bims-ginsta 2025-02-16 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2025–02–16
37 papers selected by
Jinrong Hu, National University of Singapore

Afadin mediates cadherin-catenin complex clustering on F-actin linked to cooperative binding and filament curvature.
Unravelling single-cell DNA replication timing dynamics using machine learning reveals heterogeneity in cancer progression.
Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition.
NuMA is a mitotic adaptor protein that activates dynein and connects it to microtubule minus ends.
Intrinsic electrical activity drives small-cell lung cancer progression.
ATR-hippo drives force signaling to nuclear F-actin and links mechanotransduction to neurological disorders.
RNA polymerase II at histone genes predicts outcome in human cancer.
Topological segregation of stress sensors along the gut crypt-villus axis.
Organoid modeling reveals the tumorigenic potential of the alveolar progenitor cell state.
Mitochondrial DNA removal is essential for sperm development and activity.
The RNA helicase HrpA rescues collided ribosomes in E. coli.
Dietary Branched-Chain Amino Acids Modify Postinfarct Cardiac Remodeling and Function in the Murine Heart.
Lactate controls cancer stemness and plasticity through epigenetic regulation.
A microscopy-based screen identifies cellular kinases modulating mitochondrial translation.
RIOK3 mediates the degradation of 40S ribosomes.
Mesoderm FN1 shaping the heart.
Biomolecular condensation of human IDRs initiates endogenous transcription via intrachromosomal looping or high-density promoter localization.
Mechanical forces pattern endocardial Notch activation via mTORC2-PKC pathway.
Distinct mismatch-repair complex genes set neuronal CAG-repeat expansion rate to drive selective pathogenesis in HD mice.
The structural basis for RNA slicing by human Argonaute2.
Exploring Origin-Dependent Susceptibility of Smooth Muscle Cells to Aortic Diseases Through Intersectional Genetics.
Prickle2 regulates apical junction remodeling and tissue fluidity during vertebrate neurulation.
Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis.
Nuclear position controls the activity of cortical actomyosin networks powering simultaneous morphogenetic events.
Minimal Component, Protein-Free, and Cost-effective Human Pluripotent Stem Cell Cardiomyocyte Differentiation.
The integrated stress response regulates 18S nonfunctional rRNA decay in mammals.
Trajectory analysis of hepatic stellate cell differentiation reveals metabolic regulation of cell commitment and fibrosis.
Membrane-tethered SCOTIN condensates elicit an endoplasmic reticulum stress response by sequestering luminal BiP.
Acetylation at lysine 27 on maternal H3.3 regulates minor zygotic genome activation.
Transcriptomic neuron types vary topographically in function and morphology.
Genome-wide absolute quantification of chromatin looping.
Regulation of lung progenitor plasticity and repair by fatty acid oxidation.
Scalable co-sequencing of RNA and DNA from individual nuclei.
Exploring The Differentiation Potential of EomesPOS Mouse Trophoblast Cells in Mid-Gestation.
Visualization of chromosomal reorganization induced by heterologous fusions in the mammalian nucleus.
Initiation of ERAD by the bifunctional complex of Mnl1/Htm1 mannosidase and protein disulfide isomerase.
Identification of FSH-regulated and estrous stage-specific transcriptional networks in mouse ovaries.

Sci Adv. 2025 Feb 14. 11(7): eadu0989

Afadin mediates cadherin-catenin complex clustering on F-actin linked to cooperative binding and filament curvature.

Rui Gong, Matthew J Reynolds, Xiaoyu Sun, Gregory M Alushin.

The E-cadherin-β-catenin-αE-catenin (cadherin-catenin) complex couples the cytoskeletons of neighboring cells at adherens junctions (AJs) to mediate force transmission across epithelia. Mechanical force and auxiliary binding partners converge to stabilize the cadherin-catenin complex's inherently weak binding to actin filaments (F-actin) through unclear mechanisms. Here, we show that afadin's coiled-coil (CC) domain and vinculin synergistically enhance the cadherin-catenin complex's F-actin engagement. The cryo-electron microscopy (cryo-EM) structure of an E-cadherin-β-catenin-αE-catenin-vinculin-afadin-CC supra-complex bound to F-actin reveals that afadin-CC bridges adjacent αE-catenin actin-binding domains along the filament, stabilizing flexible αE-catenin segments implicated in mechanical regulation. These cooperative binding contacts promote the formation of supra-complex clusters along F-actin. Additionally, cryo-EM variability analysis links supra-complex binding along individual F-actin strands to nanoscale filament curvature, a deformation mode associated with cytoskeletal forces. Collectively, this work elucidates a mechanistic framework by which vinculin and afadin tune cadherin-catenin complex-cytoskeleton coupling to support AJ function across varying mechanical regimes.

DOI: https://doi.org/10.1126/sciadv.adu0989
Nat Commun. 2025 Feb 08. 16(1): 1472

Unravelling single-cell DNA replication timing dynamics using machine learning reveals heterogeneity in cancer progression.

Joseph M Josephides, Chun-Long Chen.

Genomic heterogeneity has largely been overlooked in single-cell replication timing (scRT) studies. Here, we develop MnM, an efficient machine learning-based tool that allows disentangling scRT profiles from heterogenous samples. We use single-cell copy number data to accurately perform missing value imputation, identify cell replication states, and detect genomic heterogeneity. This allows us to separate somatic copy number alterations from copy number changes resulting from DNA replication. Our methodology brings critical insights into chromosomal aberrations and highlights the ubiquitous aneuploidy process during tumorigenesis. The copy number and scRT profiles obtained by analysing >119,000 high-quality human single cells from different cell lines, patient tumours and patient-derived xenograft samples leads to a multi-sample heterogeneity-resolved scRT atlas. This atlas is an important resource for cancer research and demonstrates that scRT profiles can be used to study replication timing heterogeneity in cancer. Our findings also highlight the importance of studying cancer tissue samples to comprehensively grasp the complexities of DNA replication because cell lines, although convenient, lack dynamic environmental factors. These results facilitate future research at the interface of genomic instability and replication stress during cancer progression.

DOI: https://doi.org/10.1038/s41467-025-56783-0
Nat Struct Mol Biol. 2025 Feb 11.

Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition.

Kseniia Lysakovskaia, Arjun Devadas, Björn Schwalb, Michael Lidschreiber, Patrick Cramer.

Metazoan gene transcription by RNA polymerase II (Pol II) is regulated in the promoter-proximal region. Pol II can undergo termination in the promoter-proximal region but whether this can contribute to transcription regulation in cells remains unclear. Here we extend our previous multiomics analysis to quantify changes in transcription kinetics during a human cell type transition event. We observe that upregulation of transcription involves an increase in initiation frequency and, at a set of genes, a decrease in promoter-proximal termination. In turn, downregulation of transcription involves a decrease in initiation frequency and an increase in promoter-proximal termination. Thus, promoter-proximal termination of Pol II contributes to the regulation of human gene transcription.

DOI: https://doi.org/10.1038/s41594-025-01486-9
J Cell Biol. 2025 Apr 07. pii: e202408118. [Epub ahead of print]224(4):

NuMA is a mitotic adaptor protein that activates dynein and connects it to microtubule minus ends.

Sabina Colombo, Christel Michel, Silvia Speroni, Felix Ruhnow, Maria Gili, Cláudia Brito, Thomas Surrey.

Nuclear mitotic apparatus protein (NuMA) is indispensable for the mitotic functions of the major microtubule minus-end directed motor cytoplasmic dynein 1. NuMA and dynein are both essential for correct spindle pole organization. How these proteins cooperate to gather microtubule minus ends at spindle poles remains unclear. Here, we use microscopy-based in vitro reconstitutions to demonstrate that NuMA is a dynein adaptor, activating processive dynein motility together with dynein's cofactors dynactin and Lissencephaly-1 (Lis1). Additionally, we find that NuMA binds and stabilizes microtubule minus ends, allowing dynein/dynactin/NuMA to transport microtubule minus ends as cargo to other minus ends. We further show that the microtubule-nucleating γ-tubulin ring complex (γTuRC) hinders NuMA binding and that NuMA only caps minus ends of γTuRC-nucleated microtubules after γTuRC release. These results provide new mechanistic insight into how dynein, dynactin, NuMA, and Lis1 together with γTuRC and uncapping proteins cooperate to organize spindle poles in cells.

