bims-ginsta 2025-10-05 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2025–10–05
thirty-six papers selected by
Jinrong Hu, National University of Singapore

Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells.
Cell-type-specific functionality encoded within the intrinsically disordered regions of OCT4.
Lmo3-expressing peri-isthmus progenitor cells sustain renewal and repair of the mammalian intestinal telocyte niche.
Microtubule architecture connects AMOT stability to YAP/TAZ mechanotransduction and Hippo signalling.
Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution.
Phase-separated NDF-FACT condensates facilitate transcription elongation on chromatin.
A human-specific regulatory mechanism revealed in a pre-implantation model.
Oxidative phosphorylation is required for cardiomyocyte re-differentiation and long-term fish heart regeneration.
Dietary cysteine enhances intestinal stemness via CD8+ T cell-derived IL-22.
Single-cell nascent transcription reveals sparse genome usage and plasticity.
Contractile fibroblasts form a transient niche for the branching mammary epithelium.
IGFBP2 Mediates Human iPSC-Cardiomyocyte Proliferation in a Cellular Contact-Dependent Manner.
PARP1 auto-modification promotes faithful Okazaki fragment processing and limits replication fork speed.
Ovarian development is driven by early spatiotemporal priming of the coelomic epithelium.
GCN1 couples GCN2 to ribosomal state to initiate amino acid response pathway signaling.
E2F1 induces a G0-G1 reentry transcriptional program without changing chromatin accessibility.
Chromosome-specific epigenetic control and transmission of ribosomal DNA arrays in Hominidae genomes.
Mitotic DNA repair by TMEJ suppresses replication stress-induced nuclear envelope reassembly defect.
Optimality as a framework for understanding developmental robustness.
Fine-tuning mechanical constraints reveals uncoupled patterning and gene expression programs in murine gastruloids.
Molecular basis for the activation of outer dynein arms in cilia.
Cardiomyocyte-expressed TGFβ signals to fibroblasts to program early heart maturation and adult myocyte identity.
Matrix-associated extracellular vesicles modulate human smooth muscle cell adhesion and directionality by presenting collagen VI.
Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq.
In vitro modeling of cell types in cardiogenesis and congenital heart disease.
Single-Cell Splicing Isoform Atlas of the Adult Human Heart and Heart Failure.
Muscle-derived miR-126 regulates TDP-43 axonal local synthesis and NMJ integrity in ALS models.
Derivation of embryonic stem cells across avian species.
Autoimmune response to C9orf72 protein in amyotrophic lateral sclerosis.
Spatial multiomics of acute myocardial infarction reveals immune cell infiltration through the endocardium.
Codon-specific ribosome stalling reshapes translational dynamics during branched-chain amino acid starvation.
Gene Clusters Reveal Fundamental Principles of Genome Folding and Transcriptional Regulation.
Crotonate enhances intestinal regeneration after injury via HBO1-mediated H3K14 crotonylation.
PIWI proteins tether the piRNA biogenesis machinery to mitochondria during mammalian spermatogenesis.
Regulation of NSL by TAF4A is critical for genome stability and quiescence of muscle stem cells.
A self-limiting mechanotransduction feedback loop ensures robust organ formation.

Nat Cell Biol. 2025 Sep 29.

Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells.

Kaitlin P McCreery, Aki Stubb, Rebecca Stephens, Nadezda A Fursova, Andrew Cook, Kai Kruse, Anja Michelbach, Leah C Biggs, Adib Keikhosravi, Sonja Nykänen, Roosa Pulkkanen, Christel Hydén-Granskog, Jizhong Zou, Jan-Wilm Lackmann, Carien M Niessen, Sanna Vuoristo, Yekaterina A Miroshnikova, Sara A Wickström.

Acquisition of specific cell shapes and morphologies is a central component of cell fate transitions. Although signalling circuits and gene regulatory networks that regulate pluripotent stem cell differentiation have been intensely studied, how these networks are integrated in space and time with morphological changes and mechanical deformations to control state transitions remains a fundamental open question. Here we focus on two distinct models of pluripotency, preimplantation inner cell mass cells of human embryos and primed pluripotent stem cells, to discover that cell fate transitions associate with rapid, compaction-triggered changes in nuclear shape and volume. These phenotypical changes and the associated active deformation of the nuclear envelope arise from growth factor signalling-controlled changes in cytoskeletal confinement and chromatin mechanics. The resulting osmotic stress state triggers global transcriptional repression, macromolecular crowding and remodelling of nuclear condensates that prime chromatin for a cell fate transition by attenuating repression of differentiation genes. However, while this mechano-osmotic chromatin priming has the potential to accelerate fate transitions and differentiation, sustained biochemical signals are required for robust induction of specific lineages. Our findings uncover a critical mechanochemical feedback mechanism that integrates nuclear mechanics, shape and volume with biochemical signalling and chromatin state to control cell fate transition dynamics.

DOI: https://doi.org/10.1038/s41556-025-01767-x
Nat Commun. 2025 Sep 30. 16(1): 8647

Cell-type-specific functionality encoded within the intrinsically disordered regions of OCT4.

Burak Ozkan, Mitzy Rios de Anda, Elisa Hall-Ponsele, Maria Rosa Portero Migueles, Amani Alshaikh, Marta Hanzevacki, Moriyah Naama, Katharine Furlong, Gareth A Roberts, Meryam Beniazza, My Linh Huynh, Michael R O'Dwyer, Sonia Yiakoumi, Christos Spanos, Hazar Yassen, Keisuke Kaji, Hitoshi Niwa, Yosef Buganim, Sally Lowell, Abdenour Soufi.

The cell-type-specific function of transcription factors (TFs) is crucial for determining cellular identity. However, it is unclear how a single TF can function specifically in different cell types. Here, we define the molecular features that enable OCT4 to reprogram somatic cells into pluripotent or trophoblast stem cells, maintain the self-renewal of embryonic stem cells (ESCs), and drive lineage commitment during early embryonic development. Embedded within the intrinsically disordered regions (IDRs) of OCT4, we uncover short linear peptides that are essential for reprogramming (SLiPERs) but dispensable for ESC self-renewal. SLiPERs adopt a quasi-ordered state and, during reprogramming, recruit a unique set of proteins to closed chromatin that are unnecessary for ESC self-renewal. Interestingly, SLiPERs are essential for embryos to develop beyond late gastrulation. Removing SLiPERs leads to aberrant OCT4 binding, derailing the regular transition of ESCs out of pluripotency. Our findings identify modules within IDRs that contribute to the functional versatility and specificity of TFs.

DOI: https://doi.org/10.1038/s41467-025-63806-3
Dev Cell. 2025 Sep 26. pii: S1534-5807(25)00564-7. [Epub ahead of print]

Lmo3-expressing peri-isthmus progenitor cells sustain renewal and repair of the mammalian intestinal telocyte niche.

Daxin Jiang, Guoli Zhu, Yongchao Zhang, Jiawen Wang, Nannan Qian, Zhen Jin, Qingyu Sun, Haimeng Yu, Kebei Tang, Tao Cai, Fengchao Wang, Rongwen Xi.

  Intestinal telocytes that reside immediately beneath the intestinal epithelium exert niche-supporting roles for intestinal stem cells and their progenies. They are heterogeneous cells compartmentalized along the crypt-villus axis, but the mechanisms governing the maintenance of this telocyte population remain unclear. Here, we identify a distinct population of subepithelial mesenchymal cells in the developing mouse embryo, marked by LIM Domain Only 3 (Lmo3), as the cellular origin of post-natal intestinal telocytes. The Lmo3+ cells emerge prior to villus formation at embryonic day 13.5, and after birth, they progressively acquire a spatial confinement to the intestinal isthmus region, where they persist as long-lived, slow-cycling cells, supplying both peri-villus and peri-crypt telocytes. Further, we show that Lmo3+ cells respond rapidly to tissue damage, becoming activated to promote repair of the telocyte niche. Therefore, a quiescent and damage-responsive progenitor cell population marked by Lmo3 maintains the intestinal telocyte niche.

Keywords:  BMP; FOXL1; LMO3; cell differentiation; intestinal telocyte; irradiation damage; mesenchymal cell niche; stem cell self-renewal; telocyte progenitor cell; villus formation

DOI:  https://doi.org/10.1016/j.devcel.2025.09.004
Nat Cell Biol. 2025 Oct 01.

