bims-ginsta 2025-08-10 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2025–08–10
27 papers selected by
Jinrong Hu, National University of Singapore

Mechanochemical coupling of cell shape and organ function optimizes heart size and contractile efficiency in zebrafish.
Transgene-free generation of mouse post-gastrulation whole embryo models solely from naive ESCs and iPSCs.
A programmed decline in ribosome levels governs human early neurodevelopment.
NuMA mechanically reinforces the spindle independently of its partner dynein.
A complete model of mouse embryogenesis through organogenesis enabled by chemically induced embryo founder cells.
Eliminating separase inhibition reveals absence of robust cohesin protection in oocyte metaphase II.
The intrinsically disordered regions of organellophagy receptors are interchangeable and control organelle fragmentation, ER-phagy and mitophagy flux.
Unequal segregation of mitochondria during asymmetric cell division contributes to cell fate divergence in sister cells in vivo.
Chromatin-dependent motif syntax defines differentiation trajectories.
YAP regulates transcriptional programs for layer-specific periosteal expansion during fracture repair.
Allele frequency selection and no age-related increase in human oocyte mitochondrial mutations.
Basal Cell-Contact Dynamics Influence Tissue Packing in a Proliferating Mammalian Epithelium.
Targeting CyclinD1-CDK6 to Mitigate Senescence-Driven Inflammation and Age-Associated Functional Decline.
RNA N-glycosylation enables immune evasion and homeostatic efferocytosis.
Mapping mesenchymal diversity in the developing human intestine and organoids.
NAC controls nascent chain fate through tunnel sensing and chaperone action.
Global inhibition of deadenylation stabilizes the transcriptome in mitotic cells.
Cell surface crowding is a tunable energetic barrier to cell-cell fusion.
The cardiac phospho-proteome during pressure overload in mice.
The molecular basis of human transcription-coupled DNA repair.
A mechano-resistance mechanism in skin adapts to terrestrial locomotion.
Transcription-coupled repair: protecting genome across generations.
Fibroblast depletion reveals mammalian epithelial resilience across neonatal and adult stages.
STRESS, an automated geometrical characterization of deformable particles for in vivo measurements of cell and tissue mechanical stresses.
Comprehensive transcription factor perturbations recapitulate fibroblast transcriptional states.
The RING finger E3 ligase RNF25 protects DNA replication forks independently of its canonical roles in ubiquitin signaling.
Generative model for the first cell fate bifurcation in mammalian development.

Dev Cell. 2025 Aug 05. pii: S1534-5807(25)00468-X. [Epub ahead of print]

Mechanochemical coupling of cell shape and organ function optimizes heart size and contractile efficiency in zebrafish.

Toby G R Andrews, Jake Cornwall-Scoones, Marie-Christine Ramel, Kirti Gupta, James Briscoe, Rashmi Priya.

  How simple tissue primordia sculpt complex functional organs, robustly and reproducibly, remains elusive. During zebrafish development, the embryonic myocardial wall matures into an intricate 3D architecture, composed of an outer compact layer enveloping an inner layer of multicellular trabecular ridges. How these tissue layers acquire their characteristic form suited for their function remains an open question. Here, we find that multiscale mechanochemical coupling and an emergent tissue-scale morphological transition steer functional maturation of the developing zebrafish heart. Single-celled trabecular seeds recruit outer compact layer cells to mature into clonally heterogeneous multicellular ridges, thereby amplifying cardiac contractile forces. In response, the remaining compact layer cells are stretched, which impedes their further recruitment, thereby constraining trabecular ridge density. Concomitantly, Notch-dependent actomyosin dampening triggers a sharp transition in myocardial tissue area, activating rapid organ growth that expands blood-filling capacity. Thus, multiscale self-organizing interactions optimize heart size and contractile efficiency to support embryonic life.

Keywords:  Notch signaling; cardiac trabeculation; critical transition; developmental mechanics; heart development; mechanical tipping-point; mechanochemical feedback; organogenesis; robustness; tissue morphogenesis

DOI:  https://doi.org/10.1016/j.devcel.2025.07.011
Cell Stem Cell. 2025 Aug 06. pii: S1934-5909(25)00262-0. [Epub ahead of print]

Transgene-free generation of mouse post-gastrulation whole embryo models solely from naive ESCs and iPSCs.

Alperen Yilmaz, Gulben Gurhan, Mehmet-Yunus Comar, Sergey Viukov, Inbal Serfaty, Mert Gayretli, Sergey Golenchenko, Dmitry Lokshtanov, Shahd Ashouokhi, Angel Polanco, Idan Berlad, Tae-Won Ha, Alejandro Aguilera-Castrejon, Shadi Tarazi, Marina Cohen, Nir Livnat, Komal Kumar, Hisham Cholakkal, Nathan Levy, Nir Yosef, Nizar Khatib, Reli Rachel Kakun, Merav Kedmi, Inbal Bolocan Nachman, Hadas Keren-Shaul, Yoseph Addadi, Ayelet-Hashahar Orenbuch, Karina Korovin, Alina Molchadsky, Konrad Hochedlinger, Ohad Gafni, Itay Maza, Noa Novershtern, Bernardo Oldak, Jacob H Hanna.

  The generation of post-gastrulation stem cell-derived mouse embryo models (SEMs) exclusively from naive embryonic stem cells (nESCs) has underscored their ability to give rise to embryonic and extra-embryonic lineages. However, existing protocols for mouse SEMs rely on the separate induction of extra-embryonic lineages and on ectopic expression of transcription factors to induce nESC differentiation into trophectoderm (TE) or primitive endoderm (PrE). Here, we demonstrate that mouse nESCs and naive induced pluripotent stem cells (niPSCs) can be simultaneously co-induced, via signaling pathway modulation, to generate PrE and TE extra-embryonic cells that self-organize into embryonic day (E) 8.5-E8.75 transgene-free (TF) SEMs. We also devised an alternative condition (AC) naive media that in vitro stabilizes TF-SEM-competent OCT4+/NANOG+ nESC colonies that co-express antagonistic CDX2 and/or GATA6 extra-embryonic fate master regulators and self-renew while remaining poised for TE and PrE differentiation, respectively. These findings improve mouse SEM strategies and shed light on amplifying an inherent and dormant extra-embryonic plasticity of mouse naive pluripotent cells in vitro.

