bims-ginsta 2025-04-20 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2025–04–20
37 papers selected by
Jinrong Hu, National University of Singapore

The subcortical maternal complex safeguards mouse oocyte-to-embryo transition by preventing nuclear entry of SPIN1.
DNA binding and mitotic phosphorylation protect polyglutamine proteins from assembly formation.
Stem cell-based models of early human development.
Fate and state transitions during human blood vessel organoid development.
Total whole-arm chromosome losses predict malignancy in human cancer.
High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH.
Lineage-specific CDK activity dynamics characterize early mammalian development.
Glycolytic activity instructs germ layer proportions through regulation of Nodal and Wnt signaling.
Integrator loss leads to dsRNA formation that triggers the integrated stress response.
Integrated molecular-phenotypic profiling reveals metabolic control of morphological variation in a stem-cell-based embryo model.
Apical constriction requires patterned apical surface remodeling to synchronize cellular deformation.
Desmosome mutations impact the tumor microenvironment to promote melanoma proliferation.
Mechanochemical bistability of intestinal organoids enables robust morphogenesis.
Mechanical force-driven cell competition ensures robust morphogen gradient formation.
Unified molecular approach for spatial epigenome, transcriptome, and cell lineages.
Cell and nuclear size are associated with chromosomal instability and tumorigenicity in cancer cells that undergo whole genome doubling.
Cytosolic cytochrome c represses ferroptosis.
Emerging roles of transcriptional condensates as temporal signal integrators.
Tripartite phosphorylation of SPT5 by CDK9 times pause release and tunes elongation rate of RNA polymerase II.
Cell lineage-resolved embryonic morphological map reveals signaling associated with cell fate and size asymmetry.
Coupling of ribosome biogenesis and translation initiation in human mitochondria.
Multi-zonal liver organoids from human pluripotent stem cells.
Mechanism of DNA replication fork breakage and PARP1 hyperactivation during replication catastrophe.
Genome-wide analyses identify 25 infertility loci and relationships with reproductive traits across the allele frequency spectrum.
Specific mitotic events drive left-right organizer development.
Exploring early extraembryonic cells of epiblast origin: Questions on human amniotic ectoderm and extraembryonic mesoderm.
Spatial analysis of mitochondrial gene expression reveals dynamic translation hubs and remodeling in stress.
Interplay of damage and repair in the control of epithelial tissue integrity in response to cyclic loading.
A tripartite cell-free translation system to study mammalian translation.
Rewriting regulatory DNA to dissect and reprogram gene expression.
Generation of human adult hepatocyte organoids with metabolic functions.
Granulosa cell transcription is similarly impacted by superovulation and aging and predicts early embryonic trajectories.
Evidence of substrate control of Cdk phosphorylation during the budding yeast cell cycle.
ATM priming and end resection-coupled phosphorylation of MRE11 is important for fork protection and replication restart.
ALDH7A1 protects against ferroptosis by generating membrane NADH and regulating FSP1.
SIRT7 links H3K36ac epigenetic regulation with genome maintenance in the aging mouse testis.
Glutamylation of centrosomes ensures their function by recruiting microtubule nucleation factors.

Nat Struct Mol Biol. 2025 Apr 17.

The subcortical maternal complex safeguards mouse oocyte-to-embryo transition by preventing nuclear entry of SPIN1.

Chengpeng Xu, Dandan Qin, Xukun Lu, Qianqian Qi, Yu Wu, Qizhi Wang, Zhuo Han, Xiaoqing Nie, Yongmei Jiang, Dong Deng, Wei Xie, Zheng Gao, Lei Li.

How cytoplasmic regulators control nuclear events in mammalian oocytes and early embryos remains largely enigmatic. We previously identified a subcortical maternal complex (SCMC) that specifically resides in the cytoplasm of mammalian oocytes and early embryos but is also involved in nuclear events. Nevertheless, how the cytoplasmic SCMC exerts its role in nuclear processes remains unknown. In this study, we unveil SPIN1, a histone methylation reader, as a novel member of the SCMC. The SCMC component FILIA tightly regulates the expression and cytoplasmic localization of SPIN1 through direct interaction. When the expression of FILIA is decreased because of genetic mutations of SCMC genes, SPIN1 expression is dramatically reduced but the residual SPIN1 translocates into the nucleus. The abnormal nuclear presence of SPIN1 impairs H3K4me3 reprogramming, zygotic genome activation and physiological embryonic development. Inhibiting the interaction between SPIN1 and H3K4me3 partially rescues the abnormal phenotype in FILIA-null embryos. Mechanistically, SPIN1 partially perturbs the demethylation process by competing with KDM5B for binding to H3K4me3. Collectively, our work highlights the complexity of the mammalian SCMC and oocyte-to-embryo transition, revealing an intricate regulatory mechanism that facilitates the smooth progression of this process.

DOI: https://doi.org/10.1038/s41594-025-01538-0
Cell. 2025 Apr 12. pii: S0092-8674(25)00349-6. [Epub ahead of print]

DNA binding and mitotic phosphorylation protect polyglutamine proteins from assembly formation.

Shady Saad, Tomek Swigut, Saman Tabatabaee, Pranav Lalgudi, Daniel F Jarosz, Joanna Wysocka.

  Polyglutamine (polyQ) expansion is associated with pathogenic protein aggregation in neurodegenerative disorders. However, long polyQ tracts are also found in many transcription factors (TFs), such as FOXP2, a TF implicated in human speech. Here, we explore how FOXP2 and other glutamine-rich TFs avoid unscheduled assembly. Throughout interphase, DNA binding, irrespective of sequence specificity, has a solubilizing effect. During mitosis, multiple phosphorylation events promote FOXP2's eviction from chromatin and supplant the solubilizing function of DNA. Further, human-specific amino acid substitutions linked to the evolution of speech map to a mitotic phospho-patch, the "EVO patch," and reduce the propensity of the human FOXP2 to assemble. Fusing the pathogenic form of Huntingtin to either a DNA-binding domain, a phosphomimetic variant of this EVO patch, or a negatively charged peptide is sufficient to diminish assembly formation, suggesting that hijacking mechanisms governing solubility of glutamine-rich TFs may offer new strategies for treatment of polyQ expansion diseases.

Keywords:  FOXP2; Huntington's disease; amyloid; evolution; glutamine-rich proteins; human speech; language; polyglutamine; protein assemblies; transcription factors

DOI:  https://doi.org/10.1016/j.cell.2025.03.031
Development. 2025 Apr 15. pii: dev204543. [Epub ahead of print]152(8):

Stem cell-based models of early human development.

Lizhong Liu, Jun Wu.

  Stem cell-based embryo models (SCBEMs) are structures generated from three-dimensional (3D) culture of pluripotent stem cells and their derivatives, utilizing mechanical and/or chemical cues to facilitate lineage differentiation, self-organization and morphogenesis. These models partially mimic early embryos, which would otherwise be difficult to access. SCBEMs have been established in mice, livestock, nonhuman primates and humans. Here, we focus on recently developed human models, with an emphasis on the peri-implantation stage and the aspects of human development these SCBEMs recapitulate.

Keywords:  Gastrulation; Human pluripotent stem cells; Implantation; Stem cell-based embryo models

DOI:  https://doi.org/10.1242/dev.204543
Cell. 2025 Apr 16. pii: S0092-8674(25)00387-3. [Epub ahead of print]

Fate and state transitions during human blood vessel organoid development.