Microtubule architecture connects AMOT stability to YAP/TAZ mechanotransduction and Hippo signalling.

Giada Vanni, Anna Citron, Ambela Suli, Paolo Contessotto, Robin Caire, Alessandro Gandin, Giovanna Mantovan, Francesca Zanconato, Giovanna Brusatin, Michele Di Palma, Elisa Peirano, Lisa Sofia Pozzer, Carlo Albanese, Roberto A Steiner, Michelangelo Cordenonsi, Tito Panciera, Stefano Piccolo.

Cellular mechanotransduction is a key informational system, yet its mechanisms remain elusive. Here we unveil the role of microtubules in mechanosignalling, operating downstream of subnuclear F-actin and nuclear envelope mechanics. Upon mechanical activation, microtubules reorganize from a perinuclear cage into a radial array nucleated by centrosomes. This structural rearrangement triggers degradation of AMOT proteins, which we identify as key mechanical rheostats that sequester YAP/TAZ in the cytoplasm. AMOT is stable in mechano-OFF but degraded in mechano-ON cell states, where microtubules allow AMOT rapid transport to the pericentrosomal proteasome in complex with dynein/dynactin. This process ensures swift control of YAP/TAZ function in response to changes in cell mechanics, with experimental loss of AMOT proteins rendering cells insensitive to mechanical modulations. Ras/RTK oncogenes promote YAP/TAZ-dependent tumorigenesis by corrupting this AMOT-centred mechanical checkpoint. Notably, the Hippo pathway fine-tunes mechanotransduction: LATS kinases phosphorylate AMOT, shielding it from degradation, thereby indirectly restraining YAP/TAZ. Thus, AMOT protein stability serves as a hub linking cytoskeletal reorganization and Hippo signalling to YAP/TAZ mechanosignalling.

DOI: https://doi.org/10.1038/s41556-025-01773-z
Cell. 2025 Oct 01. pii: S0092-8674(25)01037-2. [Epub ahead of print]

Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution.

Yubao Cheng, Shengyuan Dang, Yuan Zhang, Yanbo Chen, Ruihuan Yu, Miao Liu, Shengyan Jin, Ailin Han, Samuel Katz, Siyuan Wang.

  Recent breakthroughs in spatial transcriptomics technologies have enhanced our understanding of diverse cellular identities, spatial organizations, and functions. Yet existing spatial transcriptomics tools are still limited in either transcriptomic coverage or spatial resolution, hindering unbiased, hypothesis-free transcriptomic analyses at high spatial resolution. Here, we develop reverse-padlock amplicon-encoding fluorescence in situ hybridization (RAEFISH), an image-based spatial transcriptomics method with whole-genome coverage and single-molecule resolution in intact tissues. We demonstrate the spatial profiling of transcripts from 23,000 human or 22,000 mouse genes in single cells and tissue sections. Our analyses reveal transcript-specific subcellular localization, cell-type-specific and cell-type-invariant zonation-dependent transcriptomes, and gene programs underlying preferential cell-cell interactions. Finally, we further develop our technology for the direct spatial readout of guide RNAs (gRNAs) in an image-based, high-content CRISPR screen. Overall, these developments offer a broadly applicable technology that enables high-coverage, high-resolution spatial profiling of both long and short, native and engineered RNAs in many biomedical contexts.

Keywords:  high content CRISPR screen; highly multiplexed RNA imaging; spatial transcriptomics

DOI:  https://doi.org/10.1016/j.cell.2025.09.006
Nat Cell Biol. 2025 Sep 30.

Phase-separated NDF-FACT condensates facilitate transcription elongation on chromatin.

Ziwei Li, Francesca Burgos-Bravo, Kevin Xu, Chen Li, Kelvin Y Kwan, Alexander B Tong, Zelin Shan, Huan Wang, Motoki Takaku, Joey Li, Zheng Shi, Dmitry Lyumkis, Carlos Bustamante, Jia Fei.

How the facilitates chromatin transcription (FACT) complex enables RNA polymerase II to overcome chromatin barriers in cells remains poorly understood-especially given the limited direct interactions of FACT with polymerases, DNA or nucleosomes. Here we demonstrate that phase separation, mediated by nucleosome destabilizing factor (NDF), is a key mechanism enabling the function of FACT during transcription elongation. Through biochemical and single-molecule assays, we found that NDF-FACT condensates create specialized biochemical environments that enhance transcription efficiency approximately 20-fold compared with FACT alone. These dynamic condensates form on transcribing RNA polymerase II and travel along chromatin, where they promote efficient nucleosome disassembly at barriers while retaining histones on DNA to preserve chromatin integrity. In human stem cells, disruption of these condensates leads to genome-wide transcriptional defects and chromatin instability, mirroring the effects of FACT depletion. By showing that phase separation enhances FACT function during transcription elongation, our study reveals a key mechanism that preserves chromatin integrity and transcriptional homeostasis in human stem cells.

DOI: https://doi.org/10.1038/s41556-025-01778-8
Nature. 2025 Oct 01.

A human-specific regulatory mechanism revealed in a pre-implantation model.

Raquel Fueyo, Sicong Wang, Olivia J Crocker, Tomek Swigut, Hiromitsu Nakauchi, Joanna Wysocka.

Stem cell-based human embryo models offer a unique opportunity for functional studies of the human-specific features of development. Here we genetically and epigenetically manipulate human blastoids, a 3D embryo model of the blastocyst1, to investigate the functional effect of HERVK LTR5Hs, a hominoid-specific endogenous retrovirus, on pre-implantation development. We uncover a pervasive cis-regulatory contribution of LTR5Hs elements to the hominoid-specific diversification of the epiblast transcriptome in blastoids. Many of the LTR5Hs genomic insertions in the human genome are unique to our own species. We show that at least one such human-specific LTR5Hs element is essential for the blastoid-forming potential via enhancing expression of the primate-specific ZNF729 gene, encoding a KRAB zinc-finger protein. ZNF729 binds to GC-rich sequences, abundant at gene promoters associated with basic cellular functions, such as cell proliferation and metabolism. Despite mediating recruitment of TRIM28, at many of these promoters ZNF729 acts as a transcriptional activator. Together, our results illustrate how recently emerged transposable elements and genes can confer developmentally essential functions in humans.

DOI: https://doi.org/10.1038/s41586-025-09571-1
Nat Cardiovasc Res. 2025 Oct 01.

Oxidative phosphorylation is required for cardiomyocyte re-differentiation and long-term fish heart regeneration.

Konstantinos Lekkos, Zhilian Hu, Phong D Nguyen, Hessel Honkoop, Esra Sengul, Rita Alonaizan, Jana Koth, Jun Ying, Madeleine E Lemieux, Alisha Kenward, Sean Keeley, Bastiaan Spanjaard, Brett W C Kennedy, Xin Sun, Katherine Banecki, Helen G Potts, Gennaro Ruggiero, James Montgomery, Daniela Panáková, Jan Philipp Junker, Lisa C Heather, Xiaonan Wang, Juan Manuel Gonzalez-Rosa, Jeroen Bakkers, Mathilda T M Mommersteeg.

In contrast to humans, fish can fully regenerate their hearts after cardiac injury. However, not all fish have the same regenerative potential, allowing comparative inter-species and intra-species analysis to identify the mechanisms controlling successful heart regeneration. Here we report a differential regenerative response to cardiac cryo-injury among different wild-type zebrafish strains. Correlating these data with single-cell and bulk RNA sequencing data, we identify oxidative phosphorylation (OXPHOS) as a positive regulator of long-term regenerative outcome. OXPHOS levels, driven by glycolysis through the malate-aspartate shuttle, increase as soon as cardiomyocyte proliferation decreases, and this increase is required for cardiomyocyte re-differentiation and successful long-term regeneration. Reduced upregulation of OXPHOS in Astyanax mexicanus cavefish results in the absence of a dynamic temporal sarcomere gene expression program during cardiomyocyte re-differentiation. These findings challenge the assumption that OXPHOS inhibits regeneration and reveal targetable pathways to enhance heart repair in humans after myocardial infarction.

DOI: https://doi.org/10.1038/s44161-025-00718-x
Nature. 2025 Oct 01.