DOI: https://doi.org/10.1083/jcb.202408118
Nature. 2025 Feb 12.

Intrinsic electrical activity drives small-cell lung cancer progression.

Paola Peinado, Marco Stazi, Claudio Ballabio, Michael-Bogdan Margineanu, Zhaoqi Li, Caterina I Colón, Min-Shu Hsieh, Shreoshi Pal Choudhuri, Victor Stastny, Seth Hamilton, Alix Le Marois, Jodie Collingridge, Linus Conrad, Yinxing Chen, Sheng Rong Ng, Margaret Magendantz, Arjun Bhutkar, Jin-Shing Chen, Erik Sahai, Benjamin J Drapkin, Tyler Jacks, Matthew G Vander Heiden, Maksym V Kopanitsa, Hugh P C Robinson, Leanne Li.

Elevated or ectopic expression of neuronal receptors promotes tumour progression in many cancer types1,2; neuroendocrine (NE) transformation of adenocarcinomas has also been associated with increased aggressiveness3. Whether the defining neuronal feature, namely electrical excitability, exists in cancer cells and impacts cancer progression remains mostly unexplored. Small-cell lung cancer (SCLC) is an archetypal example of a highly aggressive NE cancer and comprises two major distinct subpopulations: NE cells and non-NE cells4,5. Here we show that NE cells, but not non-NE cells, are excitable, and their action potential firing directly promotes SCLC malignancy. However, the resultant high ATP demand leads to an unusual dependency on oxidative phosphorylation in NE cells. This finding contrasts with the properties of most cancer cells reported in the literature, which are non-excitable and rely heavily on aerobic glycolysis. Additionally, we found that non-NE cells metabolically support NE cells, a process akin to the astrocyte-neuron metabolite shuttle6. Finally, we observed drastic changes in the innervation landscape during SCLC progression, which coincided with increased intratumoural heterogeneity and elevated neuronal features in SCLC cells, suggesting an induction of a tumour-autonomous vicious cycle, driven by cancer cell-intrinsic electrical activity, which confers long-term tumorigenic capability and metastatic potential.

DOI: https://doi.org/10.1038/s41586-024-08575-7
Sci Adv. 2025 Feb 14. 11(7): eadr5683

ATR-hippo drives force signaling to nuclear F-actin and links mechanotransduction to neurological disorders.

Maria Chatzifrangkeskou, Tess Stanly, Delia Koennig, Luana Campos-Soares, Michael Eyres, Alexander Hasson, Alexandra Perdiou, Iolanda Vendrell, Roman Fischer, Sayoni Das, Steve Gardner, Simei Go, Ben Futcher, Ashley Newton, Paris Skourides, Francis Szele, Eric O'Neill.

The mechanical environment is sensed through cell-matrix contacts with the cytoskeleton, but how signals transit the nuclear envelope to affect cell fate decisions remains unknown. Nuclear actin coordinates chromatin motility during differentiation and genome maintenance, yet it remains unclear how nuclear actin responds to mechanical force. The DNA-damage kinase ataxia telangiectasia and Rad3-related protein (ATR) translocates to the nuclear envelope to protect the nucleus during cell motility or compression. Here, we show that ATR drives nuclear actin assembly via recruitment of Filamin-A to the inner nuclear membrane through binding of the hippo pathway scaffold and ATR substrate, RASSF1A. Moreover, we demonstrate how germline RASSF1 mutation disables nuclear mechanotransduction resulting in cerebral cortex thinning and associates with common psychological traits. Thus, defective mechanical-regulated pathways may contribute to complex neurological disorders.

DOI: https://doi.org/10.1126/sciadv.adr5683
Science. 2025 Jan 02. 387(6735): 737-743

RNA polymerase II at histone genes predicts outcome in human cancer.

Steven Henikoff, Ye Zheng, Ronald M Paranal, Yiling Xu, Jacob E Greene, Jorja G Henikoff, Zachary R Russell, Frank Szulzewsky, H Nayanga Thirimanne, Sita Kugel, Eric C Holland, Kami Ahmad.

Genome-wide hypertranscription is common in human cancer and predicts poor prognosis. To understand how hypertranscription might drive cancer, we applied our formalin-fixed paraffin-embedded (FFPE)-cleavage under targeted accessible chromatin method for mapping RNA polymerase II (RNAPII) genome-wide in FFPE sections. We demonstrate global RNAPII elevations in mouse gliomas and assorted human tumors in small clinical samples and discover regional elevations corresponding to de novo HER2 amplifications punctuated by likely selective sweeps. RNAPII occupancy at S-phase-dependent histone genes correlated with WHO grade in meningiomas, accurately predicted rapid recurrence, and corresponded to whole-arm chromosome losses. Elevated RNAPII at histone genes in meningiomas and diverse breast cancers is consistent with histone production being rate-limiting for S-phase progression and histone gene hypertranscription driving overproliferation and aneuploidy in cancer, with general implications for precision oncology.

DOI: https://doi.org/10.1126/science.ads2169
Nature. 2025 Feb 12.

Topological segregation of stress sensors along the gut crypt-villus axis.

Kouki K Touhara, Nathan D Rossen, Fei Deng, Joel Castro, Andrea M Harrington, Tifany Chu, Sonia Garcia-Caraballo, Mariana Brizuela, Tracey O'Donnell, Jinhao Xu, Onur Cil, Stuart M Brierley, Yulong Li, David Julius.

The crypt-villus structure of the small intestine serves as an essential protective barrier. The integrity of this barrier is monitored by the complex sensory system of the gut, in which serotonergic enterochromaffin (EC) cells play an important part1,2. These rare sensory epithelial cells surveil the mucosal environment for luminal stimuli and transmit signals both within and outside the gut3-6. However, whether EC cells in crypts and villi detect different stimuli or produce distinct physiological responses is unknown. Here we address these questions by developing a reporter mouse model to quantitatively measure the release and propagation of serotonin from EC cells in live intestines. Crypt EC cells exhibit a tonic low-level mode that activates epithelial serotonin 5-HT4 receptors to modulate basal ion secretion and a stimulus-induced high-level mode that activates 5-HT3 receptors on sensory nerve fibres. Both these modes can be initiated by the irritant receptor TRPA1, which is confined to crypt EC cells. The activation of TRPA1 by luminal irritants is enhanced when the protective mucus layer is compromised. Villus EC cells also signal damage through a distinct mechanism, whereby oxidative stress activates TRPM2 channels, which leads to the release of both serotonin and ATP and consequent excitation of sensory nerve fibres. This topological segregation of EC cell functionality along the mucosal architecture constitutes a mechanism for the surveillance, maintenance and protection of gut integrity under diverse physiological conditions.

DOI: https://doi.org/10.1038/s41586-024-08581-9
EMBO J. 2025 Feb 10.

Organoid modeling reveals the tumorigenic potential of the alveolar progenitor cell state.

Jingyun Li, Susanna M Dang, Shreoshi Sengupta, Paul Schurmann, Antonella F M Dost, Aaron L Moye, Maria F Trovero, Sidrah Ahmed, Margherita Paschini, Preetida J Bhetariya, Roderick Bronson, Shannan J Ho Sui, Carla F Kim.