Marina T Nikolova, Zhisong He, Makiko Seimiya, Gustav Jonsson, Wuji Cao, Ryo Okuda, Reiner A Wimmer, Ryoko Okamoto, Josef M Penninger, J Gray Camp, Barbara Treutlein.

  Human blood vessel organoids (hBVOs) have emerged as a system to model human vascular development and disease. Here, we use single-cell multi-omics together with genetic and signaling pathway perturbations to reconstruct hBVO development. Mesodermal progenitors bifurcate into endothelial and mural fates in vitro, and xenografted BVOs acquire definitive arteriovenous endothelial cell specification. We infer a gene regulatory network and use single-cell genetic perturbations to identify transcription factors (TFs) and receptors involved in cell fate specification, including a role for MECOM in endothelial and mural specification. We assess the potential of BVOs to generate organotypic states, identify TFs lacking expression in hBVOs, and find that induced LEF1 overexpression increases brain vasculature specificity. Finally, we map vascular disease-associated genes to hBVO cell states and analyze an hBVO model of diabetes. Altogether, we provide a comprehensive cell state atlas of hBVO development and illuminate the power and limitation of hBVOs for translational research.

Keywords:  arteriovenous specification; human blood vessel organoid; human development; organoid cell atlas; single-cell genomics; single-cell perturbation screen

DOI:  https://doi.org/10.1016/j.cell.2025.03.037
bioRxiv. 2025 Apr 01. pii: 2025.03.09.642243. [Epub ahead of print]

Total whole-arm chromosome losses predict malignancy in human cancer.

Ye Zheng, Kami Ahmad, Steven Henikoff.

Aneuploidy is observed as gains or losses of whole chromosomes or chromosome arms and is a common hallmark of cancer. Whereas models for the generation of aneuploidy in cancer invoke mitotic chromosome segregation errors, whole-arm losses might occur simply as a result of centromere breakage. We recently showed that elevated RNA Polymerase II (RNAPII) level over S-phase-dependent histone genes predicts rapid recurrence of human meningioma and is correlated with total whole-arm losses relative to gains. To explain this imbalance in arm losses over gains, we have proposed that histone overexpression at S-phase competes with the histone H3 variant CENP-A, resulting in centromere breaks and whole-arm losses. To test whether centromere breaks alone can drive aneuploidy, we ask whether total whole-arm aneuploids can predict outcome across different cancer types in large RNA and whole-genome sequencing databanks. We find that total whole-arm losses generally predict outcome, suggesting that centromere breakage is a major initiating factor leading to aneuploidy and the resulting changes in the selective landscape that drive most cancers. We also present evidence that centromere breakage alone is sufficient to account for whole-arm losses and gains, contrary to mitotic spindle error models for generation of aneuploidy. Our results suggest that therapeutic intervention targeting histone overexpression has the potential of reducing aneuploidy and slowing cancer progression.
Significance Statement: Gain or loss of whole chromosome arms following centromere breaks is frequent in cancer, but whether or not there is a common initiating event is unknown. Here we show that the total number of whole-arm losses predicts patient outcomes across cancer types, suggesting a causal relationship. This general excess of losses over gains is not predicted by mitotic error models of aneuploidy but rather suggests that centromere breaks themselves initiate whole-arm aneuploidies. Insofar as aneuploidy reshapes the selective landscapes that drive most cancers, our results have potential clinical implications.

DOI: https://doi.org/10.1101/2025.03.09.642243
Cell. 2025 Apr 11. pii: S0092-8674(25)00350-2. [Epub ahead of print]

High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH.

Yanyu Zhu, Ashwin Balaji, Mengting Han, Leonid Andronov, Anish R Roy, Zheng Wei, Crystal Chen, Leanne Miles, Sa Cai, Zhengxi Gu, Ariana Tse, Betty Chentzu Yu, Takeshi Uenaka, Xueqiu Lin, Andrew J Spakowitz, W E Moerner, Lei S Qi.

  Three-dimensional (3D) genome dynamics are crucial for cellular functions and disease. However, real-time, live-cell DNA visualization remains challenging, as existing methods are often confined to repetitive regions, suffer from low resolution, or require complex genome engineering. Here, we present Oligo-LiveFISH, a high-resolution, reagent-based platform for dynamically tracking non-repetitive genomic loci in diverse cell types, including primary cells. Oligo-LiveFISH utilizes fluorescent guide RNA (gRNA) oligo pools generated by computational design, in vitro transcription, and chemical labeling, delivered as ribonucleoproteins. Utilizing machine learning, we characterized the impact of gRNA design and chromatin features on imaging efficiency. Multi-color Oligo-LiveFISH achieved 20-nm spatial resolution and 50-ms temporal resolution in 3D, capturing real-time enhancer and promoter dynamics. Our measurements and dynamic modeling revealed two distinct modes of chromatin communication, and active transcription slows enhancer-promoter dynamics at endogenous genes like FOS. Oligo-LiveFISH offers a versatile platform for studying 3D genome dynamics and their links to cellular processes and disease.

Keywords:  CRISPR imaging; DNA communication; Oligo-LiveFISH; dynamic tracking; enhancer-promoter interaction; high-resolution imaging; live DNA imaging; non-repetitive genome imaging; polymer modeling; primary cell

DOI:  https://doi.org/10.1016/j.cell.2025.03.032
Cell Rep. 2025 Apr 11. pii: S2211-1247(25)00329-8. [Epub ahead of print]44(4): 115558

Lineage-specific CDK activity dynamics characterize early mammalian development.

Bechara Saykali, Andy D Tran, James A Cornwell, Matthew A Caldwell, Paniz Rezvan Sangsari, Nicole Y Morgan, Michael J Kruhlak, Steven D Cappell, Sergio Ruiz.

  Cyclin-dependent kinases (CDKs) regulate proliferation dynamics and cell fate in response to extracellular inputs. It remains largely unknown how CDK activity fluctuates and influences cell commitment during early mammalian development. Here, we generated a mouse model expressing a CDK translocation reporter that enabled quantification of CDK activity in live single cells. By examining pre- and post-implantation mouse embryos at different stages, we observed a progressive decrease in CDK activity in cells from the trophectoderm (TE) prior to implantation. This drop seems to correlate with the available levels of ICM-derived FGF4 as CDK activity downregulation is rescued by exogenous FGF4. Furthermore, we showed that cell fate decisions in the pre-implantation embryo are not determined by the establishment of oscillatory CDK activity or overall changes in CDK activity. Finally, we uncovered the existence of conserved regulatory mechanisms in mammals by revealing lineage-specific regulation of CDK activity in TE-like human cells.

Keywords:  CDK; CP: Developmental biology; cyclin-dependent kinase; embryonic stem cells; kinase translocation reporter; pre-implantation development; trophectoderm

DOI:  https://doi.org/10.1016/j.celrep.2025.115558
Cell Stem Cell. 2025 Apr 10. pii: S1934-5909(25)00101-8. [Epub ahead of print]

Glycolytic activity instructs germ layer proportions through regulation of Nodal and Wnt signaling.

Kristina S Stapornwongkul, Elisa Hahn, Patryk Poliński, Laura Salamó Palau, Krisztina Arató, LiAng Yao, Kate Williamson, Nicola Gritti, Kerim Anlas, Mireia Osuna Lopez, Kiran R Patil, Idse Heemskerk, Miki Ebisuya, Vikas Trivedi.