Keywords:  chemical reprogramming; embryo models; ex utero embryo culture; extra-embryonic lineages; naive pluripotency; primitive endoderm; synthetic embryology; trophoblast stem cells

DOI:  https://doi.org/10.1016/j.stem.2025.07.005
Nat Cell Biol. 2025 Aug 04.

A programmed decline in ribosome levels governs human early neurodevelopment.

Chunyang Ni, Yudong Wei, Barbara Vona, Dayea Park, Yulei Wei, Daniel A Schmitz, Yi Ding, Masahiro Sakurai, Emily Ballard, Leijie Li, Yan Liu, Ashwani Kumar, Chao Xing, Shenlu Qin, Sangin Kim, Martina Foglizzo, Jianchao Zhao, Hyung-Goo Kim, Cumhur Ekmekci, Ehsan Ghayoor Karimiani, Shima Imannezhad, Fatemeh Eghbal, Reza Shervin Badv, Eva Maria Christina Schwaibold, Mohammadreza Dehghani, Mohammad Yahya Vahidi Mehrjardi, Zahra Metanat, Hosein Eslamiyeh, Ebtissal Khouj, Saleh Mohammed Nasser Alhajj, Aziza Chedrawi, Khushnooda Ramzan, Jamil A Hashmi, Majed M Alluqmani, Sulman Basit, Danai Veltra, Nikolaos M Marinakis, Georgios Niotakis, Pelagia Vorgia, Christalena Sofocleous, Hane Lee, Won Chan Jeong, Muhammad Umair, Muhammad Bilal, César Augusto Pinheiro Ferreira Alves, Matthew Sieber, Michael Kruer, Henry Houlden, Fowzan S Alkuraya, Elton Zeqiraj, Roger A Greenberg, Can Cenik, Leqian Yu, Reza Maroofian, Jun Wu, Michael Buszczak.

Many neurodevelopmental defects are linked to genes involved in housekeeping functions, such as those encoding ribosome biogenesis factors. How reductions in ribosome biogenesis can result in tissue- and developmental-specific defects remains unclear. Here we describe variants in the ribosome biogenesis factor AIRIM/C1orf109 that are primarily associated with neurodevelopmental disorders. Using human cerebral organoids in combination with proteomic, single-cell RNA sequencing and single-organoid translation analyses, we identify a previously unappreciated drop in protein production during early brain development. We find that ribosome levels decrease during neuroepithelial differentiation, making differentiating cells particularly vulnerable to perturbations in ribosome biogenesis during this time. Reduced ribosome availability more profoundly impacts the translation of specific transcripts, disrupting both survival and cell fate commitment of transitioning neuroepithelia. Enhancing mTOR activity suppresses the growth and developmental defects associated with AIRIM/C1orf109 variants. This work provides evidence for the functional importance of regulated changes in global protein synthesis capacity during cellular differentiation.

DOI: https://doi.org/10.1038/s41556-025-01708-8
Curr Biol. 2025 Jul 30. pii: S0960-9822(25)00894-2. [Epub ahead of print]

NuMA mechanically reinforces the spindle independently of its partner dynein.

Nathan H Cho, Merve Aslan, Aryan Taheri, Ahmet Yildiz, Sophie Dumont.

  During cell division, both motor and non-motor proteins organize microtubules to build the spindle and maintain it against opposing forces. Nuclear mitotic apparatus (NuMA), a long microtubule-binding protein, is essential to spindle structure and function. NuMA recruits the motor dynein to actively cluster spindle microtubule minus-ends, but whether NuMA performs other spindle roles remains unknown. Here, we show that NuMA acts independently of dynein to passively reinforce the mammalian spindle. NuMA that cannot bind dynein is sufficient to protect spindle poles against fracture under external force. In contrast, NuMA with a shorter coiled coil or disrupted self-interactions cannot protect spindle poles, and NuMA turnover differences cannot explain mechanical differences. In vitro, NuMA's C terminus self-interacts and bundles microtubules without dynein, dependent on residues essential to pole protection in vivo. Together, this suggests that NuMA reinforces spindle poles by crosslinking microtubules, using its long coiled coil and self-interactions to reach multiple, far-reaching pole microtubules. We propose that NuMA acts as a mechanical "multitasker" targeting contractile motor activity and separately crosslinking microtubules, with both functions synergizing to drive spindle mechanical robustness.

Keywords:  NuMA; crosslinking; dynein; force; mechanics; microtubules; pole; robustness; self-organization; spindle

DOI:  https://doi.org/10.1016/j.cub.2025.07.028
Cell. 2025 Aug 06. pii: S0092-8674(25)00807-4. [Epub ahead of print]

A complete model of mouse embryogenesis through organogenesis enabled by chemically induced embryo founder cells.

Huanhuan Li, Wei Guan, Jiahui Huang, Penglei Shen, Jinyi Wu, Haiping Luo, Yun Yang, Shaoqiang Ning, Litao Chang, Haiyong Zhao, Chuanxin Chen, Yake Gao, Yaoyu Chen, Xianfa Yang, Yael Costa, Chen-Leng Cai, Duanqing Pei, Guangdun Peng, Guangming Wu, Jiekai Chen, Jian Zhang, Naihe Jing, José C R Silva.