  Cancers display cellular, genetic and epigenetic heterogeneity, complicating disease modeling. Multiple cell states defined by gene expression have been described in lung adenocarcinoma (LUAD). However, the functional contributions of cell state and the regulatory programs that control chromatin and gene expression in the early stages of tumor initiation are not well understood. Using single-cell RNA and ATAC sequencing in Kras/p53-driven tumor organoids, we identified two major cellular states: one more closely resembling alveolar type 2 (AT2) cells (SPC-high), and the other with epithelial-mesenchymal-transition (EMT)-associated gene expression (Hmga2-high). Each state exhibited distinct transcription factor networks, with SPC-high cells associated with TFs regulating AT2 fate and Hmga2-high cells enriched in Wnt- and NFκB-related TFs. CD44 was identified as a marker for the Hmga2-high state, enabling functional comparison of the two populations. Organoid assays and orthotopic transplantation revealed that SPC-high, CD44-negative cells exhibited higher tumorigenic potential within the lung microenvironment. These findings highlight the utility of organoids in understanding chromatin regulation in early tumorigenesis and identifying novel early-stage therapeutic targets in Kras-driven LUAD.

Keywords:  Alveolar; Cell State; Kras; Lung Cancer; Organoids

DOI:  https://doi.org/10.1038/s44318-025-00376-6
EMBO J. 2025 Feb 11.

Mitochondrial DNA removal is essential for sperm development and activity.

Zhe Chen, Fan Zhang, Annie Lee, Michaela Yamine, Zong-Heng Wang, Guofeng Zhang, Christian Combs, Hong Xu.

  Active mitochondrial DNA (mtDNA) elimination during spermatogenesis has emerged as a conserved mechanism ensuring the uniparental mitochondrial inheritance in animals. However, given the existence of post-fertilization processes degrading sperm mitochondria, the physiological significance of mtDNA removal during spermatogenesis is not clear. Here we show that mtDNA clearance is indispensable for sperm development and activity. We uncover a previously unappreciated role of Poldip2 as a mitochondrial exonuclease that is specifically expressed in late spermatogenesis and required for sperm mtDNA elimination in Drosophila. Loss of Poldip2 impairs mtDNA clearance in elongated spermatids and impedes the progression of individualization complexes that strip away cytoplasmic materials and organelles. Over time, poldip2 mutant sperm exhibit marked nuclear genome fragmentation, and the flies become completely sterile. Notably, these phenotypes were rescued by expressing a mitochondrially targeted bacterial exonuclease, which ectopically removes mtDNA. Our work illustrates the developmental necessity of mtDNA clearance for effective cytoplasm removal at the end of spermatid morphogenesis, and for preventing potential nuclear-mitochondrial genome imbalance in mature sperm, in which nuclear genome activity is shut down.

Keywords:   Drosophila spermatogenesis; EndoG; Exonuclease; Male Sterile; Maternal Inheritance

DOI:  https://doi.org/10.1038/s44318-025-00377-5
Mol Cell. 2025 Jan 30. pii: S1097-2765(25)00052-8. [Epub ahead of print]

The RNA helicase HrpA rescues collided ribosomes in E. coli.

Annabelle Campbell, Hanna F Esser, A Maxwell Burroughs, Otto Berninghausen, L Aravind, Thomas Becker, Rachel Green, Roland Beckmann, Allen R Buskirk.

  Although many antibiotics inhibit bacterial ribosomes, the loss of known factors that rescue stalled ribosomes does not lead to robust antibiotic sensitivity in E. coli, suggesting the existence of additional mechanisms. Here, we show that the RNA helicase HrpA rescues stalled ribosomes in E. coli. Acting selectively on ribosomes that have collided, HrpA uses ATP hydrolysis to split stalled ribosomes into subunits. Cryoelectron microscopy (cryo-EM) structures reveal how HrpA simultaneously binds to two collided ribosomes, explaining its selectivity, and how its helicase module engages downstream mRNA such that, by exerting a pulling force on the mRNA, it would destabilize the stalled ribosome. These studies show that ribosome splitting is a conserved mechanism that allows proteobacteria to tolerate ribosome-targeting antibiotics.

Keywords:  DEAH-box protein; HrpA; SmrB; cryo-EM; ribosome collisions; ribosome splitting

DOI:  https://doi.org/10.1016/j.molcel.2025.01.018
J Am Heart Assoc. 2025 Feb 14. e037637

Dietary Branched-Chain Amino Acids Modify Postinfarct Cardiac Remodeling and Function in the Murine Heart.

Daniel C Nguyen, Collin K Wells, Madison S Taylor, Yania Martinez-Ondaro, Richa Singhal, Kenneth R Brittian, Robert E Brainard, Joseph B Moore, Bradford G Hill.

   BACKGROUND: Branched-chain amino acids (BCAAs), which are derived from the diet, are markedly elevated in cardiac tissue following myocardial infarction (MI). Nevertheless, it remains unclear whether dietary BCAA levels influence post-MI remodeling.
METHODS: To investigate the impact of dietary BCAAs on cardiac remodeling and function after MI, we fed mice a low or a high BCAA diet for 2 weeks before MI and for 4 weeks after MI. Cardiac structural and functional changes were evaluated by echocardiography, gravimetry, and histopathological analyses. Immunoblotting was used to evaluate the effects of BCAAs on isolated cardiac myofibroblast differentiation.
RESULTS: The low BCAA diet decreased circulating BCAA concentrations by >2-fold when compared with the high BCAA diet. Although neither body weights nor heart masses were different in female mice fed the custom diets, male mice fed the high BCAA diet had significantly higher body and heart masses than those on the low BCAA diet. The low BCAA diet preserved stroke volume and cardiac output after MI, whereas the high BCAA diet promoted progressive decreases in cardiac function. Although BCAAs were required for myofibroblast differentiation in vitro, cardiac fibrosis, scar collagen topography, and cardiomyocyte cross-sectional area were not different between the dietary groups; however, male mice fed the high BCAA diet had longer cardiomyocytes and higher capillary density compared with the low BCAA group.
CONCLUSIONS: A low BCAA diet mitigates eccentric cardiomyocyte remodeling and loss of cardiac function after MI in mice, with dietary effects more prominent in males.

Keywords:  branched‐chain amino acids; fibrosis; heart failure; hypertrophy; myocardial infarction

DOI:  https://doi.org/10.1161/JAHA.124.037637
Cell Metab. 2025 Feb 04. pii: S1550-4131(25)00002-6. [Epub ahead of print]

Lactate controls cancer stemness and plasticity through epigenetic regulation.

Nguyen T B Nguyen, Sira Gevers, Rutger N U Kok, Lotte M Burgering, Hannah Neikes, Ninouk Akkerman, Max A Betjes, Marlies C Ludikhuize, Can Gulersonmez, Edwin C A Stigter, Yvonne Vercoulen, Jarno Drost, Hans Clevers, Michiel Vermeulen, Jeroen S van Zon, Sander J Tans, Boudewijn M T Burgering, Maria J Rodríguez Colman.

  Tumors arise from uncontrolled cell proliferation driven by mutations in genes that regulate stem cell renewal and differentiation. Intestinal tumors, however, retain some hierarchical organization, maintaining both cancer stem cells (CSCs) and cancer differentiated cells (CDCs). This heterogeneity, coupled with cellular plasticity enabling CDCs to revert to CSCs, contributes to therapy resistance and relapse. Using genetically encoded fluorescent reporters in human tumor organoids, combined with our machine-learning-based cell tracker, CellPhenTracker, we simultaneously traced cell-type specification, metabolic changes, and reconstructed cell lineage trajectories during tumor organoid development. Our findings reveal distinctive metabolic phenotypes in CSCs and CDCs. We find that lactate regulates tumor dynamics, suppressing CSC differentiation and inducing dedifferentiation into a proliferative CSC state. Mechanistically, lactate increases histone acetylation, epigenetically activating MYC. Given that lactate's regulation of MYC depends on the bromodomain-containing protein 4 (BRD4), targeting cancer metabolism and BRD4 inhibitors emerge as a promising strategy to prevent tumor relapse.

Keywords:  cancer metabolism; cell plasticity; cell types; cell-cell interactions; differentiation; heterogeneity; live imaging; organoids; single-cell tracking; stem cells

DOI:  https://doi.org/10.1016/j.cmet.2025.01.002
Cell Rep. 2025 Jan 28. pii: S2211-1247(24)01494-3. [Epub ahead of print]44(1): 115143

A microscopy-based screen identifies cellular kinases modulating mitochondrial translation.