Dietary cysteine enhances intestinal stemness via CD8+ T cell-derived IL-22.

Fangtao Chi, Qiming Zhang, Jessica E S Shay, Shixun Han, Johanna Ten Hoeve, Yin Yuan, Zhenning Yang, Heaji Shin, Samuel Block, Sumeet Solanki, Yatrik M Shah, Matthew G Vander Heiden, Judith Agudo, Ömer H Yilmaz.

A fundamental question in physiology is understanding how tissues adapt and alter their cellular composition in response to dietary cues1-8. The mammalian small intestine is maintained by rapidly renewing LGR5+ intestinal stem cells (ISCs) that respond to macronutrient changes such as fasting regimens and obesogenic diets, yet how specific amino acids control ISC function during homeostasis and injury remains unclear. Here we demonstrate that dietary cysteine, a semi-essential amino acid, enhances ISC-mediated intestinal regeneration following injury. Cysteine contributes to coenzyme A (CoA) biosynthesis in intestinal epithelial cells, which promotes expansion of intraepithelial CD8αβ+ T cells and their production of interleukin-22 (IL-22). This enhanced IL-22 signalling directly augments ISC reparative capacity after injury. The mechanistic involvement of the pathway in driving the effects of cysteine is demonstrated by several findings: CoA supplementation recapitulates cysteine effects, epithelial-specific loss of the cystine transporter SLC7A11 blocks the response, and mice with CD8αβ+ T cells lacking IL-22 or a depletion of CD8αβ+ T cells fail to show enhanced regeneration despite cysteine treatment. These findings highlight how coupled cysteine metabolism between ISCs and CD8+ T cells augments intestinal stemness, providing a dietary approach that exploits ISC and immune cell crosstalk for ameliorating intestinal damage.

DOI: https://doi.org/10.1038/s41586-025-09589-5
Cell. 2025 Sep 26. pii: S0092-8674(25)01034-7. [Epub ahead of print]

Single-cell nascent transcription reveals sparse genome usage and plasticity.

Shaoqian Ma, Yantao Hong, Junhan Chen, Jingzhao Xu, Xiaohua Shen.

  Understanding cell diversification from a common genome in metazoans requires single-cell transcriptional analysis. We introduce single-cell full-length EU-labeled nascent RNA sequencing (scFLUENT-seq), a single-cell nascent RNA sequencing method using brief 10-min metabolic labeling to capture genome-wide transcription. Surprisingly, individual cells-from splenic lymphocytes to pluripotent stem cells-transcribe only ∼0.02%-3.1% of the genome, versus >80% in bulk, revealing limited genome engagement and profound cell-type and cell-to-cell heterogeneity. Intergenic transcription, especially from heterochromatin, is pervasive and stochastic. Promoter-associated antisense and genic transcription rarely co-occur in the same cell. Proximal intergenic transcription involves both gene readthrough and independent initiation, while distal intergenic transcription is largely independent of neighboring genes and correlates with increased transcriptional diversity, a hallmark of cellular plasticity. Although global RNA synthesis and turnover are coupled in bulk, individual mRNA transcription and decay are poorly coordinated in single cells, suggesting noise-buffering mechanisms. Overall, scFLUENT-seq uncovers complex coding and noncoding transcriptional dynamics that underlie single-cell heterogeneity and state transitions.

Keywords:  cell state and plasticity; chromatin; heterogeneity; noncoding genome; single-cell nascent RNA-seq; transcription dynamics

DOI:  https://doi.org/10.1016/j.cell.2025.09.003
Nat Commun. 2025 Sep 29. 16(1): 8576

Contractile fibroblasts form a transient niche for the branching mammary epithelium.

Jakub Sumbal, Robin P Journot, Kriti Attri, Veronika Danek, Candice Merle, Marisa M Faraldo, Zuzana Sumbalova Koledova, Silvia Fre.

Fibroblasts are stromal cells found in connective tissue that are critical for organ development, tissue homeostasis and pathology. Single-cell transcriptomic analyses have revealed a high level of inter- and intra-organ heterogeneity of fibroblasts. However, the functional implications and lineage relations of different fibroblast subtypes remained unexplored, especially in the mammary gland. Here, we provide a comprehensive characterization of pubertal mouse mammary fibroblasts, through single-cell RNA sequencing, spatial mapping, functional assays, and in vivo lineage tracing. We unravel a transient niche-forming population of specialized contractile fibroblasts that exclusively localize around the tips of the growing mammary epithelium and are recruited from preadipocytes in the surrounding fat pad stroma. Using organoid-fibroblast co-cultures we reveal that different fibroblast populations can acquire contractile features when in direct contact with the epithelium, promoting organoid branching. The detailed in vivo characterization of these specialized cells and their lineage history provides insights into fibroblast heterogeneity and implicates their importance for creating a signalling niche during mouse mammary gland development.

DOI: https://doi.org/10.1038/s41467-025-63612-x
Circ Res. 2025 Oct 01.

IGFBP2 Mediates Human iPSC-Cardiomyocyte Proliferation in a Cellular Contact-Dependent Manner.

Soah Lee, Paul Heinrich, Daniel Lee, Yongwon Kang, Harley Robinson, Sean J Humphrey, Jihye Yun, William R Goodyer, Jan W Buikema, David T Paik, Francisco X Galdos, Boyoung Kim, Nadjet Belbachir, Sungjin Min, Seung-Woo Cho, Jaecheol Lee, Alessandra Moretti, Joseph C Wu, James Hudson, Sean M Wu.

   BACKGROUND: Induction of cardiomyocyte proliferation in situ represents a promising strategy for myocardial regeneration following injury. However, cardiomyocytes possess intrinsic inhibitory mechanisms that attenuate pro-proliferative signaling and constrain their expansion. We hypothesized that cell-cell contact is a key suppressor of cardiomyocyte proliferation. We aimed to delineate the underlying molecular pathways to enable sustained proliferation in 3-dimensional contexts.
METHODS: Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) were cultured at varying plating densities to examine the impact of cell-cell contact on cell cycle activity. Phosphoproteomic profiling was performed in sparse versus dense cultures to identify signaling alterations. Conditioned media from sparse cultures were interrogated using a human growth factor array to identify secreted pro-proliferative factors.
RESULTS: hiPSC-CM proliferation increased proportionally with plating density until intercellular contacts were established, at which point proliferation was suppressed. Dense cultures exhibited enhanced adherens junction assembly, sarcomeric organization, and contractile function. Increased cell-cell contact in dense conditions attenuated nuclear translocation of β-catenin and reduced TCF/LEF transcriptional activity, providing a mechanistic basis for the reduced hiPSC-CM proliferation. Disruption of adherens junctions or sarcomere assembly via siRNA-mediated knockdown of N-cadherin or α-actinin, respectively, resulted in increased cell cycle activation of hiPSC-CMs, but this was not sufficient to drive division of hiPSC-CMs. Additional screening for putative secreted growth factors in the conditioned media from sparsely plated hiPSC-CMs revealed the enrichment of IGFBP2, which was sufficient to drive hiPSC-CM division in the presence of cell-cell contact in 3-dimensional constructs.
CONCLUSIONS: Our findings demonstrate that cell-cell contact inhibits hiPSC-CM proliferation through adherens junction formation, sarcomeric assembly, and reduced IGFBP2 secretion. Importantly, exogenous supplementation of IGFBP2 can overcome cell contact-mediated inhibition of hiPSC-CM proliferation and facilitate the growth of 3-dimensional cardiac tissue. These insights provide valuable implications for advancing cardiac tissue engineering and regenerative therapies.

Keywords:  actinin; cadherins; catenins; myocardium; sarcomeres

DOI:  https://doi.org/10.1161/CIRCRESAHA.125.326522
Mol Cell. 2025 Oct 02. pii: S1097-2765(25)00747-6. [Epub ahead of print]85(19): 3562-3575.e10

PARP1 auto-modification promotes faithful Okazaki fragment processing and limits replication fork speed.

Jonas D Elsborg, Sebastian H N Munk, Alba Adelantado-Rubio, Ramóna Pék, Zita Fábian, Victor Imburchia, Siham Zentout, Ivo A Hendriks, Sara C Buch-Larsen, Rebecca Smith, Jiri Bartek, Julien P Duxin, Sébastien Huet, Apolinar Maya-Mendoza, Michael L Nielsen.