  Embryo models offer opportunities for understanding development and advancing medicine but rely on intricate procedures with limitations in efficiency and developmental fidelity. Here, we employ a small-molecule-only approach to induce mouse embryonic stem cells into 8- to 16-cell-like embryo founder cells, enabling the generation of a complete embryo model. These founder cells specify all blastocyst lineages, both embryonic and extraembryonic, in vivo and in vitro. The embryo model made only from embryo founder cells faithfully recapitulates development through organogenesis. During gastrulation, it forms a primitive streak via epithelial-to-mesenchymal transition, generates the three germ layers, and develops an ectoplacental cone. The model proceeds to form 6-14 somite pairs, fore-/mid-/hindbrain, a looping heart tube, optic buds, allantois, tail bud, migrating primordial germ cells, and well-defined gut. Altogether, our system using embryo founder cells enables a direct, rapid, efficient, and accurate in vitro model of embryogenesis.

Keywords:  EFC; EFC embryo model; chemical reprogramming; embryo model; gastrulation; induced embryo founder cells; organogenesis; small molecule; synthetic embryo; totipotent

DOI:  https://doi.org/10.1016/j.cell.2025.07.018
EMBO J. 2025 Aug 05.

Eliminating separase inhibition reveals absence of robust cohesin protection in oocyte metaphase II.

Safia El Jailani, Damien Cladière, Elvira Nikalayevich, Sandra A Touati, Vera Chesnokova, Shlomo Melmed, Eulalie Buffin, Katja Wassmann.

  The meiotic segregation pattern to generate haploid gametes is mediated by step-wise cohesion removal by separase, first from chromosome arms in meiosis I, and then from the pericentromere in meiosis II. In mammalian oocytes, separase is tightly controlled during the hours-long prometaphase and until chromosome segregation in meiosis I, activated for a short time window, and again inhibited until metaphase II arrest is lifted by fertilization. Centromeric cohesin is protected from cleavage by Sgo2-PP2A in meiosis I. It remained enigmatic how tight control of alternating separase activation and inactivation is achieved during the two divisions in oocytes, and when cohesin protection is put in place and removed. Using complementation assays in knock-out mouse models, we established the contributions of cyclin B1 and securin for separase inhibition during both divisions. When eliminating separase inhibition, we found that cohesin is not robustly protected at meiosis I resumption and during metaphase II arrest. Importantly, in meiosis II, the sole event required for cleavage of pericentromeric cohesin besides separase activation is prior kinetochore individualization in meiosis I.

Keywords:  Cohesin Protection; Kinetochore Individualization; Meiosis; Oocytes; Separase Inhibition

DOI:  https://doi.org/10.1038/s44318-025-00522-0
Nat Cell Biol. 2025 Aug 04.

The intrinsically disordered regions of organellophagy receptors are interchangeable and control organelle fragmentation, ER-phagy and mitophagy flux.

Mikhail Rudinskiy, Carmela Galli, Andrea Raimondi, Maurizio Molinari.

Organellophagy receptors control the generation and delivery of portions of their homing organelle to acidic degradative compartments to recycle nutrients, remove toxic or aged macromolecules and remodel the organelle upon physiologic or pathologic cues. How they operate is not understood. Here we show that organellophagy receptors are composed of a membrane-tethering module that controls organellar and suborganellar distribution and by a cytoplasmic intrinsically disordered region (IDR) with net cumulative negative charge that controls organelle fragmentation and displays an LC3-interacting region (LIR). The LIR is required for lysosomal delivery but is dispensable for organelle fragmentation. Endoplasmic reticulum (ER)-phagy receptors' IDRs trigger DRP1-assisted mitochondrial fragmentation and mitophagy when transplanted at the outer mitochondrial membrane. Mitophagy receptors' IDRs trigger ER fragmentation and ER-phagy when transplanted at the ER membrane. This offers an interesting example of function conservation on sequence divergency. Our results imply the possibility to control the integrity and activity of intracellular organelles by surface expression of organelle-targeted chimeras composed of an organelle-targeting module and an IDR module with net cumulative negative charge that, if it contains a LIR, eventually tags the organelle portions for lysosomal clearance.

DOI: https://doi.org/10.1038/s41556-025-01728-4
Nat Commun. 2025 Aug 04. 16(1): 7174

Unequal segregation of mitochondria during asymmetric cell division contributes to cell fate divergence in sister cells in vivo.

Ioannis Segos, Jens Van Eeckhoven, Simon Berger, Nikhil Mishra, Eric J Lambie, Barbara Conradt.

The unequal segregation of organelles has been proposed to be an intrinsic mechanism that contributes to cell fate divergence during asymmetric cell division; however, in vivo evidence is sparse. Using super-resolution microscopy, we analysed the segregation of organelles during the division of the neuroblast QL.p in C. elegans larvae. QL.p divides to generate a daughter that survives, QL.pa, and a daughter that dies, QL.pp. We found that mitochondria segregate unequally by density and morphology and that this is dependent on mitochondrial dynamics. Furthermore, we found that mitochondrial density in QL.pp correlates with the time it takes QL.pp to die. We propose that low mitochondrial density in QL.pp promotes the cell death fate and ensures that QL.pp dies in a highly reproducible and timely manner. Our results provide in vivo evidence that the unequal segregation of mitochondria can contribute to cell fate divergence during asymmetric cell division in a developing animal.

DOI: https://doi.org/10.1038/s41467-025-62484-5
Mol Cell. 2025 Aug 07. pii: S1097-2765(25)00606-9. [Epub ahead of print]85(15): 2900-2918.e16

Chromatin-dependent motif syntax defines differentiation trajectories.

Sevi Durdu, Murat Iskar, Luke Isbel, Leslie Hoerner, Christiane Wirbelauer, Lukas Burger, Daniel Hess, Vytautas Iesmantavicius, Dirk Schübeler.

