,7,8 Theoretical and experimental explorations of MCC have mostly focused on the contribution of growth and pressure to cell elimination and a few genetic contexts, including the activation of Ras in vivo2,8 and mutation of the polarity gene scribble in mammalian cell culture.3,4,9 However, it remains unclear whether other oncogenes can trigger MCC and whether growth is generally the only central regulator of MCC. Using the Drosophila pupal notum (a single-layer epithelium), quantitative live imaging, and vertex modeling, we revisited the mechanisms contributing to MCC. Doing so, we outlined the co-existence of two modes of wild-type (WT) cell compaction near oncogenic cells, namely compaction driven by growth versus local compaction driven by increased tension at tumoral/WT cell interfaces in zones of high 2D curvature. We highlighted distinct signatures in cell deformation and cell elimination distribution that can delineate these two modes of compaction, and we recapitulated them in silico and in vivo using genetic backgrounds affecting growth and/or interfacial tension independently. Altogether, this study reveals the contribution of interfacial-tension-driven compaction to MCC and outlines the co-existence of various modes of compaction during MCC.

Keywords:  Drosophila; N-cad; Ras; Yki; apoptosis; differential growth; epithelium; interfacial tension; mechanical cell competition; vertex model

DOI:  https://doi.org/10.1016/j.cub.2025.09.040
Mol Biol Cell. 2025 Oct 08. mbcE25060302

The biophysical mechanism of mitochondrial pearling.

Gabriel Sturm, Kayley Hake, Austin E Y T Lefebvre, Caleb J Rux, Daria Ivanova, Alfred Millett-Sikking, Kevin M Tharp, Beiduo Rao, Michael Closser, Adam James Waite, Magdalena Precido-Lopez, Alex T Ritter, Sophie Dumont, Wen Lu, Suliana Manley, Juan C Landoni, Wallace F Marshall.

Mitochondrial networks exhibit remarkable dynamics that are driven in part by fission and fusion events. However, there are other reorganizations of the network that do not involve fission and fusion. One such exception is the elusive, "beads-on-a-string" morphological transition of mitochondria. During such transitions, the cylindrical tubes of the mitochondrial membrane transiently undergo shape changes to a string of "pearls" connected along thin tubes. These dynamics have been observed in many contexts and given disparate explanations. Here we unify these observations by proposing a common underlying mechanism based on the biophysical properties of tubular fluid membranes for which it is known that, under particular regimes of tension and pressure, membranes reach an instability and undergo a shape transition to a string of connected pearls. First, we use high-speed light-sheet microscopy to show that transient, short-lived pearling events occur spontaneously in the mitochondrial network in every cell type we have examined, including during T cell activation, neuronal firing, and replicative senescence. This high-temporal data reveals two distinct classes of spontaneous pearling, triggered either by ionic flux or cytoskeleton tension. We then induce pearling with chemical, genetic, and mechanical perturbations and establish three main physical causes of mitochondrial pearling, i) ionic flux producing internal osmotic pressure, ii) membrane packing lowering bending elasticity, and iii) external mechanical force increasing membrane tension. Pearling dynamics thereby reveal a fundamental biophysical facet of mitochondrial biology. We suggest that pearling should take its place beside fission and fusion as a key process of mitochondrial dynamics, with implications for physiology, disease, and aging.

DOI: https://doi.org/10.1091/mbc.E25-06-0302
Development. 2025 Oct 01. pii: dev204821. [Epub ahead of print]152(19):

Coupling and decoupling of the cell cycle from cell differentiation in development.

Kalki Kukreja, Allon Klein.

  For over a century, biologists have examined how the cell cycle and differentiation influence one another. While it is well established that cell fate decisions can regulate the cell cycle, the reciprocal effect of the cycle on differentiation remains more contentious. Here, we review mechanisms by which cell cycle events can influence differentiation in animals, but focus primarily on the widespread evidence that these processes are often uncoupled. Erythropoiesis provides a rare example where S-phase progression appears to be strictly required for a key commitment step across different species, whereas many other tissues differentiate normally despite complete arrest of cell division. We propose that decoupling cell cycle progression from differentiation enables independent control of tissue size and cell size and allows the cell cycle to tune progenitor numbers in response to physiological and evolutionary demands. Advances in single-cell and spatial transcriptomics now allow systematic assessment of coupling across tissues and developmental stages, and can disentangle genuine dependencies from stress responses induced by classical cell cycle inhibitors. Division and differentiation interact through multiple molecular pathways, but buffering these interactions to maintain weak or no coupling may be essential for adapting developmental processes.