Roya Yousefi, Luis Daniel Cruz-Zaragoza, Anusha Valpadashi, Carina Hansohn, Drishan Dahal, Ricarda Richter-Dennerlein, Silvio Rizzoli, Henning Urlaub, Peter Rehling, David Pacheu-Grau.

  Mitochondrial DNA encodes 13 subunits of the oxidative phosphorylation (OXPHOS) system, which are synthesized inside the organelle and essential for cellular energy supply. How mitochondrial gene expression is regulated and integrated into cellular physiology is little understood. Here, we perform a high-throughput screen combining fluorescent labeling of mitochondrial translation products with small interfering RNA (siRNA)-mediated knockdown to identify cellular kinases regulating translation. As proof of principle, the screen identifies known kinases that affect mitochondrial translation, and it also reveals several kinases not yet linked to this process. Among the latter, we focus on the primarily cytosolic kinase, fructosamine 3 kinase (FN3K), which localizes partially to the mitochondria to support translation. FN3K interacts with the mitochondrial ribosome and modulates its assembly, thereby affecting translation. Overall, our work provides a reliable approach to identify protein functions for mitochondrial gene expression in a high-throughput manner.

Keywords:  CP: Metabolism; CP: Molecular biology; cellular kinases; click chemistry; mito-FUNCAT; mitochondrial translation; siRNA library

DOI:  https://doi.org/10.1016/j.celrep.2024.115143
Mol Cell. 2025 Feb 06. pii: S1097-2765(25)00048-6. [Epub ahead of print]

RIOK3 mediates the degradation of 40S ribosomes.

Zixuan Huang, Frances F Diehl, Mengjiao Wang, Yi Li, Aixia Song, Fei Xavier Chen, Nicolle A Rosa-Mercado, Roland Beckmann, Rachel Green, Jingdong Cheng.

  Cells tightly regulate ribosome homeostasis to adapt to changing environments. Ribosomes are degraded during stress, but the mechanisms responsible remain unclear. Here, we show that starvation induces the selective depletion of 40S ribosomes following their ubiquitylation by the E3 ligase RNF10. The atypical kinase RIOK3 specifically recognizes these ubiquitylated 40S ribosomes through a unique ubiquitin-interacting motif, visualized by cryoelectron microscopy (cryo-EM). RIOK3 binding and ubiquitin recognition are essential for 40S ribosome degradation during starvation. RIOK3 induces the degradation of ubiquitylated 40S ribosomes through progressive decay of their 18S rRNA beginning at the 3' end, as revealed by cryo-EM structures of degradation intermediates. Together, these data define a pathway and mechanism for stress-induced degradation of 40S ribosomes, directly connecting ubiquitylation to regulation of ribosome homeostasis.

Keywords:  40S; RIOK3; RNA degradation; cryo-EM; homeostasis; ribosome; starvation; stress response; translation; ubiquitin

DOI:  https://doi.org/10.1016/j.molcel.2025.01.013
Nat Cell Biol. 2025 Feb;27(2): 175

Mesoderm FN1 shaping the heart.

Daryl J V David.

DOI: https://doi.org/10.1038/s41556-025-01630-z
Nucleic Acids Res. 2025 Feb 08. pii: gkaf056. [Epub ahead of print]53(4):

Biomolecular condensation of human IDRs initiates endogenous transcription via intrachromosomal looping or high-density promoter localization.

Jing Li, Shizhe Liu, Sunghwan Kim, Jacob Goell, Zachary Allen Drum, John Patrick Flores, Alex J Ma, Barun Mahata, Mario Escobar, Alex Raterink, Jeong Hyun Ahn, Erik R Terán, Rosa Selenia Guerra-Resendez, Yuhao Zhou, Bo Yu, Michael R Diehl, Gang Greg Wang, Anna-Karin Gustavsson, Douglas H Phanstiel, Isaac B Hilton.

Protein intrinsically disordered regions (IDRs) are critical gene-regulatory components and aberrant fusions between IDRs and DNA-binding/chromatin-associating domains cause diverse human cancers. Despite this importance, how IDRs influence gene expression, and how aberrant IDR fusion proteins provoke oncogenesis, remains incompletely understood. Here we develop a series of synthetic dCas9-IDR fusions to establish that locus-specific recruitment of IDRs can be sufficient to stimulate endogenous gene expression. Using dCas9 fused to the paradigmatic leukemogenic NUP98 IDR, we also demonstrate that IDRs can activate transcription via localized biomolecular condensation and in a manner that is dependent upon overall IDR concentration, local binding density, and amino acid composition. To better clarify the oncogenic role of IDRs, we construct clinically observed NUP98 IDR fusions and show that, while generally non-overlapping, oncogenic NUP98-IDR fusions convergently drive a core leukemogenic gene expression program in donor-derived human hematopoietic stem cells. Interestingly, we find that this leukemic program arises through differing mechanistic routes based upon IDR fusion partner; either distributed intragenic binding and intrachromosomal looping, or dense binding at promoters. Altogether, our studies clarify the gene-regulatory roles of IDRs and, for the NUP98 IDR, connect this capacity to pathological cellular programs, creating potential opportunities for generalized and mechanistically tailored therapies.

DOI: https://doi.org/10.1093/nar/gkaf056
Elife. 2025 Feb 11. pii: RP97268. [Epub ahead of print]13

Mechanical forces pattern endocardial Notch activation via mTORC2-PKC pathway.

Yunfei Mu, Shijia Hu, Xiangyang Liu, Xin Tang, Jiayi Lin, Hongjun Shi.

  Notch signaling has been identified as a key regulatory pathway in patterning the endocardium through activation of endothelial-to-mesenchymal transition (EMT) in the atrioventricular canal (AVC) and proximal outflow tract (OFT) region. However, the precise mechanism underlying Notch activation remains elusive. By transiently blocking the heartbeat of E9.5 mouse embryos, we found that Notch activation in the arterial endothelium was dependent on its ligand Dll4, whereas the reduced expression of Dll4 in the endocardium led to a ligand-depleted field, enabling Notch to be specifically activated in AVC and OFT by regional increased shear stress. The strong shear stress altered the membrane lipid microdomain structure of endocardial cells, which activated mTORC2 and PKC and promoted Notch1 cleavage even in the absence of strong ligand stimulation. These findings highlight the role of mechanical forces as a primary cue for endocardial patterning and provide insights into the mechanisms underlying congenital heart diseases of endocardial origin.

Keywords:  EMT; cardiac patterning; developmental biology; endocardium; mechanosensing; mouse; notch; shear stress

DOI:  https://doi.org/10.7554/eLife.97268
Cell. 2025 Feb 08. pii: S0092-8674(25)00100-X. [Epub ahead of print]

Distinct mismatch-repair complex genes set neuronal CAG-repeat expansion rate to drive selective pathogenesis in HD mice.

Nan Wang, Shasha Zhang, Peter Langfelder, Lalini Ramanathan, Fuying Gao, Mary Plascencia, Raymond Vaca, Xiaofeng Gu, Linna Deng, Leonardo E Dionisio, Ha Vu, Emily Maciejewski, Jason Ernst, Brinda C Prasad, Thomas F Vogt, Steve Horvath, Jeffrey S Aaronson, Jim Rosinski, X William Yang.

  Huntington's disease (HD) modifiers include mismatch-repair (MMR) genes, but their connections to neuronal pathogenesis remain unclear. Here, we genetically tested 9 HD genome-wide association study (GWAS)/MMR genes in mutant Huntingtin (mHtt) mice with 140 inherited CAG repeats (Q140). Knockout (KO) of genes encoding a distinct MMR complex either strongly (Msh3 and Pms1) or moderately (Msh2 and Mlh1) rescues phenotypes with early onset in striatal medium-spiny neurons (MSNs) and late onset in the cortical neurons: somatic CAG-repeat expansion, transcriptionopathy, and mHtt aggregation. Msh3 deficiency ameliorates open-chromatin dysregulation in Q140 neurons. Mechanistically, the fast linear rate of mHtt modal-CAG-repeat expansion in MSNs (8.8 repeats/month) is drastically reduced or stopped by MMR mutants. Msh3 or Pms1 deficiency prevents mHtt aggregation by keeping somatic MSN CAG length below 150. Importantly, Msh3 deficiency corrects synaptic, astrocytic, and locomotor defects in HD mice. Thus, Msh3 and Pms1 drive fast somatic mHtt CAG-expansion rates in HD-vulnerable neurons to elicit repeat-length/threshold-dependent, selective, and progressive pathogenesis in vivo.