  Transcription factors (TFs) recognizing DNA motifs within regulatory regions drive cell identity. Despite recent advances, their specificity remains incompletely understood. Here, we address this by contrasting two TFs, Neurogenin-2 (NGN2) and MyoD1, which recognize ubiquitous E-box motifs yet drive distinct cell fates toward neurons and muscles, respectively. Upon induction in mouse embryonic stem cells, we monitor binding across differentiation, employing an interpretable machine learning approach that integrates preexisting DNA accessibility. This reveals a chromatin-dependent motif syntax, delineating both common and factor-specific binding, validated by cellular and in vitro assays. Shared binding sites reside in open chromatin, locally influenced by nucleosomes. In contrast, factor-specific binding in closed chromatin involves NGN2 and MyoD1 acting as pioneer factors, influenced by motif variant frequencies, motif spacing, and interaction partners, which together account for subsequent lineage divergence. Transferring our methodology to other models demonstrates how a combination of opportunistic binding and context-specific chromatin-opening underpin TF specificity, driving differentiation trajectories.

Keywords:  E-box; cell differentiation; chromatin accessibility; gene regulation; machine learning; motif syntax; motif variants; pioneer factors; predictive models; transcription factor specificity

DOI:  https://doi.org/10.1016/j.molcel.2025.07.005
Sci Adv. 2025 Aug 08. 11(32): eadw0126

YAP regulates transcriptional programs for layer-specific periosteal expansion during fracture repair.

Madhura P Nijsure, Brendan Tobin, Dakota L Jones, Annemarie Lang, Grey Hallström, Miriam Baitner, Gabrielle I Tanner, Georgios Kotsaris, Yasaman Moharrer, Christopher J Panebianco, Elizabeth G Seidl, Nathaniel A Dyment, Gregory L Szeto, Levi Wood, Joel D Boerckel.

Bone fracture repair initiates by periosteal expansion. The periosteum is a bilayered tissue composed of inner cambium and outer fibrous layers. Typically quiescent, periosteal progenitor cells proliferate upon fracture; however, the underlying transcriptional mechanisms remain unclear. Here, we show that deletion of the transcriptional regulators, yes-associated protein (YAP) and transcriptional coactivator with PDZ binding motif (TAZ), from Osterix-expressing cells, which reside in the cambium, impairs periosteal expansion. YAP activation increases chromatin accessibility, preferentially at TEA domain transcription factor (TEAD) binding sites, and regulates both cell-intrinsic and cell-extrinsic cellular functions. We identify bone morphogenetic protein 4 (Bmp4) as a YAP-TEAD target gene expressed in the cambium. In YAP/TAZ knockout mice, BMP4 delivery increased periosteal expansion through matrix accumulation and fibrous layer cell proliferation. Conversely, in wild-type mice, BMP4 delivery increased osteogenic activity and angiogenesis. Together, these data identify YAP-mediated transcriptional programs that promote layer-specific periosteal expansion.

DOI: https://doi.org/10.1126/sciadv.adw0126
Sci Adv. 2025 Aug 08. 11(32): eadw4954

Allele frequency selection and no age-related increase in human oocyte mitochondrial mutations.

Barbara Arbeithuber, Kate Anthony, Bonnie Higgins, Peter Oppelt, Omar Shebl, Irene Tiemann-Boege, Francesca Chiaromonte, Thomas Ebner, Kateryna D Makova.

Mitochondria, cellular powerhouses, harbor DNA [mitochondrial DNA (mtDNA)] inherited from the mothers. mtDNA mutations can cause diseases, yet whether they increase with age in human oocytes remains understudied. Here, using highly accurate duplex sequencing, we detected de novo mutations in single oocytes, blood, and saliva in women 20 to 42 years of age. We found that, with age, mutations increased in blood and saliva but not in oocytes. In oocytes, mutations with high allele frequencies were less prevalent in coding than noncoding regions, whereas mutations with low allele frequencies were more uniformly distributed along the mtDNA, suggesting frequency-dependent purifying selection. Thus, mtDNA in human oocytes is protected against accumulation of mutations with aging and having functional consequences. These findings are particularly timely as humans tend to reproduce later in life.

DOI: https://doi.org/10.1126/sciadv.adw4954
bioRxiv. 2025 Jul 31. pii: 2025.07.30.665610. [Epub ahead of print]

Basal Cell-Contact Dynamics Influence Tissue Packing in a Proliferating Mammalian Epithelium.

Subramanian P Ramanathan, Tanmoy Sarkar, Matej Krajnc, Rosemary Mwithiga, Azize Cerci, Chongbei Zhao, Matthew C Gibson.

Animal tissue morphology is determined by the shape, position, and proliferative capacity of individual epithelial cells. Nevertheless, it remains incompletely understood how the dynamic shape transformations implicit in mitotic proliferation influence tissue packing, particularly at the level of basal cell contacts. Here, we use an in silico vertex model to show that epithelial mitotic rounding necessitates a sequence of dynamic basal contact rearrangements, including basal diminution of the mitotic cell volume, transient multicellular rosette assembly, basal reinsertion of daughter cells, and neighbor reorganization. We then leverage a mammalian intestinal organoid model to confirm nearly identical basal cell-contact dynamics as those predicted in silico . Pharmacological inhibition of mitotic progression reveals that two events-basal diminution of the cell body and daughter cell reinsertion-independently drive distinct contact rearrangements. Together, our results uncover a previously underappreciated topological role for basal mitotic cell dynamics in shaping epithelial packing and morphogenesis.

DOI: https://doi.org/10.1101/2025.07.30.665610
bioRxiv. 2025 Aug 02. pii: 2025.08.01.668243. [Epub ahead of print]

Targeting CyclinD1-CDK6 to Mitigate Senescence-Driven Inflammation and Age-Associated Functional Decline.

Adarsh Rajesh, Aaron P Havas, Rouven Arnold, Kathryn Lande, K Garrett Evensen, Kelly Yichen Li, Sainath Mamde, Qian Yang, Armin Gandhi, Karl N Miller, Marcos Garcia Teneche, Zoe Yao, Jessica Proulx, Andrew Davis, Laurence Haddadin, Michael Alcaraz, Carolina Cano Macip, Brightany Li, Xue Lei, Charlene Miciano, Elizabeth Smoot, Allen Wang, Jeffrey H Albrecht, April E Williams, Bing Ren, Kevin Y Yip, Peter D Adams.