Keywords:  Cell Division; Cell cycle; Embryonic development; Erythropoiesis; Single cell RNA-sequencing

DOI:  https://doi.org/10.1242/dev.204821
Elife. 2025 Oct 07. pii: RP107352. [Epub ahead of print]14

Distinct waves of ovarian follicles contribute to mouse oocyte production.

Qi Yin, Allan C Spradling.

  The earliest growing mouse follicles, wave 1, rapidly develop in the ovarian medulla, while the great majority, wave 2, are stored for later use as resting primordial follicles in the cortex. Wave 1 follicles are known to mostly undergo atresia, a fate sometimes associated with the persistence of steroidogenic theca cells, but this connection is poorly understood. We characterized wave 1 follicle biology using tissue clearing, lineage tracing, and scRNA-seq to clarify their contributions to offspring and steroidogenesis. Wave 1 follicles, lineage-marked by E16.5 Foxl2 expression in granulosa cells, reach preantral stages containing theca cell layers by 2 weeks. Atresia begins about a week later, during which 80-100% of wave 1 follicles degrade their oocytes, turn over most granulosa cells, but retain theca cells which expand in number together with interstitial gland cells in the medulla. During puberty (5 weeks), these cells ultrastructurally resemble steroidogenic cells and highly express androgen biosynthetic genes. Unexpectedly, the Foxl2 lineage tag also marked about 400 primordial follicles, located near the medullary-cortical boundary, that become the earliest activated wave 2 follicles. These 'boundary' or 'wave 1.5' follicles generate 70-100% of the earliest mature oocytes, while fewer than 26 wave 1 follicles with oocytes survive. Consistent with their largely distinct fates in steroid or oocyte production, granulosa cells of antral wave 1 and 2 follicles differentially express multiple genes, including Wnt4 and Igfbp5.

Keywords:  developmental biology; follicle wave; mouse; oocyte; ovarian follicle; steroid; theca cell

DOI:  https://doi.org/10.7554/eLife.107352
PLoS Biol. 2025 Oct 06. 23(10): e3003430

Calcium signaling is required for anterior patterning in the mouse embryo.

Matthew J Stower, Richard C V Tyser, Shifaan Thowfeequ, Felix Zhou, Marta Portela, Konstantinos Miti, Jacintha Sugnaseelan, Xin Lu, Shankar Srinivas.

Anterior-posterior axis formation in the mouse embryo requires the active migration of the DVE cell population at E5.5. While intracellular Ca2+ signaling has been shown to control cell migration in multiple cell contexts, it is unknown whether it is required for DVE migration. The pattern of Ca2+ activity in the mouse embryo at early peri-implantation stages is also unknown. Using the GCaMP6f Ca2+ reporter line, we performed a detailed assessment of Ca2+ dynamics between E0.5 and E5.5 using live imaging. We find that prior to implantation, Ca2+ transients are rare, but at E5.5 widespread, periodic, Ca2+ transients in extraembryonic tissues can be observed, including in the VE and ExE. In contrast, cells of the E5.5 epiblast remain relatively quiescent but show sporadic large-scale multicellular waves. Inhibition of SERCA at E5.5 abolishes Ca2+ transients and leads to DVE arrest, indicative that these transients are required for axial patterning. Together, these results reveal the pattern of Ca2+ handling in the early mouse embryo and a novel requirement in anterior-posterior axis formation.

DOI: https://doi.org/10.1371/journal.pbio.3003430
Nat Protoc. 2025 Oct 08.

Generation of spatially patterned human neural tube-like structures using microfluidic gradient devices.

Xufeng Xue, Omar M Rahman, Shiyu Sun, Jeyoon Bok, Aoife Tang, Jianping Fu.

The functional complexity and anatomical organization of the nervous system are established during regional patterning of its embryonic precursor-the neural tube. Human pluripotent stem (hPS) cell-based models have emerged as valuable complements to animal models for studying neural development. Here we present the design and implementation of a microfluidic gradient device for modeling human neural tube formation and regional patterning with hPS cells. The microfluidic device enables the formation of tubular or spherical colonies of hPS cells at prescribed locations within microfluidic channels, allowing the cell colonies to form lumenal structures while being exposed to well-controlled chemical gradients for rostral-caudal and/or dorsal-ventral patterning, resulting in the formation of a microfluidic neural tube-like structure (μNTLS) or a forebrain-like structure (μFBLS). The μNTLS recapitulates important hallmarks of early human neural development, including well-defined lumenal morphologies, spatially organized regional marker expression, emergence of secondary signaling centers and the development of neural crest cells. The dorsal-ventral patterned μFBLS further recapitulates spatially segregated dorsal and ventral regions, as well as the layered segregation of early neurons from neural progenitors, mimicking human forebrain pallium and subpallium development. Both the μNTLS and μFBLS are compatible with long-term culture, live imaging, immunofluorescence staining and single-cell sequencing, serving as robust systems for studying human neurodevelopment and disease. This protocol can be implemented by a researcher with polydimethylsiloxane soft lithography and cell culture experience and takes ~8-41 d to complete, depending on the types of neural structure to model and their developmental stages, with an option for prolonged culture to promote neuronal maturation.