  Poly(ADP-ribose) polymerase (PARP) inhibitors have proven their efficacy for treating tumors defective in homologous recombination via synthetic lethality. In response to DNA breaks, PARP1 is the primary ADP-ribosylation writer, modifying itself (auto-modification) and other proteins to facilitate repair. However, enzymatic inhibition blocks both processes, making it difficult to dissect their distinct functional roles. Using proteomics and site-directed mutagenesis, we identified a PARP1 mutant deficient in auto-modification, yet it retains catalytic activity. This separation-of-function mutant revealed that PARP1 auto-modification slows DNA replication fork progression but is dispensable for repair factor recruitment. Instead, auto-modification promotes the timely release of PARP1 at DNA break sites and prevents the formation of replication stress. Simultaneous inhibition of FEN1 and loss of PARP1 auto-modification gives rise to synthetic lethality, implicating auto-modification in Okazaki fragment processing. Our results demonstrate that trapping of PARP at DNA breaks impedes repair factor accessibility, constituting an important dimension of PARP-inhibitor-driven cytotoxicity.

Keywords:  ADP-ribosylation; DNA replication fork; Okazaki fragment; PARP inhibitor; PARP1; PTM; auto-modification; electron-transfer dissociation; proteomics resource; replication stress

DOI:  https://doi.org/10.1016/j.molcel.2025.09.006
bioRxiv. 2025 Sep 26. pii: 2025.09.24.678234. [Epub ahead of print]

Ovarian development is driven by early spatiotemporal priming of the coelomic epithelium.

Cyril Djari, Chloé Mayère, Maëva Guy, Aitana Perea-Gomez, Paul Barreau, Agathe Rozier, Anthony S Martinez, Tyler J Gibson, Cassandre Guérin, Herta Ademi, Dagmar Wilhelm, Jennifer McKey, Marie-Christine Chaboissier, Serge Nef.

Ovarian organogenesis requires the coordinated specification of supporting and steroidogenic cell lineages from multipotent coelomic epithelium (CE) progenitors. A longstanding question is whether the CE contains transcriptionally distinct, spatially organized progenitor subpopulations with predetermined lineage biases, or whether specification into supporting and steroidogenic lineages occurs only after delamination and integration into the bipotential gonad. The developmental origins of granulosa cells and the emergence of ovarian steroidogenic/stromal progenitors (SPs) also remain poorly defined. Here, we show that CE cells covering the fetal mouse ovary are transcriptionally heterogeneous and spatially organized into subdomains already primed toward supporting or steroidogenic fates. CE priming is dynamic, with transient coexistence of supporting- and steroidogenic-biased CE progenitors before resolving into a predominantly supporting-biased CE. Local delamination of these primed cells seeds intragonadal niches where pre-granulosa cells and SPs mirror the spatio-temporal arrangements of CE-primed progenitors. We further demonstrate a dual origin for the supporting lineage, with granulosa cells deriving from both the CE and supporting-like cells (SLCs). In parallel, we show that SPs arise from steroidogenic-primed CE cells, expand to represent 52% of ovarian somatic cells at birth, persist into adulthood and contribute to both theca and steroidogenic stromal cells. Together, these findings reveal transcriptionally and spatially distinct CE subpopulations that shape somatic lineage emergence with important implications for ovarian pathophysiology.

DOI: https://doi.org/10.1101/2025.09.24.678234
Science. 2025 Oct 02. 390(6768): eads8728

GCN1 couples GCN2 to ribosomal state to initiate amino acid response pathway signaling.

Changqian Zhou, Miao Zhang, Jason Murray, Joao Paulo, Steve Gygi, Sichen Shao, Malcolm Whitman, Tracy Keller.

During nutrient deprivation, activation of the protein kinase GCN2 regulates cell survival and metabolic homeostasis. In addition to amino acid stress, GCN2 is activated by a variety of cellular stresses. GCN2 activation has been linked to its association with uncharged tRNAs, specific ribosomal proteins, and conditions of translational arrest, but their relative contribution to activation is unclear. Here, we used in vitro translation to reconstitute GCN2 activation by amino acid stress and compared collided ribosome populations induced by diverse translational stressors. Initiation of GCN2 signaling required the di-ribosome sensor GCN1, which recruits GCN2 to ribosomes in a collision-dependent manner, where GCN2 becomes activated by key ribosomal interactions and stably associated with collided ribosomes. Our findings define the molecular requirements and dynamics of GCN2 activation.

DOI: https://doi.org/10.1126/science.ads8728
bioRxiv. 2025 Sep 25. pii: 2025.09.23.678145. [Epub ahead of print]

E2F1 induces a G0-G1 reentry transcriptional program without changing chromatin accessibility.

Gerrald A Lodewijk, Benjamin R Topacio, Seungho Lee, Sayaka Kozuki, Znala Williams, Clara J Han, Abolfazl Zargari, Tilini U Wijeratne, Neda Bidoki, Silvart Arabian, Edward Wu, Eric Malekos, Joscha Weiss, Gerd A Müller, Vanessa Jonsson, Nicolas H Thomä, Seth M Rubin, S Ali Shariati.

Quiescent cells actively repress cell-cycle genes via chromatin-based mechanisms to maintain a non-dividing state, yet remain poised to reenter upon stimulation. E2F1, a canonical activator of cell-cycle genes, is sufficient to induce reentry from quiescence, but how it overcomes chromatin-mediated repression remains unclear. Here, we show that inducible E2F1 expression triggers exit from quiescence and progression through the cycle without changes in chromatin accessibility, by harnessing regulatory elements with limited, pre-existing accessibility. Using time-resolved transcriptomics, we demonstrate that E2F1 induces an accelerated transcriptional program compared to serum. Unlike serum, which triggers broad chromatin remodeling, E2F1-induced activation occurs in a context of limited accessibility. ChIP-seq reveals that E2F1 directly binds target sites in quiescent cells to upregulate canonical genes. Biochemical reconstitution shows that E2F1 binds nucleosomes and accesses internal E2F sites within histone-wrapped DNA. These findings suggest that E2F1 can engage nucleosome-associated DNA and initiate transcription without major chromatin reorganization, redefining transcription factor-chromatin dynamics during cell fate transitions and establishing E2F1 as a potent regulator of cell-cycle reentry.

DOI: https://doi.org/10.1101/2025.09.23.678145
Cell Genom. 2025 Oct 02. pii: S2666-979X(25)00287-3. [Epub ahead of print] 101031

Chromosome-specific epigenetic control and transmission of ribosomal DNA arrays in Hominidae genomes.

Tamara A Potapova, Paxton Kostos, Sean McKinney, Matthew Borchers, Jeff Haug, Andrea Guarracino, Steven J Solar, Mark Mattingly, Graciela Monfort Anez, Leonardo Gomes de Lima, Yan Wang, Chongbei Zhao, Kate Hall, Madelaine Gogol, Sophie Hoffman, Dmitry Antipov, Arang Rhie, Monika Cechova, Karen H Miga, Erik Garrison, Adam M Phillippy, Jennifer L Gerton.

  Ribosomal RNA (rRNA) genes are organized in tandem arrays known as ribosomal DNA (rDNA) on multiple chromosomes in Hominidae genomes. We measured copy number and transcriptional activity status of rRNA gene arrays across multiple individual genomes, revealing an identifiable fingerprint of rDNA copy number and activity. In some cases, entire arrays were transcriptionally silent, characterized by high DNA methylation across the rRNA gene, inaccessible chromatin, and the absence of transcription factors and transcripts. Silent arrays showed reduced association with the nucleolus and decreased interchromosomal interactions, consistent with the model that nucleolar organizer function depends on transcriptional activity. Removing rDNA methylation activated silent arrays. Array activity status remained stable through induced pluripotent stem cell reprogramming and differentiation into cerebral and intestinal organoids. Haplotype tracing in two unrelated family trios showed paternal transmission of silent arrays. We propose that the epigenetic state buffers rRNA gene dosage, specifies nucleolar organizer function, and can propagate transgenerationally.

Keywords:  DNA methylation; Treacle; UBF; apes; epigenetics; humans; nucleolus; rRNA genes; ribosomal DNA

DOI:  https://doi.org/10.1016/j.xgen.2025.101031
Nat Commun. 2025 Oct 03. 16(1): 8836

Mitotic DNA repair by TMEJ suppresses replication stress-induced nuclear envelope reassembly defect.