Cellular senescence contributes to aging and age-related diseases by driving chronic inflammation through the Senescence Associated Secretory Phenotype (SASP) and interferon-stimulated genes (ISGs). Cyclin D1 (CCND1), a key cell cycle regulator, is paradoxically upregulated in these non-proliferating cells. We show that CCND1 and its kinase partner CDK6 drive SASP and ISG expression in senescent cells by promoting DNA damage accumulation. This leads to the formation of cytoplasmic chromatin fragments (CCFs) that activate pro-inflammatory CGAS-STING signaling. The tumor suppressor p53 (TP53) and its target p21 (CDKN2A) antagonize this CCND1-CDK6-dependent DNA damage accumulation pathway to suppress the SASP. In aged mouse livers, senescent hepatocytes show increased Ccnd1 expression. Hepatocyte-specific Ccnd1 knockout or treatment with the Cdk4/6 inhibitor Palbociclib reduces DNA damage and ISGs in aged mouse liver. Notably, Palbociclib also suppresses frailty and improves physical performance of aged mice. These findings reveal a novel role for CCND1/CDK6 in regulating DNA damage and inflammation in senescence and aging, highlighting it as a promising therapeutic target.

DOI: https://doi.org/10.1101/2025.08.01.668243
Nature. 2025 Aug 06.

RNA N-glycosylation enables immune evasion and homeostatic efferocytosis.

Vincent R Graziano, Jennifer Porat, Marie Dominique Ah Kioon, Ivana Mejdrová, Alyssa J Matz, Charlotta G Lebedenko, Peiyuan Chai, John V Pluvinage, Rafael Ricci-Azevedo, Andrew G Harrison, Skylar S Wright, Xinzheng Wang, Madison S Strine, Penghua Wang, Michael R Wilson, Sivapriya Kailasan Vanaja, Beiyan Zhou, Franck J Barrat, Thomas Carell, Ryan A Flynn, Vijay A Rathinam.

Glycosylation is central to the localization and function of biomolecules1. We recently discovered that small RNAs undergo N-glycosylation2 at the modified RNA base 3-(3-amino-3-carboxypropyl) uridine (acp3U)3. However, the functional significance of N-glycosylation of RNAs is unknown. Here we show that the N-glycans on glycoRNAs prevent innate immune sensing of endogenous small RNAs. We found that de-N-glycosylation of cell-culture-derived and circulating human and mouse glycoRNA elicited potent inflammatory responses including the production of type I interferons in a Toll-like receptor 3- and Toll-like receptor 7-dependent manner. Furthermore, we show that N-glycans on cell surface RNAs prevent apoptotic cells from triggering endosomal RNA sensors in efferocytes, thus facilitating the non-inflammatory clearance of dead cells. Mechanistically, N-glycans conceal the hypermodified uracil base acp3U, which we identified as immunostimulatory when exposed in RNA. Consistent with this, genetic deletion of an enzyme (DTWD2) that synthesizes acp3U abrogated innate immune activation by de-N-glycosylated small RNAs and apoptotic cells. Furthermore, synthetic acp3U-containing RNAs are sufficient to trigger innate immune responses. Thus, our study has uncovered a natural mechanism by which N-glycans block RNAs from inducing acp3U-dependent innate immune activation, demonstrating how glycoRNAs exist on the cell surface and in the endosomal network without inducing autoinflammatory responses.

DOI: https://doi.org/10.1038/s41586-025-09310-6
bioRxiv. 2025 Jul 22. pii: 2025.07.22.665939. [Epub ahead of print]

Mapping mesenchymal diversity in the developing human intestine and organoids.

Kelli F Johnson, Xiangning Dong, Yu-Hwai Tsai, Angeline Wu, Sydney G Clark, Sha Huang, Rachel K Zwick, Ian Glass, Katherine D Walton, Ophir D Klein, Jason R Spence.

The organization of diverse mesenchymal populations during human intestinal development is critical for tissue architecture and function yet remains poorly defined. To construct a comprehensive, tissue-scale map of the developing human small intestine, we leveraged single-cell RNA-sequencing data to build a custom Xenium spatial transcriptomics gene panel covering the diversity of cell types in the human intestine. Analysis was focused on the developing mesenchyme populations (also referred to as fibroblasts or stroma) given the lack of spatiotemporal information about these cell populations. We defined 5 broad mesenchymal populations occupying discrete anatomical locations within the lamina propria and submucosa - the subepithelial cells (SEC), lamina propria fibroblasts (LPF), submucosal fibroblasts (SMF), smooth muscle cells (SMC), and CXCL13 + fibroblasts. Our data reveal dynamic spatial remodeling of fibroblast communities during development and establish molecular markers to distinguish these populations. We leverage this high-resolution atlas to benchmark pluripotent stem cell-derived human intestinal organoids and to demonstrate how this foundational resource can be used to dissect intestinal stromal signaling in a spatial manner, with broad implications for modeling development, regeneration, and disease.

DOI: https://doi.org/10.1101/2025.07.22.665939
bioRxiv. 2025 Jul 31. pii: 2025.07.27.667080. [Epub ahead of print]

NAC controls nascent chain fate through tunnel sensing and chaperone action.

Jae Ho Lee, Laurenz Rabl, Martin Gamerdinger, Vaishali Goyal, Katrin Michaela Khakzar, Natalia Moreira Barbosa, Juliana Abramovich, Fabian Morales-Polanco, Ann-Kathrin Köhler, Ekaterina Samatova, Marina V Rodnina, Elke Deuerling, Judith Frydman.