  Metabolic pathways can influence cell fate decisions, yet their regulative role during embryonic development remains poorly understood. Here, we demonstrate an instructive role of glycolytic activity in regulating signaling pathways involved in mesoderm and endoderm specification. Using a mouse embryonic stem cell (mESC)-based in vitro model for gastrulation, we found that glycolysis inhibition increases ectodermal cell fates at the expense of mesodermal and endodermal lineages. We demonstrate that this relationship is dose dependent, enabling metabolic control of germ layer proportions through exogenous glucose levels. We further show that glycolysis acts as an upstream regulator of Nodal and Wnt signaling and that its influence on cell fate specification can be decoupled from its effects on growth. Finally, we confirm the generality of our findings using a human gastrulation model. Our work underscores the dependence of signaling pathways on metabolic conditions and provides mechanistic insight into the nutritional regulation of cell fate decision-making.

Keywords:  Nodal signaling; Wnt signaling; endoderm; gastruloid; germ layer specification; glycolysis; mesoderm; metabolic signaling; nutritional environment; stem cell model of development

DOI:  https://doi.org/10.1016/j.stem.2025.03.011
Cell. 2025 Apr 10. pii: S0092-8674(25)00343-5. [Epub ahead of print]

Integrator loss leads to dsRNA formation that triggers the integrated stress response.

Apoorva Baluapuri, Nicole ChenCheng Zhao, Ryan J Marina, Kai-Lieh Huang, Anastasia Kuzkina, Maria E Amodeo, Chad B Stein, Lucie Y Ahn, Jordan S Farr, Ashleigh E Schaffer, Vikram Khurana, Eric J Wagner, Karen Adelman.

  Integrator (INT) is a metazoan-specific complex that targets promoter-proximally paused RNA polymerase II (RNAPII) for termination, preventing immature RNAPII from entering gene bodies and functionally attenuating transcription of stress-responsive genes. Mutations in INT subunits are associated with many human diseases, including cancer, ciliopathies, and neurodevelopmental disorders, but how reduced INT activity contributes to disease is unknown. Here, we demonstrate that the loss of INT-mediated termination in human cells triggers the integrated stress response (ISR). INT depletion causes upregulation of short genes such as the ISR transcription factor activating transcription factor 3 (ATF3). Further, immature RNAPII that escapes into genes upon INT depletion is prone to premature termination, generating incomplete pre-mRNAs with retained introns. Retroelements within retained introns form double-stranded RNA (dsRNA) that is recognized by protein kinase R (PKR), which drives ATF4 activation and prolonged ISR. Critically, patient cells with INT mutations exhibit dsRNA accumulation and ISR activation, thereby implicating chronic ISR in diseases caused by INT deficiency.

Keywords:  IR-Alu; Integrator; RNA polymerase II pausing; double-stranded RNA; gene regulation; integrated stress response; premature cleavage and polyadenylation; premature termination; protein kinase R

DOI:  https://doi.org/10.1016/j.cell.2025.03.025
Cell Stem Cell. 2025 Apr 11. pii: S1934-5909(25)00102-X. [Epub ahead of print]

Integrated molecular-phenotypic profiling reveals metabolic control of morphological variation in a stem-cell-based embryo model.

Alba Villaronga-Luque, Ryan G Savill, Natalia López-Anguita, Adriano Bolondi, Sumit Garai, Seher Ipek Gassaloglu, Roua Rouatbi, Kathrin Schmeisser, Aayush Poddar, Lisa Bauer, Tiago Alves, Sofia Traikov, Jonathan Rodenfels, Triantafyllos Chavakis, Aydan Bulut-Karslioglu, Jesse V Veenvliet.

  Considerable phenotypic variation under identical culture conditions limits the potential of stem-cell-based embryo models (SEMs) in basic and applied research. The biological processes causing this seemingly stochastic variation remain unclear. Here, we investigated the roots of phenotypic variation by parallel recording of transcriptomic states and morphological history in individual structures modeling embryonic trunk formation. Machine learning and integration of time-resolved single-cell RNA sequencing with imaging-based phenotypic profiling identified early features predictive of phenotypic end states. Leveraging this predictive power revealed that early imbalance of oxidative phosphorylation and glycolysis results in aberrant morphology and a neural lineage bias, which we confirmed by metabolic measurements. Accordingly, metabolic interventions improved phenotypic end states. Collectively, our work establishes divergent metabolic states as drivers of phenotypic variation and offers a broadly applicable framework to chart and predict phenotypic variation in organoids and SEMs. The strategy can be used to identify and control underlying biological processes, ultimately increasing reproducibility.

Keywords:  developmental metabolism; gastruloids; glycolysis; metabolic signaling; morphospace; neuromesodermal progenitors; organoids; oxidative phosphorylation; single-cell RNA sequencing; stem-cell-based embryo models

DOI:  https://doi.org/10.1016/j.stem.2025.03.012
Elife. 2025 Apr 17. pii: RP93496. [Epub ahead of print]13

Apical constriction requires patterned apical surface remodeling to synchronize cellular deformation.

Satoshi Yamashita, Shuji Ishihara, François Graner.

  Apical constriction is a basic mechanism for epithelial morphogenesis, making columnar cells into wedge shape and bending a flat cell sheet. It has long been thought that an apically localized myosin generates a contractile force and drives the cell deformation. However, when we tested the increased apical surface contractility in a cellular Potts model simulation, the constriction increased pressure inside the cell and pushed its lateral surface outward, making the cells adopt a drop shape instead of the expected wedge shape. To keep the lateral surface straight, we considered an alternative model in which the cell shape was determined by cell membrane elasticity and endocytosis, and the increased pressure is balanced among the cells. The cellular Potts model simulation succeeded in reproducing the apical constriction, and it also suggested that a too strong apical surface tension might prevent the tissue invagination.

Keywords:  D. melanogaster; apical constriction; cellular Potts model; developmental biology; simulation

DOI:  https://doi.org/10.7554/eLife.93496
Nat Genet. 2025 Apr 16.

Desmosome mutations impact the tumor microenvironment to promote melanoma proliferation.

Maayan Baron, Mohita Tagore, Patrick Wall, Fan Zheng, Dalia Barkley, Itai Yanai, Jing Yang, Maija Kiuru, Richard M White, Trey Ideker.

Desmosomes are transmembrane protein complexes that contribute to cell-cell adhesion in epithelia and other tissues. Here, we report the discovery of frequent genetic alterations in the desmosome in human cancers, with the strongest signal seen in cutaneous melanoma, where desmosomes are mutated in more than 70% of cases. In primary but not metastatic melanoma biopsies, the burden of coding mutations in desmosome genes is associated with a strong reduction in desmosome gene expression. Analysis by spatial transcriptomics and protein immunofluorescence suggests that these decreases in expression occur in keratinocytes in the microenvironment rather than in primary melanoma cells. In further support of a microenvironmental origin, we find that desmosome gene knockdown in keratinocytes yields markedly increased proliferation of adjacent melanoma cells in keratinocyte and melanoma cocultures. Similar increases in melanoma proliferation are observed in media preconditioned with desmosome-deficient keratinocytes. Thus, gradual accumulation of desmosome mutations in neighboring cells may prime melanoma cells for neoplastic transformation.

DOI: https://doi.org/10.1038/s41588-025-02163-9
Nat Phys. 2025 ;21(4): 608-617

Mechanochemical bistability of intestinal organoids enables robust morphogenesis.

Shi-Lei Xue, Qiutan Yang, Prisca Liberali, Edouard Hannezo.