DOI: https://doi.org/10.1038/s41596-025-01266-1
Sci Adv. 2025 Oct 10. 11(41): eadw4618

Endogenous p21 levels protect genomic stability by suppressing both excess and restrained nascent DNA syntheses.

Nicolás L Calzetta, Sabrina F Mansilla, Candelaria Mares Ahlers, Agostina P Bertolin, Lilen I Caimi, Sofía Venerus Arbilla, Jingkun Zeng, Lisa Wiesmüller, Vanesa Gottifredi.

The rate of DNA synthesis is crucial for full DNA duplication. We report a key role of p21 in controlling this rate. During normal replication, p21 promotes nascent DNA synthesis alongside the DNA polymerase iota (Pol ι)/p53 complex. When p21 is down-regulated but detectable, nascent DNA tracks are longer and discontinuous and rely on primase and DNA polymerase (PrimPol). With the complete elimination of p21, nascent DNA tracks become shorter and continuous and depend on Pol kappa (κ). Endogenous p21 levels are critical for genomic stability, as both PrimPol- and Pol κ-mediated syntheses can induce chromosomal instability. The residual expression of p21 in p53-null cells influences the involvement of PrimPol or Pol κ in nascent DNA synthesis and subsequent chromosomal instability. Our results demonstrate that endogenous levels of p21 in cycling cells, insufficient for cyclin-dependent kinase inhibition, prevent genomic instability through proliferating cell nuclear antigen binding (PCNA), limiting PrimPol and Pol κ's role in nascent DNA synthesis.

DOI: https://doi.org/10.1126/sciadv.adw4618
Nat Struct Mol Biol. 2025 Oct 06.

Reporter CRISPR screens decipher cis-regulatory and trans-regulatory principles at the Xist locus.

Till Schwämmle, Gemma Noviello, Eleni Kanata, Jonathan J Froehlich, Melissa Bothe, Alexandra Martitz, Aybuge Altay, Jade Scouarnec, Vivi-Yun Feng, Heleen Mallie, Martin Vingron, Edda G Schulz.

Developmental genes are controlled by an ensemble of cis-acting regulatory elements (REs), which in turn respond to multiple trans-acting transcription factors (TFs). Understanding how a cis-regulatory landscape integrates information from many dynamically expressed TFs has remained a challenge. Here we develop a combined CRISPR screening approach using endogenous RNA and RE reporters as readouts. Applied to the murine Xist locus, which is crucial for X-chromosome inactivation in females, this method allows us to comprehensively identify Xist-controlling TFs and map their TF-RE wiring. We find a group of transiently upregulated TFs, including ZIC3, that regulate proximal REs, driving the binary activation of Xist expression. These basal activators are more highly expressed in cells with two X chromosomes, potentially governing female-specific Xist upregulation. A second set of developmental TFs that include OTX2 is upregulated later during differentiation and targets distal REs. This regulatory axis is crucial to achieve high levels of Xist RNA, which is necessary for X-chromosome inactivation. OCT4 emerges as the strongest activator overall, regulating both proximal and distal elements. Our findings support a model for developmental gene regulation, in which factors targeting proximal REs drive binary on-off decisions, whereas factors interacting with distal REs control the transcription output.

DOI: https://doi.org/10.1038/s41594-025-01686-3
Cell Genom. 2025 Oct 07. pii: S2666-979X(25)00291-5. [Epub ahead of print] 101035

Single-cell and spatial detection of senescent cells using DeepScence.

Yilong Qu, Beijie Ji, Runze Dong, Liangcai Gu, Cliburn Chan, Jichun Xie, Carolyn Glass, Xiao-Fan Wang, Andrew B Nixon, Zhicheng Ji.

  Accurately identifying senescent cells is essential for studying their spatial and molecular features. We developed DeepScence, a method based on deep neural networks, to identify senescent cells in single-cell and spatial transcriptomics data. DeepScence is based on CoreScence, a senescence-associated gene set we curated that incorporates information from multiple published gene sets. We demonstrate that DeepScence can accurately identify senescent cells in single-cell gene expression data collected both in vitro and in vivo, as well as in spatial transcriptomics data generated by different platforms, substantially outperforming existing methods.