The nascent polypeptide-associated complex (NAC) is a conserved ribosome-bound factor with essential yet incompletely understood roles in protein biogenesis. Here, we show that NAC is a multifaceted regulator that coordinates translation elongation, cotranslational folding, and organelle targeting through distinct interactions with nascent polypeptides both inside and outside the ribosome exit tunnel. Using NAC-selective ribosome profiling in C. elegans , we identify thousands of sequence-specific NAC binding events across the nascent proteome, revealing broad cotranslational engagement with hydrophobic and helical motifs in cytosolic, nuclear, ER, and mitochondrial proteins. Unexpectedly, we discover an intra-tunnel sensing mode, where NAC engages ribosomes with extremely short nascent polypeptides inside the exit tunnel in a sequence-specific manner. These early NAC interactions induce an early elongation slowdown that tunes ribosome flux and prevent ribosome collisions, linking NAC's chaperone activity to kinetic control of translation. We propose that NAC action protects aggregation-prone intermediates by shielding amphipathic helices thus promoting cytonuclear folding and supporting mitochondrial membrane protein biogenesis and ER targeting by early recognition of signal sequences and transmembrane domain. Our findings establish NAC as an early-acting, multifaceted orchestrator of cotranslational proteostasis, with distinct mechanisms of action on nascent chains depending on their sequence features and subcellular destinations.

DOI: https://doi.org/10.1101/2025.07.27.667080
bioRxiv. 2025 Jul 22. pii: 2025.07.22.666109. [Epub ahead of print]

Global inhibition of deadenylation stabilizes the transcriptome in mitotic cells.

Ekaterina Khalizeva, Arash Latifkar, David P Bartel, Jimmy Ly, Iain M Cheeseman.

In the presence of cell division errors, mammalian cells can pause in mitosis for tens of hours with little to no transcription, while still requiring continued translation for viability. These unique aspects of mitosis require substantial adaptations to the core gene expression programs. Indeed, during interphase, the homeostatic control of mRNA levels involves a constant balance of transcription and degradation, with a median mRNA half-life of ∼2-4 hours. If such short mRNA half-lives persisted in mitosis, cells would be expected to quickly deplete their transcriptome in the absence of new transcription. Here, we report that the transcriptome is globally stabilized during prolonged mitotic delays. Typical mRNA half-lives are increased >4-fold in mitosis compared to interphase, thereby buffering mRNA levels in the absence of new synthesis. Moreover, the poly(A)-tail-length profile of mRNAs changes in mitosis, strongly suggesting a mitotic repression of deadenylation. We further show that mRNA stabilization in mitosis is dependent on cytoplasmic poly(A)-binding proteins PABPC1&4. Depletion of PABPC1&4 disrupts the maintenance of mitotic arrest, highlighting the critical physiological role of mitotic transcriptome buffering.
Highlights: The cellular transcriptome is globally stabilized during prolonged mitotic arrestDistinct poly(A)-tail-length profile of mRNAs in mitosis suggests repression of deadenylationmRNA stabilization in mitosis is dependent on PABPC1 and PABPC4Degradation of mRNAs during mitosis compromises maintenance of mitotic arrest.

DOI: https://doi.org/10.1101/2025.07.22.666109
Nat Commun. 2025 Aug 04. 16(1): 7158

Cell surface crowding is a tunable energetic barrier to cell-cell fusion.

Daniel S W Lee, Liya F Oster, Sungmin Son, Daniel A Fletcher.

Cell-cell fusion is fundamental to processes such as muscle formation and viral infection. An essential step in fusion is close membrane apposition, but cell membranes are crowded with proteins, glycoproteins, and glycolipids, which must be cleared before a fusion pore can be nucleated. Here, we find that cell surface crowding reduces fusogenicity independent of how fusion is driven. We estimate that crowding presents an energetic barrier to membrane apposition on the scale of ~ 100kBT , greater than that of bare membrane fusion alone. We show that increasing cell surface crowding reduces fusion efficiency of PEG-mediated and fusogen-mediated cell-cell fusion, as well as synthetic membranes under force. Interestingly, we find that differentiating myoblasts naturally decrease their surface crowding prior to fusion. In this work, we show that cell surface crowding presents an underappreciated biophysical barrier that may be tuned developmentally and could be targeted externally to control tissue-specific cell-cell fusion.

DOI: https://doi.org/10.1038/s41467-025-62330-8
Sci Data. 2025 Aug 02. 12(1): 1347

The cardiac phospho-proteome during pressure overload in mice.

Rhys Wardman, Steve Grein, Jennifer Schwartz, Frank Stein, Joerg Heineke.

Transaortic constriction (TAC) is a murine model of pressure overload-induced cardiac hypertrophy and heart failure. Despite its high prevalence during aortic stenosis or chronic arterial hypertension, the global alterations in cardiac phospho-proteome dynamics following TAC remain incompletely characterised. We present a database of the phospho-proteomic signature one day and seven days after TAC. Utilising proteomic and phospho-proteomic analyses, we quantified thousands of proteins and phosphorylation sites, revealing hundreds of differential phosphorylation events significantly altered in the cardiac response to pressure overload. Our analysis highlights significant changes in hypertrophic signalling, metabolic remodelling, contractile function, and the stress response pathways. We present proteomic data from the main cardiac cell types (endothelial cells, fibroblasts and cardiomyocytes) to reveal the cellular localisation of the detected phospho-proteins, offering insights into temporal and site-specific phosphorylation events, facilitating the potential discovery of novel therapeutic targets and biomarkers. By making this resource publicly available (ProteomeXchange with identifier PXD061784) we aim to enable further exploration of the molecular basis of cardiac remodelling and advance translational research in heart failure.

DOI: https://doi.org/10.1038/s41597-025-05506-7
Nat Cell Biol. 2025 Aug 05.

The molecular basis of human transcription-coupled DNA repair.

Paula J van der Meer, Martijn S Luijsterburg.