Keywords:  ATAC-seq; CAG repeat; Huntingtin; Huntington's disease; Mlh1; Msh2; Msh3; Pms1; RNA-seq; aggregate; chromatin; cortex; mismatch repair; neurons; rate; repeat expansion; repeat instability; selective vulnerability; striatum; threshold

DOI:  https://doi.org/10.1016/j.cell.2025.01.031
Cell Rep. 2025 Jan 28. pii: S2211-1247(24)01517-1. [Epub ahead of print]44(1): 115166

The structural basis for RNA slicing by human Argonaute2.

Abdallah A Mohamed, Peter Y Wang, David P Bartel, Seychelle M Vos.

  Argonaute (AGO) proteins associate with guide RNAs to form complexes that slice transcripts that pair to the guide. This slicing drives post-transcriptional gene silencing through RNA interference (RNAi), which is essential for many eukaryotes and the basis for new clinical therapies. Despite this importance, structural information on eukaryotic AGOs in a fully paired, slicing-competent conformation-hypothesized to be intrinsically unstable-has been lacking. Here, we present the cryogenic electron microscopy structure of a human AGO-guide complex bound to a fully paired target, revealing structural rearrangements that enable this conformation. Critically, the N domain of AGO rotates to allow the RNA full access to the central channel and forms contacts that license rapid slicing. Moreover, a conserved loop in the PIWI domain secures the RNA near the active site to enhance slicing rate and specificity. These results explain how AGO accommodates targets possessing pairing specificity typically observed in biological and clinical slicing substrates.

Keywords:  AGO2; Argonaute; CP: Molecular biology; RISC; RNA-protein interactions; RNAi; cryo-EM; microRNA; siRNA; slicing

DOI:  https://doi.org/10.1016/j.celrep.2024.115166
Circulation. 2025 Feb 10.

Exploring Origin-Dependent Susceptibility of Smooth Muscle Cells to Aortic Diseases Through Intersectional Genetics.

Ximeng Han, Yi Li, Enci Wang, Huan Zhu, Xiuzhen Huang, Wenjuan Pu, Mingjun Zhang, Kuo Liu, Huan Zhao, Zixin Liu, Yufei Zhao, Linghong Shen, Yan Li, Xiao Yang, Qing-Dong Wang, Xin Ma, Ruling Shen, Kathy Lui, Lixin Wang, Ben He, Bin Zhou.

   BACKGROUND: The developmental diversity among smooth muscle cells (SMCs) plays a crucial role in segment-specific aortic diseases. However, traditional genetic approaches are inadequate for enabling in vivo analysis of disease susceptibility associated with cellular origin. There is an urgent need to build genetic technologies that target different developmental origins to investigate the mechanisms of aortopathies, thereby facilitating the development of effective therapeutics.
METHODS: To address this challenge, we developed an advanced dual recombinase-mediated intersectional genetic system, specifically designed to precisely target SMCs from various developmental origins in mice. Specifically, we used Isl1-Dre, Wnt1-Dre, Meox1-DreER, and Upk3b-Dre to target SMC progenitors from the second heart field, cardiac neural crest, somites, and mesothelium, respectively. This system was combined with single-cell RNA sequencing to investigate the impact of TGF-β (transforming growth factor-β) signaling in different segments of the aorta by selectively knocking out Tgfbr2 in the ascending aorta and Smad4 in the aortic arch, respectively.
RESULTS: Through intersectional genetic approaches, we use the Myh11-Cre(ER) driver along with origin-specific Dre drivers to trace cells of diverse developmental origins within the SMC population. We found that a deficiency of Tgfbr2 in SMCs of the ascending aorta leads to aneurysm formation in this specific region. We also demonstrate the critical role of Smad4 in preserving aortic wall integrity and homeostasis in SMCs of the aortic arch.
CONCLUSIONS: Our approach to genetically targeting SMC subtypes provides a novel platform for exploring origin-dependent or location-specific aortic vascular diseases. This genetic system enables comprehensive analysis of contributions from different cell lineages to SMC behavior and pathology, thereby paving the way for targeted research and therapeutic interventions in the future.

Keywords:  TGF-β; aortic diseases; developmental origin; lineage tracing; smooth muscle cell

DOI:  https://doi.org/10.1161/CIRCULATIONAHA.124.070782
J Cell Biol. 2025 Apr 07. pii: e202407025. [Epub ahead of print]224(4):

Prickle2 regulates apical junction remodeling and tissue fluidity during vertebrate neurulation.

Miho Matsuda, Sergei Y Sokol.

The process of folding the flat neuroectoderm into an elongated neural tube depends on tissue fluidity, a property that allows epithelial deformation while preserving tissue integrity. Neural tube folding also requires the planar cell polarity (PCP) pathway. Here, we report that Prickle2 (Pk2), a core PCP component, increases tissue fluidity by promoting the remodeling of apical junctions (AJs) in Xenopus embryos. This Pk2 activity is mediated by the unique evolutionarily conserved Ser/Thr-rich region (STR) in the carboxyterminal half of the protein. Mechanistically, the effects of Pk2 require Rac1 and are accompanied by increased dynamics of C-cadherin and tricellular junctions, the hotspots of AJ remodeling. Notably, Pk2 depletion leads to the accumulation of mediolaterally oriented cells in the neuroectoderm, whereas the overexpression of Pk2 or Pk1 containing the Pk2-derived STR promotes cell elongation along the anteroposterior axis. We propose that Pk2-dependent regulation of tissue fluidity contributes to anteroposterior tissue elongation in response to extrinsic cues.

DOI: https://doi.org/10.1083/jcb.202407025
Nat Genet. 2025 Feb 13.

Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis.

Bryce Lim, Aryan Kamal, Borja Gomez Ramos, Juan M Adrian Segarra, Ignacio L Ibarra, Lennart Dignas, Tim Kindinger, Kai Volz, Mohammad Rahbari, Nuh Rahbari, Eric Poisel, Kanela Kafetzopoulou, Lio Böse, Marco Breinig, Danijela Heide, Suchira Gallage, Jose E Barragan Avila, Hendrik Wiethoff, Ivan Berest, Sarah Schnabellehner, Martin Schneider, Jonas Becker, Dominic Helm, Dirk Grimm, Taija Mäkinen, Darjus F Tschaharganeh, Mathias Heikenwalder, Judith B Zaugg, Moritz Mall.

Cell fate plasticity enables development, yet unlocked plasticity is a cancer hallmark. While transcription master regulators induce lineage-specific genes to restrict plasticity, it remains unclear whether plasticity is actively suppressed by lineage-specific repressors. Here we computationally predict so-called safeguard repressors for 18 cell types that block phenotypic plasticity lifelong. We validated hepatocyte-specific candidates using reprogramming, revealing that prospero homeobox protein 1 (PROX1) enhanced hepatocyte identity by direct repression of alternative fate master regulators. In mice, Prox1 was required for efficient hepatocyte regeneration after injury and was sufficient to prevent liver tumorigenesis. In line with patient data, Prox1 depletion caused hepatocyte fate loss in vivo and enabled the transition of hepatocellular carcinoma to cholangiocarcinoma. Conversely, overexpression promoted cholangiocarcinoma to hepatocellular carcinoma transdifferentiation. Our findings provide evidence for PROX1 as a hepatocyte-specific safeguard and support a model where cell-type-specific repressors actively suppress plasticity throughout life to safeguard lineage identity and thus prevent disease.