Keywords:  aging; cellular senescence; machine learning; scRNA-seq; senescence gene set; senescence identification; spatial transcriptomics

DOI:  https://doi.org/10.1016/j.xgen.2025.101035
Nat Commun. 2025 Oct 08. 16(1): 8955

Fosl2 facilitates chromatin accessibility to determine developmental events during follicular maturation.

Hongyong Zhang, Zechen Li, Yanmei Zhu, Wencong Lyu, Wenlu Wei, Haochen Wang, Shuangjie Tian, Wei Yue, Jiajing Zhong, Qing-Yuan Sun, Yiting Guan.

Granulosa cells (GCs) are the most dynamically responsive cell lineage to encourage continuous folliculogenesis; however, developmental dynamics and interplay with downstream transcription circuitry remain unclear. Here, we unravel the redistribution of genome-wide chromatin areas that drive broad developmental-related transcriptomic alterations during follicular maturation in murine and porcine GCs. Distinct GC-activated accessibility regions (GAAs) at the ovulatory phase are responsible for augmenting flanking GC-involved developmental gene (GDG) expression, which are essential for transcriptional responses to developmental cues. Mechanistically, the transcription factor Fosl2 is strongly recruited to GAAs, facilitating chromatin accessibility state transition. Elevated GAA signals driven by Fosl2 loading induce a significant upregulation of adjacent GDG expression. Additionally, GC-specific Fosl2 deletion in mice perturbs GC cellularity, leading to subfertility related to reproductive aging. Together, we highlight a dynamic chromatin accessibility landscape during follicular maturation, revealing the indispensable Fosl2 function not only controls transcriptional activation via a reconfigured chromatin state, but also orchestrates intricate signaling pathways that are fundamental for ovulation and reproduction.

DOI: https://doi.org/10.1038/s41467-025-64009-6
Cell Metab. 2025 Oct 07. pii: S1550-4131(25)00389-4. [Epub ahead of print]

AMPKα2 signals amino acid insufficiency to inhibit protein synthesis.

Yunzi Mao, Mei Cui, Yanfeng Jiang, Haowen Yu, Meng Wang, Gang Li, Haihui Zhang, Cheng Zhao, Yanxin Shen, Yupeng Hu, Yanpeng An, Yan Lin, Yiyuan Yuan, Pengcheng Lin, Xingdong Chen, Wei Xu, Shi-Min Zhao.

  The functional difference between the two catalytic subunits, α1 and α2, of AMP-activated protein kinase (AMPK) complexes remains elusive. Herein, we report that AMPKα2 specifically transduces amino acid insufficiency signals to protein synthesis. Low amino acid levels, high protein levels, and reduced phosphorylation of AMPKα threonine 172 (p-T172) are observed in blood samples in patients with Alzheimer's disease (AD) from a cohort of 1,000,000 Chinese individuals. Loss of α2, but not α1, recaptures these observations and induces AD-like cognitive dysfunction in mice. Mechanistically, low amino acid-activated general control nonderepressible 2 (GCN2) specifically phosphorylates α2 at T172 independent of AMP and fructose 1,6-bisphosphate to inhibit protein synthesis. α2-p-T172 loss renders protein over-synthesis and AD-pathologic protein aggregation in cells and in mouse brain. AMPK activators metformin and 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranoside (AICAR), as well as branched-chain amino acid (BCAA) or protein restriction, α2-p-T172-dependently prevent AD-like symptoms in mice. We identify AMPKα2 as a specific amino acid abundance detector for protein synthesis.

Keywords:  AMPK; Alzheimer’s disease; amino acids; translation

DOI:  https://doi.org/10.1016/j.cmet.2025.09.004
Proc Natl Acad Sci U S A. 2025 Oct 14. 122(41): e2510685122

An Orc6 tether mediates ORC binding-site switching during replication origin licensing.

David Driscoll, Larry J Friedman, Jeff Gelles, Stephen P Bell.