The stalling of RNA polymerase II (RNAPII) on DNA lesions triggers transcription-coupled DNA repair (TCR). Although the initial assembly of the TCR complex is known, recent advances have substantially deepened our understanding of its mechanisms. The elongation factor ELOF1 and DNA-binding protein STK19 have been identified as key TCR factors, with new insights into their functions. Cryo-electron microscopy of repair intermediates and mutational analyses have elucidated how TCR proteins interact with damage-stalled RNAPII. A newly discovered transcription-coupled pathway resolves DNA-protein crosslinks using only early TCR proteins. Here we integrate these advances, outlining the TCR mechanism step by step. First we discuss how early TCR factors ubiquitylate RNAPII, then we examine the transition to later nucleotide excision repair stages, and finally, the fate of damage-stalled RNAPII. Despite these advancements, significant gaps remain in our understanding of TCR mechanisms and we discuss these along with potential future research directions.

DOI: https://doi.org/10.1038/s41556-025-01715-9
Cell. 2025 Aug 01. pii: S0092-8674(25)00801-3. [Epub ahead of print]

A mechano-resistance mechanism in skin adapts to terrestrial locomotion.

Ruonan Di, Qianqian Du, Yuhua Xie, Yanhua Lu, Wenxuan Gao, Lei Zhang, Xiaoli Qi, Yanyan Fan, Jiao Li, Fengchao Wang, She Chen, Ting Chen.

  The transition from water to land required animals to evolve specialized paw skin to support body weight and enable locomotion. We identify an evolutionarily emerged mechanism in skin epithelial cells that adapts to this mechanical demand. We show that the Slurp1 gene, conserved across tetrapods, is specifically expressed in palmoplantar skin. In humans, mutations in SLURP1 cause palmoplantar keratoderma (PPK), a condition marked by pathologically thickened skin epidermis on the soles and palms. Remarkably, reducing mechanical pressure on Slurp1 knockout paw skin fully rescues the PPK phenotype. Mechanistically, SLURP1 localizes to the endoplasmic reticulum (ER) membrane, where it binds the calcium pump SERCA2b. By preserving SERCA2b activity under mechanical pressure, SLURP1 maintains low cytoplasmic calcium levels and inhibits pressure-induced activation of the pPERK-NRF2 signaling-a pathway that can be genetically targeted to reverse PPK. These findings reveal an ER-based mechano-resistance mechanism that enhances cellular defense against prolonged mechanical pressure.

Keywords:  SERCA2b; SLURP1; calcium; endoplasmic reticulum; mechanical pressure; palmoplantar keratoderma

DOI:  https://doi.org/10.1016/j.cell.2025.07.012
Curr Opin Genet Dev. 2025 Aug 05. pii: S0959-437X(25)00077-2. [Epub ahead of print]94 102385

Transcription-coupled repair: protecting genome across generations.

Bibhusita Pani, Evgeny Nudler.

The primary objective of life is to ensure the faithful transmission of genetic material across generations, despite the constant threat posed by DNA-damaging factors. To counter these challenges, life has evolved intricate mechanisms to detect, signal, and repair DNA damage, thereby preventing mutations that can cause developmental abnormalities or diseases. DNA repair is especially vital during development - a period of rapid cell proliferation and differentiation. Failure to repair DNA damage in somatic cells can result in tissue dysfunction, while during embryonic development, it is often fatal. Transcription machinery plays a key role in the mechanisms of DNA repair. This review highlights current insights into DNA repair pathways that are driven or facilitated by transcription and their essential contribution to preserving genome stability.

DOI: https://doi.org/10.1016/j.gde.2025.102385
bioRxiv. 2025 Jul 31. pii: 2025.07.29.667423. [Epub ahead of print]

Fibroblast depletion reveals mammalian epithelial resilience across neonatal and adult stages.

Isabella M Gaeta, Shuangshuang Du, Clémentine Villeneuve, David G Gonzalez, Catherine Matte-Martone, Smirthy Ganesan, Deandra Simpson, Jessica L Moore, Chen Yuan Kam, Sara Gallini, Haoyang Wei, Fabien Bertillot, Dagmar Zeuschner, Lauren E Gonzalez, Kaelyn D Sumigray, Sara A Wickström, Valentina Greco.

Regenerative organs, like the skin, depend on niche-stem cell interactions that sustain continuous cellular turnover. In cell culture, skin fibroblasts promote epidermal stem cell proliferation and differentiation. Yet, it remains elusive how fibroblasts regulate epidermal stem cell behaviors and differentiation in vivo . Here, we asked how fibroblast depletion may impact epidermal stem cell proliferation in the context of adult homeostasis. Surprisingly, we find that significant depletion of fibroblast density does not affect epidermal stem cell proliferative capacity during adult stages in vivo . We next probed earlier neonatal stages when skin is actively remodeling but found no change in epidermal stem cell proliferative capacity following fibroblast depletion. These results demonstrate that across different ages, epidermal stem cell proliferative capacity can persist in the face of a largely reduced fibroblast population. Interestingly, neonatal fibroblast depletion does not significantly reduce their secreted collagen I density but affects basement membrane mechanics and epidermal stem cell delamination. Despite these changes to basement membrane mechanics and delamination, the skin continues to maintain its protective barrier function. Thus, our work demonstrates the skin regenerative program employs robust compensatory mechanisms in the face of fibroblast depletion to maintain functional capacity.

DOI: https://doi.org/10.1101/2025.07.29.667423
Sci Rep. 2025 Aug 05. 15(1): 28599

STRESS, an automated geometrical characterization of deformable particles for in vivo measurements of cell and tissue mechanical stresses.

Ben Jeffrey Gross, Johannes Richard Soltwedel, Elijah Shelton, Carlos Gomez, Otger Campàs.

