bims-cebooc 2025-02-23 papers

bims-cebooc

Biomed News

on Cell biology of oocytes

Issue of 2025–02–23
seventeen papers selected by
Gabriele Zaffagnini, Universität zu Köln

SPO11 dimers are sufficient to catalyse DNA double-strand breaks in vitro.
In vitro reconstitution of meiotic DNA double-strand-break formation.
NAT10-mediated mRNA N4-acetylation is essential for the translational regulation during oocyte meiotic maturation in mice.
Distinct requirements for PI3K isoforms p110α and p110δ for PIP3 synthesis in mouse oocytes and early embryos.
Noninvasive characterization of oocyte deformability in microconstrictions.
A simple immunohistochemical method for perinatal mammalian ovaries revealed different kinetics of oocyte apoptosis caused by DNA damage and asynapsis.
Trps1 regulates mouse zygotic genome activation and preimplantation embryo development via the PDE4D/AKT/CREB signaling pathway.
Tudor domain containing protein 5-like (Tdrd5l) identifies a novel germline body and regulates maternal RNAs during oogenesis in Drosophila.
Destabilisation of bam transcripts terminates the mitotic phase of Drosophila female germline differentiation.
Crossovers are regulated by a conserved and disordered synaptonemal complex domain.
Dynamic R-loops at centromeres ensure chromosome alignment during oocyte meiotic divisions in mice.
Mitophagy at the oocyte-to-zygote transition promotes species immortality.
Disruption of oocyte SUMOylation impacts critical regulatory processes during folliculogenesis in mice.
The conserved ATPase PCH-2 controls the number and distribution of crossovers by antagonizing their formation in Caenorhabditis elegans.
Gap junctions allow transfer of metabolites between germ cells and somatic cells to promote germ cell growth in the Drosophila ovary.
AI-based approach to dissect the variability of mouse stem cell-derived embryo models.
SMARCAD1 and TOPBP1 contribute to heterochromatin maintenance at the transition from the 2C-like to the pluripotent state.

Nature. 2025 Feb 19.

SPO11 dimers are sufficient to catalyse DNA double-strand breaks in vitro.

Cédric Oger, Corentin Claeys Bouuaert.

SPO11 initiates meiotic recombination through the induction of programmed DNA double-strand breaks (DSBs)1,2, but this catalytic activity has never been reconstituted in vitro3,4. Here, using Mus musculus SPO11, we report a biochemical system that recapitulates all the hallmarks of meiotic DSB formation. We show that SPO11 catalyses break formation in the absence of any partners and remains covalently attached to the 5' broken strands. We find that target site selection by SPO11 is influenced by the sequence, bendability and topology of the DNA substrate, and provide evidence that SPO11 can reseal single-strand DNA breaks. In addition, we show that SPO11 is monomeric in solution and that cleavage requires dimerization for the reconstitution of two hybrid active sites. SPO11 and its partner TOP6BL form a 1:1 complex that catalyses DNA cleavage with an activity similar to that of SPO11 alone. However, this complex binds DNA ends with higher affinity, suggesting a potential role after cleavage. We propose a model in which additional partners of SPO11 required for DSB formation in vivo assemble biomolecular condensates that recruit SPO11-TOP6BL, enabling dimerization and cleavage. Our work establishes SPO11 dimerization as the fundamental mechanism that controls the induction of meiotic DSBs.

DOI: https://doi.org/10.1038/s41586-024-08574-8
Nature. 2025 Feb 19.

In vitro reconstitution of meiotic DNA double-strand-break formation.

Xinzhe Tang, Zetao Hu, Jian Ding, Meixia Wu, Pin Guan, Yawei Song, Yue Yin, Wei Wu, Jinbiao Ma, Ying Huang, Ming-Han Tong.