  Reproducible pattern and form generation during embryogenesis is poorly understood. Intestinal organoid morphogenesis involves a number of mechanochemical regulators such as cell-type-specific cytoskeletal forces and osmotically driven lumen volume changes. It is unclear how these forces are coordinated in time and space to ensure robust morphogenesis. Here we show how mechanosensitive feedback on cytoskeletal tension gives rise to morphological bistability in a minimal model of organoid morphogenesis. In the model, lumen volume changes can impact the epithelial shape via both direct mechanical and indirect mechanosensitive mechanisms. We find that both bulged and budded crypt states are possible and dependent on the history of volume changes. We test key modelling assumptions via biophysical and pharmacological experiments to demonstrate how bistability can explain experimental observations, such as the importance of the timing of lumen shrinkage and robustness of the final morphogenetic state to mechanical perturbations. This suggests that bistability arising from feedback between cellular tensions and fluid pressure could be a general mechanism that coordinates multicellular shape changes in developing systems.

Keywords:  Biological physics; Computational biophysics

DOI:  https://doi.org/10.1038/s41567-025-02792-1
Semin Cell Dev Biol. 2025 Apr 11. pii: S1084-9521(25)00017-5. [Epub ahead of print]170 103607

Mechanical force-driven cell competition ensures robust morphogen gradient formation.

Kana Aoki, Tohru Ishitani.

  Morphogen gradients provide positional data and maintain tissue patterns by instructing cells to adopt distinct fates. In contrast, morphogen gradient-forming tissues undergo dynamic morphogenetic movements that generate mechanical forces and can disturb morphogen signal transduction. However, the interactions between morphogen gradients and these forces remain largely unknown. In this study, we described how mechanical force-mediated cell competition corrects noisy morphogen gradients to ensure robust tissue patterns. The Wnt/β-catenin morphogen gradient-that patterns the embryonic anterior-posterior axis-generates cadherin-actomyosin interaction-mediated intercellular tension gradients-termed mechano-gradients. Naturally generated unfit cells that produce noisy Wnt/β-catenin gradients induce local deformation of the mechano-gradients. Neighboring fit cells sense this deformation, resulting in the activation of Piezo family mechanosensitive calcium channels and secretion of annexinA1, which specifically kills unfit cells to recover morphogen gradients. Therefore, mechanical force-mediated cell competition between the morphogen-receiver cells supports robust gradient formation. Additionally, we discuss the potential roles of mechanical force-driven cell competition in other contexts, including organogenesis and cancer.

Keywords:  Cadherin; Cell competition; Mechanical force; Morphogen; Piezo; Shh; Wnt

DOI:  https://doi.org/10.1016/j.semcdb.2025.103607
Proc Natl Acad Sci U S A. 2025 Apr 22. 122(16): e2424070122

Unified molecular approach for spatial epigenome, transcriptome, and cell lineages.

Yung-Hsin Huang, Julia A Belk, Ruochi Zhang, Natasha E Weiser, Zachary Chiang, Matthew G Jones, Paul S Mischel, Jason D Buenrostro, Howard Y Chang.

  Spatial epigenomics and multiomics can provide fine-grained insights into cellular states but their widespread adoption is limited by the requirement for bespoke slides and capture chemistries for each data modality. Here, we present SPatial assay for Accessible chromatin, Cell lineages, and gene Expression with sequencing (SPACE-seq), a method that utilizes polyadenine-tailed epigenomic libraries to enable facile spatial multiomics using standard whole transcriptome reagents. Applying SPACE-seq to a human glioblastoma specimen, we reveal the state of the tumor microenvironment, extrachromosomal DNA copy numbers, and identify putative mitochondrial DNA variants.

Keywords:  cell lineages; chromatin accessibility; spatial genomics; spatial multiomics

DOI:  https://doi.org/10.1073/pnas.2424070122
bioRxiv. 2025 Apr 02. pii: 2025.03.28.645986. [Epub ahead of print]

Cell and nuclear size are associated with chromosomal instability and tumorigenicity in cancer cells that undergo whole genome doubling.

Mathew Bloomfield, Sydney Huth, Daniella McCausland, Ron Saad, Nazia Bano, Tran N Chau, Megan Sweet, Nicolaas C Baudoin, Andrew McCaffrey, Kai Fluet, Eva M Schmelz, Uri Ben-David, Daniela Cimini.

Whole genome doubling (WGD) is a frequent event in cancer evolution associated with chromosomal instability, metastasis, and poor prognosis. While the genomic consequences of WGD are well documented, the effects of non-genetic alterations that accompany WGD, such as changes to cell and nuclear size, on tetraploid (4N) cancer cell physiology are less understood. Here, we show that cell and nuclear volume do not always scale with DNA content after WGD in cancer cells, resulting in 4N cells that differ in size. We find that small size is associated with enhanced cell fitness, mitotic fidelity, and tumorigenicity in 4N cancer cells and with poor patient survival in WGD-positive human cancers. Overall, these results suggest that cell and nuclear size contribute to the tumorigenic potential of 4N cancer cells and could be an important prognostic marker in human tumors that undergo WGD.

DOI: https://doi.org/10.1101/2025.03.28.645986
Cell Metab. 2025 Apr 08. pii: S1550-4131(25)00149-4. [Epub ahead of print]

Cytosolic cytochrome c represses ferroptosis.

Xinxin Song, Zhuan Zhou, Jiao Liu, Jingbo Li, Chunhua Yu, Herbert J Zeh, Daniel J Klionsky, Brent R Stockwell, Jiayi Wang, Rui Kang, Guido Kroemer, Daolin Tang.

  The release of cytochrome c, somatic (CYCS) from mitochondria to the cytosol is an established trigger of caspase-dependent apoptosis. Here, we unveil an unexpected role for cytosolic CYCS in inhibiting ferroptosis-a form of oxidative cell death driven by uncontrolled lipid peroxidation. Mass spectrometry and site-directed mutagenesis revealed the existence of a cytosolic complex composed of inositol polyphosphate-4-phosphatase type I A (INPP4A) and CYCS. This CYCS-INPP4A complex is distinct from the CYCS-apoptotic peptidase activating factor 1 (APAF1)-caspase-9 apoptosome formed during mitochondrial apoptosis. CYCS boosts INPP4A activity, leading to increased formation of phosphatidylinositol-3-phosphate, which prevents phospholipid peroxidation and plasma membrane rupture, thus averting ferroptotic cell death. Unbiased screening led to the identification of the small-molecule compound 10A3, which disrupts the CYCS-INPP4A interaction. 10A3 sensitized cultured cells and tumors implanted in immunocompetent mice to ferroptosis. Collectively, these findings redefine our understanding of cytosolic CYCS complexes that govern diverse cell death pathways.

Keywords:  apoptosis; cytochrome c; ferroptosis; protein complex

DOI:  https://doi.org/10.1016/j.cmet.2025.03.014
Nat Rev Genet. 2025 Apr 16.

Emerging roles of transcriptional condensates as temporal signal integrators.

Kirstin Meyer, Bo Huang, Orion D Weiner.

Transcription factors relay information from the external environment to gene regulatory networks that control cell physiology. To confer signalling specificity, robustness and coordination, these signalling networks use temporal communication codes, such as the amplitude, duration or frequency of signals. Although much is known about how temporal information is encoded, a mechanistic understanding of how gene regulatory networks decode signalling dynamics is lacking. Recent advances in our understanding of phase separation of transcriptional condensates provide new biophysical frameworks for both temporal encoding and decoding mechanisms. In this Perspective, we summarize the mechanisms by which transcriptional condensates could enable temporal decoding through signal adaptation, memory and persistence. We further outline methods to probe and manipulate dynamic communication codes of transcription factors and condensates to rationally control gene activation.