From cellular mechanotransduction to the formation of embryonic tissues and organs, mechanics has been shown to play an important role in the control of cell behavior and embryonic development. Most of our existing knowledge of how mechanics affects cell behavior comes from in vitro studies, mainly because measuring cell and tissue mechanics in 3D multicellular systems, and especially in vivo, remains challenging. Oil microdroplet sensors, and more recently gel microbeads, use surface deformations to directly quantify mechanical stresses within developing tissues, in vivo and in situ, as well as in 3D in vitro systems like organoids or multicellular spheroids. However, an automated analysis software able to quantify the spatiotemporal evolution of stresses and their characteristics from particle deformations is lacking. Here we develop STRESS (Surface Topography Reconstruction for Evaluation of Spatiotemporal Stresses), an analysis software to quantify the geometry of deformable particles of spherical topology, such as microdroplets or gel microbeads, that enables the automatic quantification of the temporal evolution of stresses in the system and the spatiotemporal features of stress inhomogeneities in the tissue. As a test case, we apply these new code to measure the temporal evolution of mechanical stresses using oil microdroplets in developing zebrafish tissues. Starting from a 3D timelapse of a droplet, the software automatically calculates the statistics of local anisotropic stresses, decouples the deformation modes associated with tissue- and cell-scale stresses, obtains their spatial features on the droplet surface and analyzes their spatiotemporal variations using spatial and temporal stress autocorrelations. We provide fully automated software in Matlab/Python and also in Napari (napari-STRESS), which allows the visualization of mechanical stresses on the droplet surface together with the microscopy images of the biological systems. The automated nature of the analysis will help users obtain quantitative information about mechanical stresses in a wide range of 3D multicellular systems, from developing embryos or tissue explants to organoids.

DOI: https://doi.org/10.1038/s41598-025-13419-z
Nat Genet. 2025 Aug 06.

Comprehensive transcription factor perturbations recapitulate fibroblast transcriptional states.

Kaden M Southard, Rico C Ardy, Anran Tang, Deirdre D O'Sullivan, Eli Metzner, Karthik Guruvayurappan, Thomas M Norman.

Cell atlas projects have revealed that common cell types often comprise distinct, recurrent transcriptional states, but the function and regulation of these states remain poorly understood. Here, we show that systematic activation of transcription factors can recreate such states in vitro, providing tractable models for mechanistic and functional studies. Using a scalable CRISPR activation (CRISPRa) Perturb-seq platform, we activated 1,836 transcription factors in two cell types. CRISPRa induced gene expression within physiological ranges, with chromatin features predicting responsiveness. Comparisons with atlas datasets showed that transcription factor perturbations recapitulated key fibroblast states and identified their regulators, including KLF2 and KLF4 for a universal state present in many tissues, and PLAGL1 for a disease-associated inflammatory state. Inducing the universal state suppressed the inflammatory state, suggesting therapeutic potential. These findings position CRISPRa as a nuanced tool for perturbing differentiated cells and establish a general strategy for studying clinically relevant transcriptional states ex vivo.

DOI: https://doi.org/10.1038/s41588-025-02284-1
Nat Commun. 2025 Aug 05. 16(1): 7214

The RING finger E3 ligase RNF25 protects DNA replication forks independently of its canonical roles in ubiquitin signaling.

Lilly F Chiou, Gaith N Droby, Deepika Jayaprakash, Jay R Anand, Xingyuan Zhang, Yang Yang, C Allie Mills, Thomas S Webb, Natalie K Barker, Jialiu Xie, Di Wu, Laura E Herring, Junya Tomida, Jessica L Bowser, Cyrus Vaziri.

The DNA damage response (DDR) mechanisms that allow cells to tolerate DNA replication stress are critically important for genome stability and cell viability. Using an unbiased genetic screen, we identify a role for the RING finger E3 ubiquitin ligase RNF25 in promoting DNA replication stress tolerance. In response to DNA replication stress, RNF25-deficient cells generate aberrantly high levels of single-stranded DNA (ssDNA), accumulate in S-phase and show reduced mitotic entry. Using single-molecule DNA fiber analysis, we show that RNF25 protects reversed DNA replication forks generated by the fork remodeler HLTF from nucleolytic degradation by MRE11 and CtIP. Mechanistically, RNF25 interacts with the replication fork protection factor REV7 and recruits REV7 to nascent DNA after replication stress. The role of RNF25 in protecting replication forks is fully separable from its canonical functions in ubiquitin conjugation. This work reveals the RNF25-REV7 signaling axis as an important protective mechanism in cells experiencing replication stress.

DOI: https://doi.org/10.1038/s41467-025-62368-8
Development. 2025 Aug 05. pii: dev.204717. [Epub ahead of print]

Generative model for the first cell fate bifurcation in mammalian development.

Maria Avdeeva, Madeleine Chalifoux, Bradley Joyce, Stanislav Y Shvartsman, Eszter Posfai.

  The first cell fate bifurcation in mammalian development directs cells toward either the trophectoderm (TE) or inner cell mass (ICM) compartments in preimplantation embryos. This decision is regulated by the subcellular localization of a transcriptional co-activator YAP and takes place over several progressively asynchronous cleavage divisions. As a result of this asynchrony and variable arrangement of blastomeres, reconstructing the dynamics of the TE/ICM cell specification from fixed embryos is extremely challenging. To address this, we developed a live imaging approach and applied it to measure pairwise dynamics of nuclear YAP and its direct target genes, CDX2 and SOX2, key transcription factors of TE and ICM, respectively. Using these datasets, we constructed a generative model of the first cell fate bifurcation, which reveals the time-dependent statistics of the TE and ICM cell allocation. In addition to making testable predictions for the joint dynamics of the full YAP/CDX2/SOX2 motif, the model revealed the stochastic nature of the induction timing of the key cell fate determinants and identified the features of YAP dynamics that are necessary or sufficient for this induction. Notably, temporal heterogeneity was particularly prominent for SOX2 expression among ICM cells. As heterogeneities within the ICM have been linked to the initiation of the second cell fate decision in the embryo, understanding the origins of this variability is of key significance. The presented approach reveals the dynamics of the first cell fate choice and lays the groundwork for dissecting the next cell fate decisions in mouse development.

Keywords:  Bayesian modeling; First cell fate decision; Live imaging; Mouse; Preimplantation

DOI:  https://doi.org/10.1242/dev.204717