DOI: https://doi.org/10.1038/s41588-025-02081-w
Nat Commun. 2025 Feb 12. 16(1): 1587

Nuclear position controls the activity of cortical actomyosin networks powering simultaneous morphogenetic events.

Nicolas Roby, Matteo Rauzi.

Tissue morphogenesis shapes epithelial sheets via cell remodelling to form functional living organisms. While the mechanisms underlying single morphogenetic events are well studied, how one tissue undergoes multiple concomitant shape changes remains largely unexplored. To tackle this, we study the process of simultaneous mesoderm folding and extension in the gastrulating Drosophila embryo. This composite transformation relies on a sharply timed reorganization of the cortical actomyosin network into two distinct subcellular tiers to drive concomitant cell apical constriction and lateral intercalation for tissue folding and convergence-extension, respectively. Here we elucidate the spatio-temporal control of the two-tiered actomyosin network. We show that, within the geometric constraints imposed by the columnar shape of mesoderm epithelial cells, the nucleus acts as a barrier shielding the lateral cortex from interactions with the microtubule network, thereby regulating the distribution of the key signalling molecule RhoGEF2. The relocation of the nucleus, driven by the contraction of the first actomyosin tier and the resulting cytoplasmic flow, unshields the lateral cortex for RhoGEF2 delivery to direct the stereotypic formation of the second tier. Thus, the nucleus and its position function as a spatio-temporal cytoskeleton compartmentalizer establishing a modular scaffold powering multiple simultaneous cell remodeling for composite morphogenesis.

DOI: https://doi.org/10.1038/s41467-025-56880-0
Curr Protoc. 2025 Feb;5(2): e70099

Minimal Component, Protein-Free, and Cost-effective Human Pluripotent Stem Cell Cardiomyocyte Differentiation.

Jessika B Iwanski, Odunayo S Lawal, William T Kwon, Isabella Vazquez, Jared M Churko.

  Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) have become a powerful source for the in vitro modeling of cardiac diseases and various other essential applications, including cardiotoxicity screening and regenerative cell replacement therapies. Although many differentiation protocols have been developed to generate cardiomyocytes from human pluripotent stem cells, these protocols are costly and complex, requiring expensive and often unnecessary components (e.g., B27 medium supplement). In addition, the use of animal-derived growth factors limits their use for regenerative medicine purposes. To address these issues, herein, we have developed an efficient, cost-effective, and protein-free hPSC-CM protocol using only two components: DMEM/F12 basal medium and l-ascorbic acid 2-phosphate. By eliminating xenobiotic and complex components, the efficiency of directed differentiations is increased, the variability between cardiac differentiations is decreased, and the scalability of cell production is enhanced. Adaptation of this efficient, low-cost, and user-friendly cardiac differentiation protocol will enrich the utility and applicability of hPSC-CMs in drug discovery, cell therapies, tissue engineering, disease modeling, precision medicine, and cardiac regenerative medicine. © 2025 Wiley Periodicals LLC. Basic Protocol 1: hPSC cell culture Basic Protocol 2: hPSC-CM differentiation Basic Protocol 3: Characterization of hPSC-CMs by immunofluorescence (IF) imaging.

Keywords:  animal‐free; cardiomyocytes; hPSC‐CM; protein‐free; stem cells

DOI:  https://doi.org/10.1002/cpz1.70099
Mol Cell. 2025 Feb 07. pii: S1097-2765(25)00047-4. [Epub ahead of print]

The integrated stress response regulates 18S nonfunctional rRNA decay in mammals.

Aaztli R Coria, Akruti Shah, Mohammad Shafieinouri, Sarah J Taylor, Emilien Orgebin, Wilfried Guiblet, Jennifer T Miller, Indra Mani Sharma, Colin Chih-Chien Wu.

  18S nonfunctional rRNA decay (NRD) detects and eliminates translationally nonfunctional 18S rRNA. Although this process is critical for ribosome quality control, the mechanisms underlying nonfunctional 18S rRNA turnover remain elusive, particularly in mammals. Here, we show that mammalian 18S NRD initiates through the integrated stress response (ISR) via GCN2. Nonfunctional 18S rRNA induces translational arrest at start sites. Biochemical analyses demonstrate that ISR activation limits translation initiation and attenuates collisions between scanning 43S preinitiation complexes and stalled nonfunctional ribosomes. The ISR promotes 18S NRD and 40S ribosomal protein turnover by RNF10-mediated ubiquitination. Ultimately, RIOK3 binds the resulting ubiquitinated 40S subunits and facilitates 18S rRNA decay. Overall, mammalian 18S NRD acts through GCN2, followed by ubiquitin-dependent 18S rRNA degradation involving the ubiquitin E3 ligase RNF10 and the atypical protein kinase RIOK3. These findings establish a dynamic feedback mechanism by which the GCN2-RNF10-RIOK3 axis surveils ribosome functionality at the translation initiation step.

Keywords:  GCN2; RIOK3; integrated stress response; nonfunctional 18S rRNA; ribosome stalling

DOI:  https://doi.org/10.1016/j.molcel.2025.01.017
Nat Commun. 2025 Feb 10. 16(1): 1489

Trajectory analysis of hepatic stellate cell differentiation reveals metabolic regulation of cell commitment and fibrosis.

Raquel A Martínez García de la Torre, Julia Vallverdú, Zhenqing Xu, Silvia Ariño, Raquel Ferrer-Lorente, Laura Zanatto, Maria Mercado-Gómez, Beatriz Aguilar-Bravo, Paloma Ruiz-Blázquez, Maria Fernandez-Fernandez, Artur Navarro-Gascon, Albert Blasco-Roset, Paula Sànchez-Fernàndez-de-Landa, Joan Pera, Damia Romero-Moya, Paula Ayuso Garcia, Celia Martínez Sánchez, Laura Sererols Viñas, Paula Cantallops Vilà, Carmen I Cárcamo Giráldez, Andrew McQuillin, Marsha Y Morgan, Daniel Moya-Rull, Núria Montserrat, Delphine Eberlé, Bart Staels, Bénédicte Antoine, Mikel Azkargorta, Juan-José Lozano, Maria L Martínez-Chantar, Alessandra Giorgetti, Félix Elortza, Anna Planavila, Marta Varela-Rey, Ashwin Woodhoo, Antonio Zorzano, Isabel Graupera, Anna Moles, Mar Coll, Silvia Affo, Pau Sancho-Bru.

Defining the trajectory of cells during differentiation and disease is key for uncovering the mechanisms driving cell fate and identity. However, trajectories of human cells remain largely unexplored due to the challenges of studying them with human samples. In this study, we investigate the proteome trajectory of iPSCs differentiation to hepatic stellate cells (diHSCs) and identify RORA as a key transcription factor governing the metabolic reprogramming of HSCs necessary for diHSCs' commitment, identity, and activation. Using RORA deficient iPSCs and pharmacologic interventions, we show that RORA is required for early differentiation and prevents diHSCs activation by reducing the high energetic state of the cells. While RORA knockout mice have enhanced fibrosis, RORA agonists rescue multi-organ fibrosis in in vivo models. Notably, RORA expression correlates negatively with liver fibrosis and HSCs activation markers in patients with liver disease. This study reveals that RORA regulates cell metabolic plasticity, important for mesoderm differentiation, pericyte quiescence, and fibrosis, influencing cell commitment and disease.

DOI: https://doi.org/10.1038/s41467-025-56024-4
Cell Rep. 2025 Feb 12. pii: S2211-1247(25)00068-3. [Epub ahead of print]44(2): 115297

Membrane-tethered SCOTIN condensates elicit an endoplasmic reticulum stress response by sequestering luminal BiP.

Areum Jo, Minkyo Jung, Ji Young Mun, Young Jin Kim, Joo-Yeon Yoo.