DOI: https://doi.org/10.1038/s41576-025-00837-y
Mol Cell. 2025 Apr 10. pii: S1097-2765(25)00265-5. [Epub ahead of print]

Tripartite phosphorylation of SPT5 by CDK9 times pause release and tunes elongation rate of RNA polymerase II.

Rui Sun, Robert P Fisher.

  The RNA polymerase II (RNAPII) transcription cycle is regulated throughout its duration by protein phosphorylation. Previously, two regions phosphorylated by cyclin-dependent kinase 9 (CDK9) in elongation factor SPT5-the linker between Kyrpides-Ouzounis-Woese (KOW) x-4 and 5 domains and carboxy-terminal repeat (CTR) 1-were implicated in promoter-proximal pausing and termination, respectively. Here, we show that phosphorylations in the linker, CTR1, and a third region, CTR2, coordinately control pause release, elongation speed, and termination in HCT116 human colon cancer cells. Pausing was unaffected or increased by mutations preventing CTR1 or CTR2 phosphorylation, respectively, but attenuated when both CTRs were mutated. Whereas loss of CTR1 phosphorylation slowed elongation and repressed nascent transcription, simultaneous CTR2 mutation partially reversed both effects. Nevertheless, mutating both CTRs had additive effects on splicing, termination, steady-state mRNA levels, and cell proliferation. Therefore, tripartite SPT5 phosphorylation times pause release and tunes RNAPII elongation rate to ensure productive transcription and cell viability.

Keywords:  CDK9; DRB sensitivity-inducing factor; DSIF; P-TEFb; RNA polymerase II; RNAPII; SPT5; chemical genetics; cyclin-dependent kinase 9; phosphorylation; positive transcription elongation factor b; pre-mRNA splicing; promoter-proximal pausing; transcription; transcription elongation; transcription termination

DOI:  https://doi.org/10.1016/j.molcel.2025.03.021
Nat Commun. 2025 Apr 18. 16(1): 3700

Cell lineage-resolved embryonic morphological map reveals signaling associated with cell fate and size asymmetry.

Guoye Guan, Zelin Li, Yiming Ma, Pohao Ye, Jianfeng Cao, Ming-Kin Wong, Vincy Wing Sze Ho, Lu-Yan Chan, Hong Yan, Chao Tang, Zhongying Zhao.

How cells change shape is crucial for the development of tissues, organs and embryos. However, studying these shape changes in detail is challenging. Here we present a comprehensive real-time cellular map that covers over 95% of the cells formed during Caenorhabditis elegans embryogenesis, featuring nearly 400,000 3D cell regions. This map includes information on each cell's identity, lineage, fate, shape, volume, surface area, contact area, and gene expression profiles, all accessible through our user-friendly software and website. Our map allows for detailed analysis of key developmental processes, including dorsal intercalation, intestinal formation, and muscle assembly. We show how Notch and Wnt signaling pathways, along with mechanical forces from cell interactions, regulate cell fate decisions and size asymmetries. Our findings suggest that repeated Notch signaling drives size disparities in the large excretory cell, which functions like a kidney. This work sets the stage for in-depth studies of the mechanisms controlling cell fate differentiation and morphogenesis.

DOI: https://doi.org/10.1038/s41467-025-58878-0
Nat Commun. 2025 Apr 17. 16(1): 3641

Coupling of ribosome biogenesis and translation initiation in human mitochondria.

Marleen Heinrichs, Anna Franziska Finke, Shintaro Aibara, Angelique Krempler, Angela Boshnakovska, Peter Rehling, Hauke S Hillen, Ricarda Richter-Dennerlein.

Biogenesis of mitoribosomes requires dedicated chaperones, RNA-modifying enzymes, and GTPases, and defects in mitoribosome assembly lead to severe mitochondriopathies in humans. Here, we characterize late-step assembly states of the small mitoribosomal subunit (mtSSU) by combining genetic perturbation and mutagenesis analysis with biochemical and structural approaches. Isolation of native mtSSU biogenesis intermediates via a FLAG-tagged variant of the GTPase MTG3 reveals three distinct assembly states, which show how factors cooperate to mature the 12S rRNA. In addition, we observe four distinct primed initiation mtSSU states with an incompletely matured rRNA, suggesting that biogenesis and translation initiation are not mutually exclusive processes but can occur simultaneously. Together, these results provide insights into mtSSU biogenesis and suggest a functional coupling between ribosome biogenesis and translation initiation in human mitochondria.

DOI: https://doi.org/10.1038/s41467-025-58827-x
Nature. 2025 Apr 16.

Multi-zonal liver organoids from human pluripotent stem cells.

Hasan Al Reza, Connie Santangelo, Kentaro Iwasawa, Abid Al Reza, Sachiko Sekiya, Kathryn Glaser, Alexander Bondoc, Jonathan Merola, Takanori Takebe.

Distinct hepatocyte subpopulations are spatially segregated along the portal-central axis and are critical to understanding metabolic homeostasis and injury in the liver1. Although several bioactive molecules, including ascorbate and bilirubin, have been described as having a role in directing zonal fates, zonal liver architecture has not yet been replicated in vitro2,3. Here, to evaluate hepatic zonal polarity, we developed a self-assembling zone-specific liver organoid by co-culturing ascorbate- and bilirubin-enriched hepatic progenitors derived from human induced pluripotent stem cells. We found that preconditioned hepatocyte-like cells exhibited zone-specific functions associated with the urea cycle, glutathione synthesis and glutamate synthesis. Single-nucleus RNA-sequencing analysis of these zonally patterned organoids identifies a hepatoblast differentiation trajectory that dictates periportal, interzonal and pericentral human hepatocytes. Epigenetic and transcriptomic analysis showed that zonal identity is orchestrated by ascorbate- or bilirubin-dependent binding of EP300 to TET1 or HIF1α. Transplantation of the self-assembled zonally patterned human organoids improved survival of immunodeficient rats who underwent bile duct ligation by ameliorating the hyperammonaemia and hyperbilirubinaemia. Overall, this multi-zonal organoid system serves as an in vitro human model to better recapitulate hepatic architecture relevant to liver development and disease.

DOI: https://doi.org/10.1038/s41586-025-08850-1
Sci Adv. 2025 Apr 18. 11(16): eadu0437

Mechanism of DNA replication fork breakage and PARP1 hyperactivation during replication catastrophe.

Pedro Ortega, Elodie Bournique, Junyi Li, Ambrocio Sanchez, Gisselle Santiago, Brooke R Harris, Josefine Striepen, John Maciejowski, Abby M Green, Rémi Buisson.

Ataxia telangiectasia and Rad3-related (ATR) inhibition triggers a surge in origin firing, resulting in increased levels of single-stranded DNA (ssDNA) that rapidly deplete all available RPA. This leaves ssDNA unprotected and susceptible to breakage, a phenomenon known as replication catastrophe. However, the mechanism by which unprotected ssDNA breaks remains unclear. Here, we reveal that APOBEC3B is the key enzyme targeting unprotected ssDNA at replication forks, initiating a reaction cascade that induces fork collapse and poly(ADP-ribose) polymerase 1 (PARP1) hyperactivation. Mechanistically, we demonstrate that uracils generated by APOBEC3B at replication forks are removed by UNG2, resulting in abasic sites that are subsequently cleaved by APE1 endonuclease. Moreover, we show that APE1-mediated DNA cleavage is the critical enzymatic step for PARP1 hyperactivation in cells, regardless of how abasic sites are generated on DNA. Last, we demonstrate that APOBEC3B-induced PARP1 trapping and DNA double-strand breaks drive cell sensitivity to ATR inhibition, creating a context of synthetic lethality when coupled with PARP inhibitors.