  During origin licensing, the origin recognition complex (ORC) loads two Mcm2-7 helicases onto DNA in a head-to-head conformation, establishing the foundation for subsequent bidirectional replication. Single-molecule experiments support a helicase-loading model in which one ORC loads both Mcm2-7 helicases at origins. For this to occur, ORC must release from its initial Mcm2-7 and DNA binding sites, flip over the helicase, and bind the opposite end of the Mcm2-7 complex and adjacent DNA to form the MO complex. Importantly, this binding-site transition occurs without ORC releasing into solution. Using a single-molecule FRET assay, we show that the N-terminal half of Orc6 tethers ORC to the N-terminal region of Mcm2 during ORC's binding-site transition. This interaction involves both the folded Orc6 N-terminal domain (Orc6N) and the adjacent unstructured linker and forms before ORC releases from its initial Mcm2-7 interaction. The absence of this interaction increases the rate of ORC release into solution, consistent with a tethering function. CDK phosphorylation of ORC inhibits the tethering interaction, providing a mechanism for the known CDK inhibition of MO complex formation. Interestingly, we identify mutations in the Orc6 linker region that support MO complex formation but prevent double-hexamer formation by inhibiting stable second Mcm2-7 recruitment. Our study provides a molecular explanation for a one-ORC mechanism of helicase loading and demonstrates that Orc6 is involved in multiple stages of origin licensing.

Keywords:  DNA replication initiation; Mcm2-7 helicase; origin licensing; origin recognition complex (ORC); single-molecule FRET

DOI:  https://doi.org/10.1073/pnas.2510685122
Science. 2025 Oct 09. 390(6769): eado8279

mRNA initiation and termination are spatially coordinated.

Ezequiel Calvo-Roitberg, Christine L Carroll, GyeungYun Kim, Valeria Sanabria, Sergey V Venev, Steven T Mick, Joseph D Paquette, Maritere Uriostegui-Arcos, Job Dekker, Ana Fiszbein, Athma A Pai.

Transcriptional initiation and termination decisions drive messenger RNA (mRNA) isoform diversity but the relationship between them remains poorly understood. By systematically profiling joint usage of transcription start and end sites, we observed that mRNA using upstream starts preferentially use upstream end sites and that the usage of downstream sites is similarly coupled. Our results suggest a positional initiation termination axis (PITA), in which usage of alternative terminal sites are coupled based on their genomic order. PITA is enriched in longer genes with distinct chromatin features. We find that mRNA 5' start choice directly influences 3' ends depending on RNA polymerase II trafficking speed. Our results indicate that spatial organization and transcriptional dynamics couple transcription initiation and mRNA 3' end decisions to define mRNA isoform expression.

DOI: https://doi.org/10.1126/science.ado8279
Nat Cell Biol. 2025 Oct 06.

Antagonistic stem cell fates under stress govern decisions between hair greying and melanoma.

Yasuaki Mohri, Jialiang Nie, Hironobu Morinaga, Tomoki Kato, Takahiro Aoto, Takashi Yamanashi, Daisuke Nanba, Hiroyuki Matsumura, Sakura Kirino, Kouji Kobiyama, Ken J Ishii, Masahiro Hayashi, Tamio Suzuki, Takeshi Namiki, Jun Seita, Emi K Nishimura.

The exposome, an individual's lifelong environmental exposure, profoundly impacts health. Somatic tissues undergo functional decline with age, exhibiting characteristic ageing phenotypes, including hair greying and cancer. However, the specific genotoxins, signals and cellular mechanisms underlying each phenotype remain largely unknown. Here we report that melanocyte stem cells (McSCs) and their niche coordinately determine individual stem cell fate through antagonistic, stress-responsive pathways, depending on the type of genotoxic damage incurred. McSC fate tracking in mice revealed that McSCs undergo cellular senescence-coupled differentiation (seno-differentiation) in response to DNA double-strand breaks, resulting in their selective depletion and hair greying, and effectively protecting against melanoma. Conversely, carcinogens can suppress McSC seno-differentiation, even in cells harbouring double-strand breaks, by activating arachidonic acid metabolism and the niche-derived KIT ligand, thereby promoting McSC self-renewal. Collectively, the fate of individual stem cell clones-expansion versus exhaustion-cumulatively and antagonistically governs ageing phenotypes through interaction with the niche.

DOI: https://doi.org/10.1038/s41556-025-01769-9
Nat Cell Biol. 2025 Oct 07.

Translational regulation in stress biology.

Naomi R Genuth, Andrew Dillin.

Organisms must constantly respond to stress to maintain homeostasis, and the successful implementation of cellular stress responses is directly linked to lifespan regulation. In this Review we examine how three age-associated stressors-loss of proteostasis, oxidative damage and dysregulated nutrient sensing-alter protein synthesis. We describe how these stressors inflict cellular damage via their effects on translation and how translational changes can serve as both sensors and responses to the stressor. Finally, we compare stress-induced translational programmes to protein synthesis alterations that occur with age and discuss whether these changes are adaptive or deleterious to longevity and healthy ageing.

DOI: https://doi.org/10.1038/s41556-025-01765-z