  The endoplasmic reticulum (ER) stress response controls the balance between cellular survival and death. Here, we implicate SCOTIN, an interferon-inducible ER protein, in activating the ER stress response and modulating cell fate through its proline-rich domain (PRD)-mediated cytosolic condensation. SCOTIN overexpression leads to the formation of condensates enveloping multiple layers of the ER, accompanied by morphological signs of organelle stress. Luminal BiP chaperone proteins are sequestered within these SCOTIN condensates, which elicit ER stress responses. The colocalization of luminal BiP with SCOTIN is strictly contingent upon the PRD-mediated condensation of SCOTIN in the cytosolic compartment, closely associated with the ER membrane. The cysteine-rich domain (CRD) of SCOTIN, along with the condensation-prone PRD domain, is required for ER stress induction. We propose that membrane-associated condensation transduces signals across the ER membrane, leading to the induction of BiP assembly and the ER stress response.

Keywords:  CP: Cell biology; ER stress; SCOTIN; SHISA-5; biomolecular condensate; cell death; endoplasmic reticulum; phase separation; signal transmission; unfolded protein response

DOI:  https://doi.org/10.1016/j.celrep.2025.115297
Cell Rep. 2025 Jan 28. pii: S2211-1247(24)01499-2. [Epub ahead of print]44(1): 115148

Acetylation at lysine 27 on maternal H3.3 regulates minor zygotic genome activation.

Jiaming Zhang, Xuanwen Li, Qi Zhao, Jingzhang Ji, Hongdi Cui, Weibo Hou, Xinyu Wang, Entong Song, Songling Xiao, Shukuan Ling, Shaorong Gao, Xiaoyu Liu, Duancheng Wen, Qingran Kong.

  Zygotic genome activation (ZGA) initiates transcription in early embryogenesis and requires extensive chromatin remodeling, including rapid incorporation of the histone variant H3.3. The distinct sources of H3.3 from paternal and maternal alleles (paH3.3 and maH3.3) complicate tracking their individual contributions. Here, using an H3.3B-hemagglutinin (HA)-tagged mouse model, we profile the temporal dynamics of paH3.3 and maH3.3, revealing a unique pattern of maH3.3 enrichment at the promoter regions from zygotes to 2-cell embryos, highlighting the crucial role of maternally stored H3.3 mRNAs and proteins (mH3.3) in pre-implantation development. Knockdown of mH3.3 compromises cleavage and minor ZGA. Mechanistically, mH3.3 facilitates minor ZGA through H3.3S31ph-dependent H3K27ac deposition. Profiling of H3.3 landscape in parthenogenetic (PG) and androgenetic (AG) embryos highlights the role of mH3.3 in remodeling the paternal genome by establishing H3K27ac. These findings demonstrate that mH3.3-mediated parental chromatin reprogramming is essential for orchestrating minor ZGA.

Keywords:  CP: Developmental biology; CP: Molecular biology; early embryonic development; epigenetic reprogramming; histone variants; maternal H3.3; zygotic genome activation

DOI:  https://doi.org/10.1016/j.celrep.2024.115148
Nature. 2025 Feb 12.

Transcriptomic neuron types vary topographically in function and morphology.

Inbal Shainer, Johannes M Kappel, Eva Laurell, Joseph C Donovan, Martin W Schneider, Enrico Kuehn, Irene Arnold-Ammer, Manuel Stemmer, Johannes Larsch, Herwig Baier.

Neuronal phenotypic traits such as morphology, connectivity and function are dictated, to a large extent, by a specific combination of differentially expressed genes. Clusters of neurons in transcriptomic space correspond to distinct cell types and in some cases-for example, Caenorhabditis elegans neurons1 and retinal ganglion cells2-4-have been shown to share morphology and function. The zebrafish optic tectum is composed of a spatial array of neurons that transforms visual inputs into motor outputs. Although the visuotopic map is continuous, subregions of the tectum are functionally specialized5,6. Here, to uncover the cell-type architecture of the tectum, we transcriptionally profiled its neurons, revealing more than 60 cell types that are organized in distinct anatomical layers. We measured the visual responses of thousands of tectal neurons by two-photon calcium imaging and matched them with their transcriptional profiles. Furthermore, we characterized the morphologies of transcriptionally identified neurons using specific transgenic lines. Notably, we found that neurons that are transcriptionally similar can diverge in shape, connectivity and visual responses. Incorporating the spatial coordinates of neurons within the tectal volume revealed functionally and morphologically defined anatomical subclusters within individual transcriptomic clusters. Our findings demonstrate that extrinsic, position-dependent factors expand the phenotypic repertoire of genetically similar neurons.

DOI: https://doi.org/10.1038/s41586-024-08518-2
bioRxiv. 2025 Jan 15. pii: 2025.01.13.632736. [Epub ahead of print]

Genome-wide absolute quantification of chromatin looping.

James M Jusuf, Simon Grosse-Holz, Michele Gabriele, Pia Mach, Ilya M Flyamer, Christoph Zechner, Luca Giorgetti, Leonid A Mirny, Anders S Hansen.

3D genomics methods such as Hi-C and Micro-C have uncovered chromatin loops across the genome and linked these loops to gene regulation. However, these methods only measure 3D interaction probabilities on a relative scale. Here, we overcome this limitation by using live imaging data to calibrate Micro-C in mouse embryonic stem cells, thus obtaining absolute looping probabilities for 36,804 chromatin loops across the genome. We find that the looped state is generally rare, with a mean probability of 2.3% and a maximum of 26% across the quantified loops. On average, CTCF-CTCF loops are stronger than loops between cis-regulatory elements (3.2% vs. 1.1%). Our findings can be extended to human stem cells and differentiated cells under certain assumptions. Overall, we establish an approach for genome-wide absolute loop quantification and report that loops generally occur with low probabilities, generalizing recent live imaging results to the whole genome.

DOI: https://doi.org/10.1101/2025.01.13.632736
JCI Insight. 2025 Feb 10. pii: e165837. [Epub ahead of print]10(3):

Regulation of lung progenitor plasticity and repair by fatty acid oxidation.

Quetzalli D Angeles-Lopez, Jhonny Rodriguez-Lopez, Paula Agudelo Garcia, Jazmin Calyeca, Diana Álvarez, Marta Bueno, Lan N Tu, Myriam Salazar-Terreros, Natalia Vanegas-Avendaño, Jordan E Krull, Aigul Moldobaeva, Srimathi Bogamuwa, Stephanie S Scott, Victor Peters, Brenda F Reader, Sruti Shiva, Michael Jurczak, Mahboobe Ghaedi, Qin Ma, Toren Finkel, Mauricio Rojas, Ana L Mora.

  Idiopathic pulmonary fibrosis (IPF) is an age-related interstitial lung disease, characterized by inadequate alveolar regeneration and ectopic bronchiolization. While some molecular pathways regulating lung progenitor cells have been described, the role of metabolic pathways in alveolar regeneration is poorly understood. We report that expression of fatty acid oxidation (FAO) genes is significantly diminished in alveolar epithelial cells of IPF lungs by single-cell RNA sequencing and tissue staining. Genetic and pharmacological inhibition in AT2 cells of carnitine palmitoyltransferase 1a (CPT1a), the rate-limiting enzyme of FAO, promoted mitochondrial dysfunction and acquisition of aberrant intermediate states expressing basaloid, and airway secretory cell markers SCGB1A1 and SCGB3A2. Furthermore, mice with deficiency of CPT1a in AT2 cells show enhanced susceptibility to developing lung fibrosis with an accumulation of epithelial cells expressing markers of intermediate cells, airway secretory cells, and senescence. We found that deficiency of CPT1a causes a decrease in SMAD7 protein levels and TGF-β signaling pathway activation. These findings suggest that the mitochondrial FAO metabolic pathway contributes to the regulation of lung progenitor cell repair responses and deficiency of FAO contributes to aberrant lung repair and the development of lung fibrosis.

Keywords:  Fatty acid oxidation; Fibrosis; Metabolism; Mitochondria; Pulmonology

DOI:  https://doi.org/10.1172/jci.insight.165837
Nat Methods. 2025 Feb 12.

Scalable co-sequencing of RNA and DNA from individual nuclei.

Timothy R Olsen, Pranay Talla, Romella K Sagatelian, Julia Furnari, Jeffrey N Bruce, Peter Canoll, Shan Zha, Peter A Sims.