Guojun Ye, Yide He, Yihui Zhang, Dongchen Li, Fuhai Liu, Yi Li, Qinglian Ge, Qiong Guo, Shuya Han, Chunyu Song, Weiping Chang, Haoyue Zhang, Qin Peng, Kun Sun, Weike Ji, Lin Deng.

Replication stress (RS), if not effectively and timely addressed, could result in DNA damage in mitosis. However, the relationship between RS and other mitotic events, such as nuclear envelope (NE) breakdown and reassembly, remains poorly understood. Here we report that RS can lead to NE defect. Importantly, rather than de novo NE rupture, the defect per se is a result of nuclear envelope reassembly defect (NERD) during mitosis. Interestingly, NERD is associated with mitotic DNA damage, and repair of the damage by DNA polymerase theta (Polθ)-mediated end joining (TMEJ) ameliorates NERD. Genomic mapping of lamina associated domains (LADs) by cleavage under targets and tagmentation (CUT&Tag) identifies a population of replication stress-sensitive LADs (RESSLADs). Strikingly, a substantial portion of RESSLADs reside in the common fragile sites (CFSs). The loss of RESSLADs-NE interaction under RS might be attributed to the sustained phosphorylation of Lamin A/C at the sites of NERD. In addition, prominent NE defect is observed under multiple conditions of synthetic lethality. Altogether, these findings establish a link between genome instability and nuclear vulnerability under replication stress.

DOI: https://doi.org/10.1038/s41467-025-63942-w
Trends Cell Biol. 2025 Sep 30. pii: S0962-8924(25)00204-1. [Epub ahead of print]

Optimality as a framework for understanding developmental robustness.

Prachiti Moghe, Edouard Hannezo, Takashi Hiiragi.

  Embryo growth, morphogenesis, and patterning are complex processes that coordinate between cellular dynamics, fate specification, and multiscale physical forces. Understanding how robustness in embryo development is achieved despite inherent heterogeneities in gene expression, cell properties, and tissue growth is a fundamental question. Although various feedback between gene expression, signaling, and cell and tissue mechanics have been uncovered to confer robustness on developmental systems, measuring variability and robustness from a quantitative perspective often remains challenging. Furthermore, cell fate plasticity, a key mechanism that can confer robustness, is lacking in many developing tissues. This review highlights how recent technological and conceptual advances in quantitative approaches to biology help to overcome these bottlenecks, with a particular focus on how mechanochemical feedback, or alternatively, selectively tuned control parameters, ensure developmental robustness.

Keywords:  embryogenesis; mechanochemical feedback; morphogenesis; patterning precision; quantitative biology; tuning of control parameters

DOI:  https://doi.org/10.1016/j.tcb.2025.08.009
Development. 2025 Sep 15. pii: dev204711. [Epub ahead of print]152(18):

Fine-tuning mechanical constraints reveals uncoupled patterning and gene expression programs in murine gastruloids.

Judith Pineau, Jerome Wong-Ng, Alexandre Mayran, Lucille Lopez-Delisle, Pierre Osteil, Armin Shoushtarizadeh, Denis Duboule, Samy Gobaa, Thomas Gregor.

  The interplay between mechanical forces and genetic programs is fundamental to embryonic development, yet how these factors influence morphogenesis and cell fate decisions remains unclear. Here, we fine-tune the mechanical environment of murine gastruloids, three-dimensional in vitro models of early embryogenesis, by embedding them in bioinert hydrogels with tunable stiffness and timing. This strategy reveals that external constraints can selectively influence transcriptional profiles, patterning or morphology, depending on the level and timing of mechanical modulation. Gastruloids in ultra-soft hydrogels (<30 Pa) elongate robustly, preserving anteroposterior patterning and transcriptional profiles. In contrast, embedding at higher stiffness disrupts polarization while leaving gene expression largely unaffected. Conversely, earlier embedding significantly impacts transcriptional profiles independently of polarization defects, highlighting the uncoupling of patterning and transcription. These findings suggest that distinct cellular states respond differently to external constraints. Live imaging and cell tracking further suggest that impaired cell motility underlies polarization defects, underscoring the role of mechanical forces in shaping morphogenesis independently of transcriptional changes. By precisely controlling mechanical boundaries, our approach provides a powerful platform to dissect how physical and biochemical factors interact to orchestrate embryonic development.

Keywords:  Morphogenesis; Polarization; Pseudoembryos; Synthetic extracellular matrix

DOI:  https://doi.org/10.1242/dev.204711
Nat Struct Mol Biol. 2025 Sep 29.

Molecular basis for the activation of outer dynein arms in cilia.

Karim Housseini B Issa, Muyang Ren, Bradley Burnet, Hao Lu, Charlotte Melia, Kate Heesom, Anthony J Roberts, Sudipto Roy, Girish R Mali.

Multiciliogenesis requires large-scale biosynthesis of motility-powering axonemal inner and outer dynein arm motors (IDAs and ODAs) before their intraflagellar transport (IFT) into cilia. ODAs are inhibited by the packaging chaperone Shulin during ciliogenesis in Tetrahymena thermophila. How Shulin is released for ODAs to become active inside cilia remains unclear. Here we uncover a molecular mechanism for ODA activation. We establish interactions between DNAAF9 (human Shulin) and mammalian ODA subunits, IFT proteins and the ciliary small guanosine triphosphatase (GTPase) ARL3 using proteomics and in vitro reconstitutions. Mutagenesis combined with biochemical and structural studies reveal that DNAAF9 and Shulin preferentially bind active Arl3-GTP highlighting a cross-species conservation of this interaction. GTP-loaded Arl3 can access, bind and displace Shulin from the packaged ODA-Shulin complex. We propose that, once the inhibited ODA complex enters growing cilia, Arl3-GTP displaces Shulin (DNAAF9) and sequesters it away from ODAs, promoting activation of their motility specifically inside cilia.

DOI: https://doi.org/10.1038/s41594-025-01680-9
bioRxiv. 2025 Sep 22. pii: 2025.09.22.677845. [Epub ahead of print]

Cardiomyocyte-expressed TGFβ signals to fibroblasts to program early heart maturation and adult myocyte identity.

Rachel A Minerath, Rajesh K Kasam, Casey O Swoboda, Vikram Prasad, Kelly M Grimes, N Scott Blair, Hadi Khalil, Christina M Alfieri, Logan Eads, Anthony A Saviola, Mohamad Azhar, Lianjie Miao, Mingfu Wu, Michelle V Tallquist, Kirk Hansen, Matthew T Weirauch, Katherine Yutzey, Douglas Millay, Jeffery D Molkentin.

Transforming growth factor β (TGFβ) is a secreted growth factor that is sequestered to the extracellular matrix (ECM) as a latent complex. In adult disease TGFβ release in the heart transforms fibroblasts into a differentiated state that synthesizes more ECM. However, it is not known how TGFβ functions in the early developing heart to impact resident fibroblasts. Here, we observe that deletion of the Tgfb1, Tgfb2, and Tgfb3 genes (TGFβ ligands) from cardiomyocytes in the early developing heart results in cardiac dysfunction by 6 weeks of age with altered fibroblast activity and altered ECM content. Early postnatal hearts from Tgfb1/2/3 cardiomyocyte-deleted mice are dysmorphic and cardiac fibroblasts have incorrect activity and produce inappropriate ECM with reduced stiffness. Gene expression profiling of hearts from myocyte-specific Tgfb1/2/3 deleted mice reveal defects in both cardiomyocyte and fibroblast maturation with ectopic expression of multiple skeletal muscle-specific genes beginning at embryonic day 17.5 and progressing with age. However, cardiomyocyte-specific deletion of TGFβ receptors I/II encoding genes (Tgfbr1/2) or Smad2/3 encoding genes (Smad2/3) do not recapitulate this phenotype suggesting that TGFβ directly programs early heart fibroblast development that in turn specifies cardiomyocyte maturation. Importantly, Col1a2-/-;Col6a2-/- mice with defective cardiac ECM stiffness, mice lacking cardiomyocyte Itgb1 with reduced ECM load sensing, and Tcf21-/- embryos at E17.5 lacking cardiac fibroblasts each fail to generate the same pathologic ECM program with ectopic cardiomyocyte differentiation observed with Tgfb1/2/3 myocyte-specific deletion. These and additional results indicate that TGFβ generated by cardiomyocytes in the embryonic heart mediates fibroblast differentiation that co-evolves the ECM environment that in turn programs cardiomyocyte maturation to establish their identity.