DOI: https://doi.org/10.1126/sciadv.adu0437
Nat Genet. 2025 Apr 14.

Genome-wide analyses identify 25 infertility loci and relationships with reproductive traits across the allele frequency spectrum.

Genes & Health Research Team

Genome-wide association studies (GWASs) may help inform the etiology of infertility. Here, we perform GWAS meta-analyses across seven cohorts in up to 42,629 cases and 740,619 controls and identify 25 genetic risk loci for male and female infertility. We additionally identify up to 269 genetic loci associated with follicle-stimulating hormone, luteinizing hormone, estradiol and testosterone through sex-specific GWAS meta-analyses (n = 6,095-246,862). Exome sequencing analyses reveal that women carrying testosterone-lowering rare variants in some genes are at risk of infertility. However, we find no local or genome-wide genetic correlation between female infertility and reproductive hormones. While infertility is genetically correlated with endometriosis and polycystic ovary syndrome, we find limited genetic overlap between infertility and obesity. Finally, we show that the evolutionary persistence of infertility-risk alleles may be explained by directional selection. Taken together, we provide a comprehensive view of the genetic determinants of infertility across multiple diagnostic criteria.

DOI: https://doi.org/10.1038/s41588-025-02156-8
Development. 2025 Apr 15. pii: dev.204687. [Epub ahead of print]

Specific mitotic events drive left-right organizer development.

Yan Wu, Yiling Lan, Favour Ononiwu, Abigail Poole, Kirsten Rasmussen, Jonah Da Silva, Abdalla Wael Shamil, Li-En Jao, Heidi Hehnly.

  Cell proliferation is crucial for tissue development. Here, we investigate its role in the Left-Right Organizer (LRO), which establishes the left-right (LR) axis. In zebrafish, we mapped mitotic events in Kupffer's Vesicle (KV) and identified an anteriorly enriched, FGF-dependent mitotic pattern. Laser ablation of mitotic cells and pericentrin-null mutants, both reducing mitotic events, resulted in smaller lumens, confirming that cell division is essential for KV development. Pericentrin-null mutants also exhibited defects in leftward cardiac jogging, indicative of KV dysfunction. Using a KV-specific fluorescent microtubule marker, we found that the KV rosette is a transient, centrally organized cluster interconnected by cytokinetic bridges and containing microtubule bundles. This structure emerges after the first four divisions and precedes lumen formation. Mitotic events during KV rounding coincide with rosette formation, spindle rotation, and cell extrusion, likely driven by increased packing. Eliminating the first four mitotic events disrupted rosette formation and prevented normal KV rounding. These findings demonstrate that mitotic events are critical for KV development, with cell division timing shaping KV architecture and function.

Keywords:  Cell Patterning; Cilia; Cytokinesis; Left-Right Organizer; Lumen Formation; Microtubules; Mitosis; Rosette

DOI:  https://doi.org/10.1242/dev.204687
Dev Biol. 2025 Apr 12. pii: S0012-1606(25)00105-8. [Epub ahead of print]

Exploring early extraembryonic cells of epiblast origin: Questions on human amniotic ectoderm and extraembryonic mesoderm.

Shota Nakanoh.

Extraembryonic tissues are essential for proper fetal development and exhibit great diversity across species. Despite its importance, human extraembryonic development has been relatively overlooked. Previously, we established an in vitro model to study human amniogenesis and extraembryonic mesoderm formation. In this article, I develop discussions on four topics inspired by this study: (1) Features of amniotic cell populations described to date. A recently reported early amniotic cell type is examined based on its signature genes to consider how this population should be incorporated into models of primate amniogenesis. (2) Molecular mechanisms underlying the effect of cell density in regulating non-neural ectoderm specification. Fate specification by positional cues in mouse is revisited and possible mechanisms are suggested by drawing insights from human epiblast models. (3) Potential applications of the three-dimensional culture we established. Primate amniotic ectoderm is postulated as a gastrulation-inducing signaling center, and our technique could be used to effectively model its interactions with epiblast. (4) Extraembryonic mesoderm development in human embryos. The obscure origin of primate extraembryonic mesoderm and implications from recent in vitro differentiation models using human pluripotent stem cells are explained. The key concepts explored here will stimulate further studies into both amnion and extraembryonic mesoderm during human and non-human primate development.

DOI: https://doi.org/10.1016/j.ydbio.2025.04.010
Sci Adv. 2025 Apr 18. 11(16): eads6830

Spatial analysis of mitochondrial gene expression reveals dynamic translation hubs and remodeling in stress.

Adam Begeman, John A Smolka, Ahmad Shami, Tejashree Pradip Waingankar, Samantha C Lewis.

Protein- and RNA-rich bodies contribute to the spatial organization of gene expression in the cell and are also sites of quality control critical to cell fitness. In most eukaryotes, mitochondria harbor their own genome, and all steps of mitochondrial gene expression co-occur within a single compartment-the matrix. Here, we report that processed mitochondrial RNAs are consolidated into micrometer-scale translation hubs distal to mitochondrial DNA transcription and RNA processing sites in human cells. We find that, during stress, mitochondrial messenger and ribosomal RNA are sequestered in mesoscale bodies containing mitoribosome components, concurrent with suppression of active translation. Stress bodies are triggered by proteotoxic stress downstream of double-stranded RNA accumulation in cells lacking unwinding activity of the highly conserved helicase SUPV3L1/SUV3. We propose that the spatial organization of nascent polypeptide synthesis into discrete domains serves to throttle the flow of genetic information to support recovery of mitochondrial quality control.

DOI: https://doi.org/10.1126/sciadv.ads6830
Curr Opin Cell Biol. 2025 Apr 14. pii: S0955-0674(25)00049-3. [Epub ahead of print]94 102511

Interplay of damage and repair in the control of epithelial tissue integrity in response to cyclic loading.

Eleni Papafilippou, Lucia Baldauf, Guillaume Charras, Alexandre J Kabla, Alessandra Bonfanti.

Epithelial tissues are continuously exposed to cyclic stretch in vivo. Physiological stretching has been found to regulate soft tissue function at the molecular, cellular, and tissue scales, allowing tissues to preserve their homeostasis and adapt to challenges. In contrast, dysregulated or pathological stretching can induce damage and tissue fragilisation. Many mechanisms have been described for the repair of epithelial tissues across a range of timescales. In this review, we present the timescales of (i) physiological cyclic loading regimes, (ii) strain-regulated remodeling and damage accumulation, and (iii) repair mechanisms in epithelial tissues. We discuss how the response to cyclic loading in biological tissues differs from synthetic materials, in that damage can be partially or fully reversed by repair mechanisms acting on timescales shorter than cyclic loading. We highlight that timescales are critical to understanding the interplay between damage and repair in tissues that experience cyclic loading, opening up new avenues for exploring soft tissue homeostasis.

DOI: https://doi.org/10.1016/j.ceb.2025.102511
Nat Protoc. 2025 Apr 16.

A tripartite cell-free translation system to study mammalian translation.

Frederic S W Arendrup, Kasper L Andersen, Anders H Lund.