The ideal technology for directly investigating the relationship between genotype and phenotype would analyze both RNA and DNA genome-wide and with single-cell resolution; however, existing tools lack the throughput required for comprehensive analysis of complex tumors and tissues. We introduce a highly scalable method for jointly profiling DNA and expression following nucleosome depletion (DEFND-seq). In DEFND-seq, nuclei are nucleosome-depleted, tagmented and separated into individual droplets for messenger RNA and genomic DNA barcoding. Once nuclei have been depleted of nucleosomes, subsequent steps can be performed using the widely available 10x Genomics droplet microfluidic technology and commercial kits. We demonstrate the production of high-complexity mRNA and gDNA sequencing libraries from thousands of individual nuclei from cell lines, fresh and archived surgical specimens for associating gene expression with both copy number and single-nucleotide variants.

DOI: https://doi.org/10.1038/s41592-024-02579-x
Dev Biol. 2025 Feb 06. pii: S0012-1606(25)00032-6. [Epub ahead of print]

Exploring The Differentiation Potential of EomesPOS Mouse Trophoblast Cells in Mid-Gestation.

Avery J McGinnis, Megan E Cull, Nichole T Peterson, Matthew K Tang, Bryony V Natale, David R C Natale.

  Mouse trophoblast stem (mTS) cells can be derived from the blastocyst or extraembryonic ectoderm as late as embryonic day (E) 6.5and when cultured in vitro, can differentiate to all trophoblast subtypes of the mature placenta. Expression of the T-box transcription factor, Eomes, is required for the maintenance of, and used to identify mTS cells. During development, Eomes is restricted to the ExE and, by E7.5, to the chorion, after which its expression declines. The placental junctional zone and labyrinth layers are thought to develop exclusively from the ectoplacental cone and chorion, respectively. While it is well established that mTS cells express Eomes in vitro, it is unknown if Eomes-positive (EomesPOS) trophoblast that reside in the chorion after E6.5 are restricted in their developmental potential to the labyrinth layer in vivo. This study utilized a lineage tracing technique to evaluate the in vivo differentiation of EomesPOS trophoblast. Using an Ai6 reporter mouse crossed with a tamoxifen-inducible Eomes-Cre-ERT2 mouse, Cre was activated from E7.5 to E9.5, permanently marking all EomesPOS trophoblast and daughter cells with the ZsGreen fluorescent protein. This approach was complemented with immunofluorescence staining to assess how the EomesPOS trophoblast had contributed to the differentiated trophoblast population within the placenta by E17.5. Importantly, the results show that daughter cells of EomesPOS trophoblast in which Cre was activated, contributed to both placental layers; specifically, spongiotrophoblast and glycogen trophoblast within the junctional zone and syncytiotrophoblast and sinusoidal trophoblast giant cells within the labyrinth. This confirms that EomesPOS trophoblast maintain the capacity to contribute to both placental layers in vivo and do so after E7.5. This study expands our understanding of trophoblast differentiation in vivo and may prove useful in assessing how EomesPOS trophoblast contribute placental development later in gestation and in the context of placental pathology, where Eomes expression has been reported.

Keywords:  Eomes; Lineage Tracing; Placenta; Trophoblast; Trophoblast Stem Cells

DOI:  https://doi.org/10.1016/j.ydbio.2025.02.002
Nat Commun. 2025 Feb 10. 16(1): 1485

Visualization of chromosomal reorganization induced by heterologous fusions in the mammalian nucleus.

Meng Yan, Xiaoyu Merlin Zhang, Zhenhua Yang, Miao Jia, Rongyu Liao, Jinsong Li.

Chromosomes are spatially organized and functionally folded into a specific macro-structure in the nucleus. Recently, we and others created haploid cells with chromosome fusions. However, there is still lack of an effective strategy for precisely investigating how the genome copes with fusions. Here, we developed a down-sampling method to convert the populational Hi-C dataset into single cell-like Khimaira Matrix (K-matrix). K-matrix preserves not only the most prominent functional genomic features but also cell-to-cell variations. K-matrix-originated genome 3D models display spatial approach of fused chromosomes and minor global structure alterations. Combined with a layered positional decomposition analysis, our models indicate slight re-adjustment of chromosome distributions accordingly with an increasing tendency following more fusions involved. Nevertheless, the radial distribution of the A/B compartment is not affected dramatically. By contrast, natural populations harboring Rb fusions display significant alterations of chromosome radial location. Overall, K-matrix-originated models enable visualization of chromosomal reorganization with high resolution.

DOI: https://doi.org/10.1038/s41467-024-55582-3
Nat Struct Mol Biol. 2025 Feb 10.

Initiation of ERAD by the bifunctional complex of Mnl1/Htm1 mannosidase and protein disulfide isomerase.

Dan Zhao, Xudong Wu, Tom A Rapoport.

Misfolded glycoproteins in the endoplasmic reticulum (ER) lumen are translocated into the cytosol and degraded by the proteasome, a conserved process called ER-associated protein degradation (ERAD). In Saccharomyces cerevisiae, the glycan of these proteins is trimmed by the luminal mannosidase Mnl1 (Htm1) to generate a degradation signal. Interestingly, Mnl1 is associated with protein disulfide isomerase (Pdi1). Here we used cryo-electron microscopy, biochemical and in vivo experiments to elucidate how this complex initiates ERAD. The Mnl1-Pdi1 complex first demannosylates misfolded, globular proteins that are recognized through the C-terminal domain (CTD) of Mnl1; Pdi1 causes the CTD to ignore completely unfolded polypeptides. The disulfides of these globular proteins are then reduced by the Pdi1 component of the complex. Mnl1 blocks the canonical oxidative function of Pdi1, allowing it to function as a disulfide reductase in ERAD. The generated unfolded polypeptides can then be translocated across the membrane into the cytosol.

DOI: https://doi.org/10.1038/s41594-025-01491-y
Proc Natl Acad Sci U S A. 2025 Feb 18. 122(7): e2411977122

Identification of FSH-regulated and estrous stage-specific transcriptional networks in mouse ovaries.

Kathryn Walters, Amber Baldwin, Zhenghui Liu, Mark Larsen, Neelanjan Mukherjee, T Rajendra Kumar.

  Follicle-stimulating hormone (FSH) acts by binding to FSHRs expressed on ovarian granulosa cells and produces estradiol. FSH is essential for female fertility because mice lacking FSH (Fshb KO) are anestrous and infertile. Although several in vitro cell culture and ex vivo approaches combined with pharmacological hormone treatment were used to identify FSH-regulated genes, how FSH orchestrates ovarian gene networks in vivo has not been investigated. Whether FSH-regulated genes display estrous stage-specific expression changes has also not been studied. Here, we functionally rescued Fshb null mice with a gonadotrope-targeted HFSHB transgene and performed RNA-Seq analysis on ovarian RNAs obtained from FSH-intact (WT), FSH-deficient (Fshb KO), and FSH-rescue (HFSHB+ rescue) mice. By comparing WT vs. Fshb KO and Fshb KO vs. HFSHB+ rescue ovarian gene expression datasets, we identified FSH-responsive genes in vivo. Cross interrogation of these datasets further allowed us to identify several transcription factors (TFs) and RNA-binding proteins specific to FSH-regulated genes. In an independent set of experiments, we performed RNA-Seq analysis on ovarian RNAs from mice in diestrous (DE), proestrous (PE), and estrous (E) and identified estrous stage-specific ovarian gene expression patterns. Interestingly, many of the FSH-regulated TFs themselves were estrous-stage specifically expressed. We found that ESR2 and GATA6, two known FSH-responsive TFs, and their target genes are reciprocally regulated with distinct patterns of expression in estrous stages. Together, our in vivo models and RNA-Seq analyses identify FSH-regulated ovarian genes in specific estrous stages that are under transcriptional and posttranscriptional control.

Keywords:  FSH; RNA-binding proteins; estrus cycles; ovary; transcription factors

DOI:  https://doi.org/10.1073/pnas.2411977122