DOI: https://doi.org/10.1101/2025.09.22.677845
Elife. 2025 Sep 30. pii: RP90375. [Epub ahead of print]12

Matrix-associated extracellular vesicles modulate human smooth muscle cell adhesion and directionality by presenting collagen VI.

Alexander N Kapustin, Sofia Serena Tsakali, Meredith Whitehead, George Chennell, Meng-Ying Wu, Chris Molenaar, Anton Kutikhin, Yimeng Chen, Sadia Ahmad, Leo Bogdanov, Maxim Sinitsky, Kseniya Rubina, Aled Clayton, Frederik J Verweij, Dirk Michiel Pegtel, Simona Zingaro, Arseniy Lobov, Bozhana Zainullina, Dylan Owen, Maddy Parsons, Richard E Cheney, Derek T Warren, Martin James Humphries, Thomas Iskratsch, Mark Holt, Catherine M Shanahan.

  The extracellular matrix (ECM) supports blood vessel architecture and functionality and undergoes active remodelling during vascular repair and atherogenesis. Vascular smooth muscle cells (VSMCs) are essential for vessel repair and, via their secretome, can invade from the vessel media into the intima to mediate ECM remodelling. Accumulation of fibronectin (FN) is a hallmark of early vascular repair and atherosclerosis. Here, we show that FN stimulates human VSMCs to secrete small extracellular vesicles (sEVs) by activating the β1 integrin/FAK/Src pathway as well as Arp2/3-dependent branching of the actin cytoskeleton. We found that sEVs are trapped by the ECM in vitro and colocalise with FN in symptomatic atherosclerotic plaques in vivo. Functionally, ECM-trapped sEVs induced the formation of focal adhesions (FA) with enhanced pulling forces at the cellular periphery preventing cellular spreading and adhesion. Proteomic and GO pathway analysis revealed that VSMC-derived sEVs display a cell adhesion signature and are specifically enriched with collagen VI on the sEV surface. In vitro assays identified collagen VI as playing a key role in cell adhesion and invasion directionality. Taken together, our data suggests that the accumulation of FN is a key early event in vessel repair acting to promote secretion of collagen VI enriched sEVs by VSMCs. These sEVs stimulate directional invasion, most likely by triggering peripheral focal adhesion formation and actomyosin contraction to exert sufficient traction force to enable VSMC movement within the complex vascular ECM network.

Keywords:  cell adhesion; cell biology; cell migration; extracellular matrix; human; regeneration

DOI:  https://doi.org/10.7554/eLife.90375
Nat Genet. 2025 Oct 03.

Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq.

Wangjie Liu, Wouter Saelens, Pernille Rainer, Marjan Biočanin, Vincent Gardeux, Antoni Jakub Gralak, Guido van Mierlo, Angelika Gebhart, Julie Russeil, Tingdang Liu, Wanze Chen, Bart Deplancke.

Reprogramming often yields heterogeneous cell fates, yet the underlying mechanisms remain poorly understood. To address this, we developed single-cell transcription factor sequencing (scTF-seq), a single-cell technique that induces barcoded, doxycycline-inducible TF overexpression and quantifies TF dose-dependent transcriptomic changes. Applied to mouse embryonic multipotent stromal cells, scTF-seq generated a gain-of-function atlas for 384 mouse TFs, identifying key regulators of lineage specification, cell cycle control and their interplay. Leveraging single-cell resolution, we uncovered how TF dose shapes reprogramming heterogeneity, revealing both dose-dependent and stochastic cell state transitions. We classified TFs into low-capacity and high-capacity groups, with the latter further subdivided by dose sensitivity. Combinatorial scTF-seq demonstrated that TF interactions can shift from synergistic to antagonistic depending on the relative dose. Altogether, scTF-seq enables the dissection of TF function, dose and cell fate control, providing a high-resolution framework to understand and predict reprogramming outcomes, advancing gene regulation research and the design of cell engineering strategies.

DOI: https://doi.org/10.1038/s41588-025-02343-7
Semin Cell Dev Biol. 2025 Sep 29. pii: S1084-9521(25)00066-7. [Epub ahead of print]175 103656

In vitro modeling of cell types in cardiogenesis and congenital heart disease.

Sanjeev S Ranade.

  Congenital heart defects (CHD) are present in nearly 1 % of live births and are a leading cause of infant mortality. Despite advances in genome sequencing technologies and an increased understanding of the genes necessary for heart development, the etiology of a majority of CHD cases remains undefined. Recent breakthroughs in single-cell genomics, lineage tracing, and live imaging in animal models of cardiogenesis have revealed the precise spatiotemporal dynamics of discrete cell types in heart development. Here, I review how these findings have informed the development of new human pluripotent stem cell methods to generate a diverse range of cells in cardiogenesis. A key unifying theme is that multipotent cardiac progenitor cells are extraordinarily responsive to slight changes to signaling factors administered at various stages of cardiac differentiation. I highlight how the ability to make a range of cardiac cell types can be used to define context specific mechanisms of CHD. I then describe how in vitro human models of cardiogenesis are especially important in cases of severe forms of CHD, such as single ventricle disorders, for which the complex genetic underlying mechanisms are poorly defined and animal models are lacking.

Keywords:  Congenital heart disease; Disease modeling; Heart development; Pluripotent stem cells; Single cell genomics

DOI:  https://doi.org/10.1016/j.semcdb.2025.103656
Circulation. 2025 Sep 29.

Single-Cell Splicing Isoform Atlas of the Adult Human Heart and Heart Failure.

Timothy Pan, Lina Lu, Keith Youker, Cheng-Kai Shiau, Minhua Wang, Hsiao-Yun Lin, Anh Nguyen, Yueying He, Eric Tong, Pei Zhu, Rajul Ranka, Yuanqing Yan, Arjun Sinha, Ankit Bharat, Todd Eagar, Jane Wilcox, Arvind Bhimaraj, Ruli Gao.

   BACKGROUND: Alternative splicing plays crucial roles in normal heart development and cardiac disease by influencing protein-coding sequences, functional domains, and molecular networks. However, a detailed characterization of the human heart isoform landscape remains incomplete.
METHODS: Leveraging long-read single-nucleus RNA sequencing and computational analysis, we dissected full-length isoform heterogeneities, expression patterns, and usage shifts across cell types, cell states, and cardiac conditions of the adult left ventricle. We applied in silico approaches to assess the functional relevance of identified isoforms; validated isoform compositions of representative cardiac genes using reverse transcription quantitative polymerase chain reaction and targeted amplicon sequencing; and developed a web server for interactive navigation of our results.
RESULTS: The data revealed that isoform heterogeneity is widespread in the cardiac cellular system, serving as a posttranscriptional buffer system that calibrates the molecule reservoirs in human hearts. In healthy left ventricles, ≈30% of cell type-specific genes were polyform, using multiple isoforms tailored to cell type-specific programs. Among ubiquitously expressed genes, >300 showed differential isoform usage with cell type specificity. Compared with heart failure, 379 genes in cardiomyocytes demonstrated marked isoform usage shifts, most of which are predicted to change protein coding outcomes through direct changes in protein coding sequences and switches between intron retention and non-protein-coding biotypes. In contrast, cell state-specific programs tend to operate on monoform genes associated with changes among cell states. In addition, our data revealed heart failure-associated differential isoform usage events in stromal and immune cell types in the cardiac microenvironment.
CONCLUSIONS: We present a comprehensive atlas of splicing isoforms in the normal adult heart and heart failure through long-read single-nucleus RNA sequencing and comprehensive computational analyses. The results suggest crucial roles of isoforms in buffering core cellular programs and contributing to disease-associated cell states. The full-length details of these cell-specific isoforms serve as an important reference for downstream translational and mechanistic studies and are available on our online data portal at https://github.com/gaolabtools/heart-isoform-atlas.

Keywords:  heart; heart ventricles; sequence analysis, RNA

DOI:  https://doi.org/10.1161/CIRCULATIONAHA.125.074959
Nat Neurosci. 2025 Oct 03.