Genetic manipulation of cellular systems often leads to the adaptation of gene expression programs, rendering detailed mechanistic insights challenging to isolate and elucidate. The proteome constitutes the ultimate manifestation of gene expression programs with multiple layers of regulation to ensure faithful execution. While current high-throughput techniques to investigate regulation at the level of translation, such as Ribo-Seq and nascent proteomics, can capture nuanced changes in the translational landscape, they suffer from potential confounding factors imposed by adaptation of the cellular states. Cell-free translation systems have been used to elucidate molecular mechanisms for decades, but experimental setups have rigid composition and often rely on non-human model systems and artificially designed mRNA constructs. Here we detail a tripartite cell-free translation system based on the separation of mRNAs, ribosomes and ribosome-depleted cytoplasmic lysate from human cells, allowing for flexible reconstitution of translation reactions, which can be performed in 1-4 days. In this setup, cellular parts such as the cytoplasmic lysate can be kept constant, while ribosome complexes or mRNA can be varied or subjected to treatments or vice versa. We detail how complete mRNA populations can be used as input with subsequent detection of nascent peptides using autoradiography or mass spectrometry. We utilize this protocol to resolve which aspects of the translational machinery are selectively affected by environmental and cellular stress conditions that trigger ribosome stalling and collisions, which have been unresolvable until now.

DOI: https://doi.org/10.1038/s41596-025-01155-7
Cell. 2025 Apr 14. pii: S0092-8674(25)00352-6. [Epub ahead of print]

Rewriting regulatory DNA to dissect and reprogram gene expression.

Gabriella E Martyn, Michael T Montgomery, Hank Jones, Katherine Guo, Benjamin R Doughty, Johannes Linder, Deepa Bisht, Fan Xia, Xiangmeng S Cai, Ziwei Chen, Kelly Cochran, Kathryn A Lawrence, Glen Munson, Anusri Pampari, Charles P Fulco, Nidhi Sahni, David R Kelley, Eric S Lander, Anshul Kundaje, Jesse M Engreitz.

  Regulatory DNA provides a platform for transcription factor binding to encode cell-type-specific patterns of gene expression. However, the effects and programmability of regulatory DNA sequences remain difficult to map or predict. Here, we develop variant effects from flow-sorting experiments with CRISPR targeting screens (Variant-EFFECTS) to introduce hundreds of designed edits to endogenous regulatory DNA and quantify their effects on gene expression. We systematically dissect and reprogram 3 regulatory elements for 2 genes in 2 cell types. These data reveal endogenous binding sites with effects specific to genomic context, transcription factor motifs with cell-type-specific activities, and limitations of computational models for predicting the effect sizes of variants. We identify small edits that can tune gene expression over a large dynamic range, suggesting new possibilities for prime-editing-based therapeutics targeting regulatory DNA. Variant-EFFECTS provides a generalizable tool to dissect regulatory DNA and to identify genome editing reagents that tune gene expression in an endogenous context.

Keywords:  CRISPR; RNA FlowFISH; enhancers; gene regulation; high-throughput screening; non-coding variants; predictive models; prime editing; sequence design; transcription factors

DOI:  https://doi.org/10.1016/j.cell.2025.03.034
Nature. 2025 Apr 16.

Generation of human adult hepatocyte organoids with metabolic functions.

Ryo Igarashi, Mayumi Oda, Ryo Okada, Tomoki Yano, Sirirat Takahashi, Strahil Pastuhov, Mami Matano, Norio Masuda, Kazuhiro Togasaki, Yuki Ohta, Saeko Sato, Takako Hishiki, Makoto Suematsu, Manabu Itoh, Masayuki Fujii, Toshiro Sato.

Proliferating hepatocytes often undergo ductal metaplasia to balance the energy trade-off between cellular functions and replication, hindering the expansion of human adult hepatocytes with functional competency1. Here we demonstrate that the combined activation of Wnt and STAT3 signalling enables long-term self-renewal of human adult hepatocyte organoids. YAP activation facilitates hepatocyte proliferation but commits it towards the biliary duct lineage. By contrast, STAT3 activation by oncostatin M induces hepatocyte proliferation while counteracting ductal metaplasia and maintaining the hepatic identity. Xenotransplanted hepatocyte organoids repopulate the recipient mouse liver and reconstitute the metabolic zonation structure. Upon niche factor removal and hormone supplementation, hepatocyte organoids form cord-like structures with bile canalicular networks and exhibit major liver metabolic functions comparable to those of in vivo hepatocytes. Hepatocyte organoids are amenable to gene editing, prompting functional modelling of inherent metabolic liver diseases. The new culture system offers a promising avenue for developing therapeutic strategies against human liver diseases.

DOI: https://doi.org/10.1038/s41586-025-08861-y
Nat Commun. 2025 Apr 17. 16(1): 3658

Granulosa cell transcription is similarly impacted by superovulation and aging and predicts early embryonic trajectories.

Klaudija Daugelaite, Perrine Lacour, Ivana Winkler, Marie-Luise Koch, Anja Schneider, Nina Schneider, Francesca Coraggio, Alexander Tolkachov, Xuan Phuoc Nguyen, Adriana Vilkaite, Julia Rehnitz, Duncan T Odom, Angela Goncalves.

In vitro fertilization efficiency is limited in part because a fraction of retrieved oocytes fails to fertilize. Accurately evaluating their quality could significantly improve in vitro fertilization efficiency, which would require better understanding how their maturation may be disrupted. Here, we quantitatively investigate the interplay between superovulation and aging in mouse oocytes and their paired granulosa cells using a newly adapted experimental methodology. We test the hypothesis that superovulation disrupts oocyte maturation, revealing the key intercellular communication pathways dysregulated at the transcriptional level by forced hormonal stimulation. We further demonstrate that granulosa cell transcriptional markers can prospectively predict an associated oocyte's early developmental potential. By using naturally ovulated old mice as a non-stimulated reference, we show that aging and superovulation dysregulate similar genes and interact with each other. By comparing mice and human transcriptional responses of granulosa cells, we find that age-related dysregulation of hormonal responses and cell cycle pathways are shared, though substantial divergence exists in other pathways.

DOI: https://doi.org/10.1038/s41467-025-58451-9
Cell Rep. 2025 Apr 11. pii: S2211-1247(25)00305-5. [Epub ahead of print]44(4): 115534

Evidence of substrate control of Cdk phosphorylation during the budding yeast cell cycle.

Luca Takacs, Lina Gerontogianni, Kimberly Quililan, Helen Flynn, Frank Uhlmann.

  A series of sequential events orchestrates cell growth and division, set in motion by cyclin-dependent kinases (Cdks). In the "qualitative model" for Cdk control, order is achieved by cell cycle stage-specific cyclins. However, single-cyclin cells retain cell cycle order. In an alternative "quantitative model," increasing Cdk activity triggers substrate phosphorylation at sequential thresholds. Here, we test a key prediction from the quantitative model: the best Cdk substrates should be the first to be phosphorylated. Phosphoproteome analysis of synchronous budding yeast cultures, against expectations, reveals little correlation between known in vitro Cdk phosphorylation rates and observed in vivo phosphorylation timing. Incorporating Cdk-counteracting phosphatases that impose phosphorylation thresholds does not improve the correlation. Instead of kinase-phosphatase control (i.e., "regulator control"), our phosphoproteome patterns reveal signatures of "substrate control," including substrate-defined phosphorylation waves. The changing behavior of the substrates themselves therefore contributes to ordering their Cdk phosphorylation during the budding yeast cell cycle.