Muscle-derived miR-126 regulates TDP-43 axonal local synthesis and NMJ integrity in ALS models.

Ariel Ionescu, Lior Ankol, Anand Ganapathy Subramaniam, Topaz Altman, Iddo Magen, Yahel Cohen, Yehuda Danino, Tal Gradus-Pery, Yoav Niv, Ori Bar Avi, Danielle Geller, Amjd Ibraheem, Ruilei Cheng, Noam Steinberg, Leenor Alfahel, Pauline Duc, Zeynep Ergul-Ulger, Doruk Arslan, Ersin Tan, Florence Rage, Nilo Riva, Angello Quattrini, Can Ebru Bekircan-Kurt, Adrian Israelson, Amir Dori, Eran Hornstein, Eran Perlson.

Amyotrophic lateral sclerosis (ALS) is characterized by neuromuscular junction (NMJ) disruption and neurodegeneration. Recent findings highlight a pivotal role for TAR DNA-binding protein 43 (TDP-43) in forming axonal pathological condensates and facilitating NMJ disruption through inhibition of local protein synthesis. However, the mechanisms that drive local TDP-43 accumulation remain unknown. Here we identify that the TDP-43 axonal accumulation in peripheral nerves of SOD1 patients and mice stems from its aberrant local synthesis. This is a non-cell-autonomous process driven by muscle-derived miR-126a-5p extracellular vesicles (EVs). Inhibiting muscle secretion of miR-126a-5p prompts presynaptic TDP-43 synthesis and accumulation, which disrupts axonal translation and causes NMJ degeneration. Introducing miR-126 to SOD1G93A mice, primary co-cultures and human induced pluripotent stem cell (iPSC)-derived co-cultures with ALS mutations exhibits neuroprotective effects and delays motor decline. These findings identify a transcellular communication axis between muscles and motor neurons that regulates axonal local synthesis and NMJ maintenance, offering insights into ALS onset and progression.

DOI: https://doi.org/10.1038/s41593-025-02062-6
Nat Biotechnol. 2025 Sep 30.

Derivation of embryonic stem cells across avian species.

Xi Chen, Zheng Guo, Xinyi Tong, Xizi Wang, Xugeng Liu, Hiroki Nagai, Ping Wu, Jiayi Lu, David Huss, Martin Tran, Carol Readhead, Christina Wu, Lin Cao, Yixin Huang, Zhaohan Zeng, Fan Feng, Nima Adhami, Sirjan Mor, Rusty Lansford, Cheng-Ming Chuong, Guojun Sheng, Carlos Lois, Qi-Long Ying.

Germline-competent embryonic stem (ES) cells have been successfully derived from mice and rats, but not from other species. Here we report the development of culture conditions for deriving ES cells from chickens and seven other avian species. Chicken ES cells express core pluripotency markers and can differentiate into cells of all embryonic germ layers, as well as extra-embryonic lineages. Notably, chicken ES cells contribute to high rates of chimerism when injected into chicken embryos and give rise to germ cells both in vitro and in ovo, confirming their germline competence. In addition, we demonstrated that ES cell self-renewal pathways are conserved among avian species, allowing ES cells from multiple avian species to be established using optimized chicken ES cell culture conditions. The establishment of authentic avian ES cells lays the groundwork for future applications in genetic engineering and the conservation of avian biodiversity.

DOI: https://doi.org/10.1038/s41587-025-02833-3
Nature. 2025 Oct 01.

Autoimmune response to C9orf72 protein in amyotrophic lateral sclerosis.

Tanner Michaelis, Cecilia S Lindestam Arlehamn, Emil Johansson, April Frazier, James D Berry, Merit Cudkowicz, Namita A Goyal, Christina Fournier, Allison Snyder, Justin Y Kwan, Jody Crook, Elizabeth J Phillips, Simon A Mallal, John Ravits, Karen S Marder, John Sidney, David Sulzer, Alessandro Sette.

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by a progressive loss of motor neurons. Neuroinflammation is apparent in affected tissues, including increased T cell infiltration and activation of microglia, particularly in the spinal cord1,2. Autoimmune responses are thought to have a key role in ALS pathology, and it is hypothesized that T cells contribute to the rapid loss of neurons during disease progression3,4. However, until now there has been no reported target for such an autoimmune response. Here we show that ALS is associated with recognition of the C9orf72 antigen, and we map the specific epitopes that are recognized. We show that these responses are mediated by CD4+ T cells that preferentially release IL-5 and IL-10, and that IL-10-mediated T cell responses are significantly greater in donors who have a longer predicted survival time. Our results reinforce the previous hypothesis that neuroinflammation has an important role in ALS disease progression, possibly because of a disrupted balance of inflammatory and counter-inflammatory T cell responses4. These findings highlight the potential of therapeutic strategies aimed at enhancing regulatory T cells5, and identify a key target for antigen-specific T cell responses that could enable precision therapeutics in ALS.

DOI: https://doi.org/10.1038/s41586-025-09588-6
Nat Cardiovasc Res. 2025 Oct 03.

Spatial multiomics of acute myocardial infarction reveals immune cell infiltration through the endocardium.

Florian Wünnemann, Florian Sicklinger, Kresimir Bestak, Jose Nimo, Tobias Thiemann, Junedh M Amrute, Mathias Nordbeck, Niklas Hartmann, Miguel A Ibarra-Arellano, Jovan Tanevski, Margot Chazotte, Clara Heine, Norbert Frey, Kory J Lavine, Fabian Coscia, Julio Saez-Rodriguez, Florian Leuschner, Denis Schapiro.

Myocardial infarction (MI) continues to be a leading cause of death worldwide. Even though it is well established that the complex interplay between different cell types determines the overall healing response after MI, the precise changes in the tissue architecture are still poorly understood. In this study, we generated an integrative cellular map of the acute phase after murine MI using a combination of imaging-based transcriptomics (Molecular Cartography) and antibody-based highly multiplexed imaging (Sequential Immunofluorescence). This enabled us to evaluate cell type compositions and changes at subcellular resolution over time. We observed the recruitment of leukocytes to the infarcted heart through the endocardium and performed unbiased spatial proteomic analysis using Deep Visual Proteomics (DVP) to investigate the underlying mechanisms. DVP identified von Willebrand factor (vWF) as an upregulated mediator of inflammation 24 hours after MI, and functional blocking of vWF reduced the infiltration of C-C chemokine receptor 2 (Ccr2)-positive monocytes and worsened cardiac function after MI.

DOI: https://doi.org/10.1038/s44161-025-00717-y
Genome Biol. 2025 Sep 27. 26(1): 315

Codon-specific ribosome stalling reshapes translational dynamics during branched-chain amino acid starvation.

Lina Worpenberg, Cédric Gobet, Felix Naef.

   BACKGROUND: Cells regulate protein synthesis in response to fluctuating nutrient availability through mechanisms that affect both translation initiation and elongation. Branched-chain amino acids, leucine, isoleucine, and valine, are essential nutrients. However, how their depletion affects translation remains largely unclear. Here, we investigate the immediate effects of single, double, and triple branched-chain amino acid deprivation on translational dynamics in NIH3T3 cells using RNA-seq and ribosome profiling.
RESULTS: All starvation conditions increased ribosome dwell times, with pronounced stalling at all valine codons during valine and triple starvation, whereas leucine and isoleucine starvation produced milder, codon-specific effects. Notably, stalling under isoleucine deprivation largely decreased under triple starvation. Positional enrichment of valine codons near the 5' end and downstream isoleucine codons potentially contributes to these patterns, suggesting a possible elongation bottleneck that influences translational responses under branched-chain amino acid starvation. The presence of multiple valine stalling sites was associated with decreased protein levels. Finally, codon-specific dwell time changes correlated strongly with patterns of tRNA isoacceptor charging.
CONCLUSIONS: Together, these findings suggest that differential ribosome stalling under branched-chain amino acid starvation reflects a balance between amino acid supply, tRNA charging dynamics, codon position, and stress-response signaling.

Keywords:  Amino acid starvation; Codon-specific stalling; Elongation bottleneck; Nutrient stress response; Ribosome profiling; Translation regulation; tRNA charging

DOI:  https://doi.org/10.1186/s13059-025-03800-6
Annu Rev Cell Dev Biol. 2025 Oct;41(1): 579-603

Gene Clusters Reveal Fundamental Principles of Genome Folding and Transcriptional Regulation.