Keywords:  CP: Cell biology; CP: Molecular biology; S. cerevisiae; cell cycle; cyclin-dependent kinase, Cdk; phosphatases; phosphoproteomics; qualitative Cdk control; quantitative Cdk control; substrate control

DOI:  https://doi.org/10.1016/j.celrep.2025.115534
Proc Natl Acad Sci U S A. 2025 Apr 22. 122(16): e2422720122

ATM priming and end resection-coupled phosphorylation of MRE11 is important for fork protection and replication restart.

Huimin Zhang, Youhang Li, Sameer Bikram Shah, Shibo Li, Qingrong Li, Joshua Oaks, Tinghong Lv, Linda Z Shi, Hailong Wang, Dong Wang, Xiaohua Wu.

  The MRE11/RAD50/NBS1 (MRN) complex plays multiple roles in the maintenance of genome stability. MRN is associated with replication forks to preserve fork integrity and is also required for end resection at double-strand breaks (DSBs) to facilitate homologous recombination (HR). The critical need for proper control of the MRE11 nuclease activity is highlighted by the extensive nascent strand DNA degradation driven by MRE11 in BRCA-deficient cells, leading to genome instability and increased sensitivity to chemotherapeutics. In this study, we identified a tightly controlled mechanism, elicited by sequential phosphorylation of MRE11 by ATM and ATR to regulate MRE11 nuclease activities through its DNA binding. Specifically, at DSBs, MRE11 phosphorylation by ATM at the C-terminal S676/S678 primes it for subsequent phosphorylation by ATR, whose activation is triggered by end resection which requires the MRE11 nuclease activity. This ATR-mediated phosphorylation in turn induces MRE11 dissociation from DNA, providing a feedback mechanism to regulate the extent of end resection. At stalled replication forks, however, without ATM priming, MRN is stably associated with forks despite ATR activation. Furthermore, the ATR phosphorylation-defective MRE11 mutants are retained at single-ended DSBs formed by fork reversal upon replication stress, leading to extensive degradation of nascent DNA strands. Importantly, this end resection-coupled MRE11 phosphorylation elicits another critical layer of fork protection of nascent DNA in addition to BRCA2, ensuring proper end resection that is sufficient for replication restart at reversed forks while maintaining fork stability.

Keywords:  ATM; ATR; MRE11; end resection; fork protection

DOI:  https://doi.org/10.1073/pnas.2422720122
Cell. 2025 Apr 08. pii: S0092-8674(25)00292-2. [Epub ahead of print]

ALDH7A1 protects against ferroptosis by generating membrane NADH and regulating FSP1.

Jia-Shu Yang, Andrew J Morris, Koki Kamizaki, Jianzhong Chen, Jillian Stark, William M Oldham, Toshitaka Nakamura, Eikan Mishima, Joseph Loscalzo, Yasuhiro Minami, Marcus Conrad, Whitney S Henry, Victor W Hsu.

  Ferroptosis is a form of cell death due to iron-induced lipid peroxidation. Ferroptosis suppressor protein 1 (FSP1) protects against this death by generating antioxidants, which requires nicotinamide adenine dinucleotide, reduced form (NADH) as a cofactor. We initially uncover that NADH exists at significant levels on cellular membranes and then find that this form of NADH is generated by aldehyde dehydrogenase 7A1 (ALDH7A1) to support FSP1 activity. ALDH7A1 activity also acts directly to decrease lipid peroxidation by consuming reactive aldehydes. Furthermore, ALDH7A1 promotes the membrane recruitment of FSP1, which is instigated by ferroptotic stress activating AMP-activated protein kinase (AMPK) to promote the membrane localization of ALDH7A1 that stabilizes FSP1 on membranes. These findings advance a fundamental understanding of NADH by revealing a previously unappreciated pool on cellular membranes, with the elucidation of its function providing a major understanding of how FSP1 acts and how an aldehyde dehydrogenase protects against ferroptosis.

Keywords:  aldehyde dehydrogenase 7A1; ferroptosis; ferroptosis suppressor protein 1; nicotinamide adenine dinucleotide reduced form

DOI:  https://doi.org/10.1016/j.cell.2025.03.019
bioRxiv. 2025 Apr 01. pii: 2025.03.31.645534. [Epub ahead of print]

SIRT7 links H3K36ac epigenetic regulation with genome maintenance in the aging mouse testis.

Anna Guitart-Solanes, Mayra Romero, Irene Fernandez-Duran, Bryan A Niedenberger, Cristina Madrid-Sandín, Ignasi Roig, Christopher B Geyer, Alejandro Vaquero, Karen Schindler, Berta N Vazquez.

Reproductive aging is an increasing health concern affecting family planning and overall well-being. While extensively studied in females, the mechanisms driving male reproductive aging remain largely unexamined. Here we found that mammalian Sirtuin 7 (SIRT7) sustains spermatogenesis in an age-dependent manner through the control of histone 3 lysine 36 acetylation (H3K36ac). SIRT7 deficiency in mice resulted in increased levels of H3K36ac in spermatogonia and spermatocytes. In a germ cell line, SIRT7 deficiency disrupted nucleosome stability and increased vulnerability to genotoxic stress. Importantly, undifferentiated spermatogonia, which are required for continuous sperm production, decreased prematurely in Sirt7 -/- mice and showed genome damage accumulation. These changes were concurrent with age-dependent defects in homologous chromosome synapsis and partial meiotic arrest. Taken together, our results indicate that SIRT7 connects H3K36ac epigenetic regulation to long-term genome stability in male germ cells, ensuring steady-state spermatogenesis during the lengthy male reproductive lifespan.

DOI: https://doi.org/10.1101/2025.03.31.645534
EMBO J. 2025 Apr 14.

Glutamylation of centrosomes ensures their function by recruiting microtubule nucleation factors.

Shi-Rong Hong, Yi-Chien Chuang, Wen-Ting Yang, Chiou-Shian Song, Hung-Wei Yeh, Bing-Huan Wu, I-Hsuan Lin, Po-Chun Chou, Shiau-Chi Chen, Lohitaksh Sharma, Jui-Chen Lu, Rou-Ying Li, Ya-Chu Chang, Kuan-Ju Liao, Hui-Chun Cheng, Won-Jing Wang, Lily Hui-Ching Wang, Yu-Chun Lin.

  Centrosomes are tubulin-based organelles that undergo glutamylation, a post-translational modification that conjugates glutamic acid residues to tubulins. Although centrosomal glutamylation has been known for several decades, how this modification regulates centrosome structure and function remains unclear. To address this long-standing issue, we developed a method to spatiotemporally reduce centrosomal glutamylation by recruiting an engineered deglutamylase to centrosomes. We found that centrosome structure remains largely unaffected by centrosomal hypoglutamylation. Intriguingly, glutamylation physically recruits, via electrostatic forces, the NEDD1/CEP192/γ-tubulin complex to centrosomes, ensuring microtubule nucleation and proper trafficking of centriolar satellites. The consequent defect in centriolar satellite trafficking leads to reduced levels of the ciliogenesis factor Talpid3, suppressing ciliogenesis. Centrosome glutamylation also promotes proper mitotic spindle formation and mitosis. In summary, our study provides a new approach to spatiotemporally manipulate glutamylation at centrosomes, and offers novel insights into how centrosomes are organized and regulated by glutamylation.

Keywords:  Centriolar satellites; Centrosomes; Glutamylation; Microtubules; Primary Cilia

DOI:  https://doi.org/10.1038/s44318-025-00435-y