Alex Buckley, Carlo Vetralla, Daniele Canzio.

  Gene clusters generate proteome diversity required for cell fate and function. Given their genomic organization, wherein tandemly arranged genes with nearly identical promoter sequences neighbor shared enhancers, gene clusters present extreme cases of enhancer-promoter specificity, long-range enhancer-promoter communication, and chromatin compartmentalization. Here, we review recent advances in the regulation of protocadherin (Pcdh) and olfactory receptor (OR) gene clusters. These clusters present similar challenges in that cells must express a limited number of each type of gene stochastically. Probabilistic Pcdh and OR choice is accomplished through tunable enhancer-promoter interactions, but these interactions are regulated by distinct mechanisms. At the Pcdh locus, cohesin-mediated DNA loop extrusion dictates enhancer-promoter communication, whereas OR genes communicate with their enhancers through multichromosome assemblies involving the protein LDB1. In reviewing principles of Pcdh and OR regulation, we propose that gene clusters offer valuable paradigms for deciphering principles of gene expression regulation, with broad mechanistic and physiological implications for mammalian genome folding.

Keywords:  enhancer–promoter communication; gene clusters; genome folding; transcriptional regulation

DOI:  https://doi.org/10.1146/annurev-cellbio-111822-122324
Nat Commun. 2025 Oct 02. 16(1): 8800

Crotonate enhances intestinal regeneration after injury via HBO1-mediated H3K14 crotonylation.

Yanhui Xiao, Shicheng Yu, Mengxian Zhang, Nanshan Zhong, Shan Hua, Zhi Fang, Zhe Zhang, Huidong Liu, Ronghui Tan, Yuan Liu, Ye-Guang Chen.

The intestinal epithelium undergoes rapid turnover driven by Lgr5+ intestinal stem cells at the crypt base, and can recover upon damage. Histone crotonylation plays a critical role in chromatin regulation and gene expression. However, the role of histone crotonylation, specifically H3K14 crotonylation (H3K14cr) in the intestine remains poorly understood. Here we demonstrate that both crotonate and H3K14cr levels are increased in the regenerating crypts. Treatment with sodium crotonate significantly alleviates dextran sulfate sodium induced colitis, an effect largely dependent on HBO1-mediated H3K14cr. Notably, HBO1 deficiency severely dampens regeneration, correlating with reduced H3K14ac and H3K14cr levels, decreased chromatin accessibility at transcriptional start sites, and impaired expression of stem and fetal genes. Single-cell RNA sequencing analysis reveals that HBO1 is expressed in stem cells and regenerative cells during recovery after irradiation, further supporting the critical role of HBO1 in intestinal regeneration. Together, our findings uncover a mechanism by which crotonate, HBO1, and H3K14cr contribute to epithelial regeneration and suggest that crotonate may represent a promising therapeutic agent for the treatment of gastrointestinal diseases.

DOI: https://doi.org/10.1038/s41467-025-63869-2
EMBO J. 2025 Sep 29.

PIWI proteins tether the piRNA biogenesis machinery to mitochondria during mammalian spermatogenesis.

Jie Gao, Canmei Chen, Guanyi Shang, Wenyang Yu, Ting Zhao, Yunfang Zhang, Chen Chen, Deqiang Ding.

  piRNA biogenesis occurs in the intermitochondrial cement (IMC) in mammalian germ cells. The mechanisms by which IMC components engage mitochondria to form an efficient piRNA biogenesis machinery remain elusive. Here, we demonstrate that PIWI proteins orchestrate the assembly and disassembly of the piRNA biogenesis machinery in mice. The mitochondrial-anchored protein ASZ1 specifically interacts with PIWIL2 and recruits PIWIL2 to IMC granules. Sequentially, piRNAs competitively bind PIWIL2, leading to ASZ1-PIWIL2 dissociation. In fetal male germ cells, ASZ1-PIWIL2-TDRD1 forms a seed complex to initiate the assembly of the piRNA biogenesis machinery. During postnatal meiosis, the TDRKH-PIWIL1-TDRD1 complex synergizes with the ASZ1-PIWIL2-TDRD1 complex to induce substantial IMC assembly and pachytene piRNA biogenesis through TDRD1-mediated phase separation. PIWI proteins act as bridges, tethering non-mitochondrial proteins to mitochondrial-anchored proteins in IMC granules with the assistance of TDRD1. Together, our findings establish the pivotal role of PIWI proteins in governing the spatiotemporal dynamics of piRNA biogenesis machinery during mammalian spermatogenesis.

Keywords:  Germ Granule; Mitochondrion; PIWI Protein; PIWI-Interacting RNA; Spermatogenesis

DOI:  https://doi.org/10.1038/s44318-025-00579-x
Nat Commun. 2025 Sep 30. 16(1): 8726

Regulation of NSL by TAF4A is critical for genome stability and quiescence of muscle stem cells.

Angelina M Georgieva, Krishna Sreenivasan, Dong Ding, Clementine Villeneuve, Sara A Wickström, Stefan Günther, Carsten Kuenne, Ulrich Gärtner, Xinyue Guo, Yonggang Zhou, Xuejun Yuan, Thomas Braun.

Acetylation of lamin A/C by the non-specific lethal complex, containing MOF and KANSL2, is instrumental for maintaining nuclear architecture and genome stability, but the mechanisms controlling expression of its components in different cell types are poorly characterized. Here, we show that TAF4A, primarily known as a subunit of TFIID, forms a complex with the heterotrimeric transcription factor NF-Y and is critical for cell type-specific regulation of Kansl2 in muscle stem cells. Inactivation of Taf4a reduces expression of Kansl2 and alters post-translational modification of lamin A/C, thereby decreasing nuclear stiffness, which disrupts the nuclear architecture and results in severe genomic instability. Reduced expression of Kansl2 in Taf4a-mutant muscle stem cells changes expression of numerous genes involved in chromatin regulation. The subsequent loss of heterochromatin, in combination with pronounced genomic instability, activates muscle stem cells but impairs their proliferation, which depletes the stem cell pool and abolishes skeletal muscle regeneration. We conclude that TAF4A-NF-Y-dependent transcription regulation safeguards heterochromatin and genome stability of muscle stem cells via the non-specific lethal complex.

DOI: https://doi.org/10.1038/s41467-025-64402-1
bioRxiv. 2025 Sep 25. pii: 2025.09.25.678607. [Epub ahead of print]

A self-limiting mechanotransduction feedback loop ensures robust organ formation.

Yusuke Mori, Paul Robin, Anne Belle Briggs, Daniel S Levic, Jiacheng Wang, Kira L Heikes, Michel Bagnat, Edouard Hannezo, Akankshi Munjal.

Organ development requires integration of mechanical forces, biochemical signals, and transcriptional programs to achieve proper size and architecture. Mechanotransduction feedback loops convert mechanical forces into gene-expression changes that, in turn, regulate cell behaviors such as growth and extracellular matrix (ECM) production. How these loops are coupled to developmental programs to ensure robust morphogenetic outcomes remains poorly understood. Here, we show that Yap-dependent mechanotransduction establishes a self-limiting positive feedback loop that drives the successful formation of semicircular canals in zebrafish. These canals form through reproducible steps of bud initiation, extension, and fusion within the otic epithelium. Local swelling of a hyaluronan-rich ECM initiates bud formation. We demonstrate that this ECM expansion activates Yap in a spatially patterned manner within the bud. Activated Yap induces its target, ccn1l1, which drives further ECM production, establishing a positive feedback loop. The ensuing rapid ECM expansion sustains bud extension. Graded perturbations to the mechanotransduction loop reduced extension, with bud fusion remaining robust at lower levels of disruption but blocked at the highest dose. Critically, the loop contains its own termination mechanism: when buds fuse, the PKA-CREB signaling is activated by the adhesion GPCR Gpr126 to suppress ccn1l1 , preventing overgrowth. These findings reveal how mechanotransduction-driven positive feedback loops can be coupled to their own termination, providing developmental control through the integration of mechanical forces with transcriptional responses and morphogenetic outcomes.

DOI: https://doi.org/10.1101/2025.09.25.678607