The Spo11 complex catalyses the formation of DNA double-strand breaks (DSBs), initiating meiotic recombination-a process that is essential for fertility and genetic diversity1,2. Although the function of Spo11 has been known for 27 years, previous efforts to reconstitute DSB formation in vitro have been unsuccessful. Here we biochemically characterize the mouse SPO11-TOP6BL protein complex, and show that this complex cleaves DNA and covalently attaches to the 5' terminus of DNA breaks in vitro. Using a point-mutation strategy, we reveal that Mg2+ is essential for the DNA-cleavage activity of this complex in vitro, as confirmed by knock-in mice carrying a point mutation in SPO11 that disrupts its binding to Mg2+, thereby abolishing DSB formation. However, the activity of the SPO11 complex is ATP-independent. We also present evidence that the mouse SPO11 complex is biochemically distinct from the ancestral topoisomerase VI. Our findings establish a mechanistic framework for understanding the first steps of meiotic recombination.

DOI: https://doi.org/10.1038/s41586-024-08551-1
Sci Adv. 2025 Feb 21. 11(8): eadp5163

NAT10-mediated mRNA N4-acetylation is essential for the translational regulation during oocyte meiotic maturation in mice.

Lu Chen, Wen-Jing Wang, Shao-Yuan Liu, Rui-Bao Su, Yu-Ke Wu, Xuan Wu, Song-Ying Zhang, Jie Qiao, Qian-Qian Sha, Heng-Yu Fan.

The precise translational regulation of maternal messenger RNAs (mRNAs) drives mammalian oocyte maturation. However, the function and mechanism of posttranscriptional chemical modifications, especially the newly identified N4-acetylcytidine (ac4C) modification catalyzed by N-acetyltransferase 10 (NAT10), are unknown. In this study, we developed a low-input ac4C sequencing technology, ac4C LACE-seq, and mapped 8241 ac4C peaks at the whole-transcriptome level using 50 mouse oocytes at the germinal vesicle stage. Oocyte-specific Nat10 knockout wiped out ac4C signals in oocytes and caused severe defects in meiotic maturation and female infertility. Mechanically, Nat10 deletion led to a failure of ac4C deposition on mRNAs encoding key maternal factors, which regulate transcriptome stability and maternal-to-zygotic transition. Nat10-deleted oocytes showed decreased mRNA translation efficiency due to the direct inhibition of ac4C sites on specific transcripts during meiotic maturation. In summary, we developed a low-input, high-sensitivity mRNA ac4C profiling approach and highlighted the important physiological function of ac4C in the precise regulation of oocyte meiotic maturation by enhancing translation efficiency.

DOI: https://doi.org/10.1126/sciadv.adp5163
Development. 2025 Feb 21. pii: dev.204398. [Epub ahead of print]

Distinct requirements for PI3K isoforms p110α and p110δ for PIP3 synthesis in mouse oocytes and early embryos.

Anne Bourdais, Patricia Viard, Jenny Bormann, Côme Sesboüé, Daniel Guerrier, Nicole Therville, Julie Guillermet-Guibert, John Carroll, Guillaume Halet.

  The PI3K/Akt pathway is thought to regulate key steps of mammalian oogenesis, such as dormant oocyte awakening during follicular activation, meiotic resumption and oocyte maturation. Supporting evidence is however indirect, as oocyte PI3K activation has never been formally demonstrated, and the PI3K isoforms involved have not been revealed. Here, we employed fluorescent PIP3 biosensors to characterize PI3K dynamics in mouse oocytes and we investigated the contribution of PI3K isoform p110α via conditional genetic ablation. Prophase oocytes showed baseline PI3K/Akt activation that could be further stimulated by adding Kit ligand (KitL). Contrary to previous reports, maternal PI3K proved dispensable for oocyte maturation in vitro, yet it was required for PIP3 synthesis in early embryos. We further show that oocyte p110α is not essential for oogenesis and female fertility. Accordingly, our data suggest that KitL activates isoform p110δ for PIP3 synthesis in oocytes. In contrast, constitutive PIP3 synthesis in early embryos is achieved by maternal p110α acting redundantly with p110δ. This study highlights the relevance of PIP3 biosensors in establishing the dynamics, mechanisms and roles of maternal PI3K signaling during mammalian oogenesis.

Keywords:  AKT; Kit; Mouse; Oocyte; PI3K; PIP3

DOI:  https://doi.org/10.1242/dev.204398
Sci Adv. 2025 Feb 21. 11(8): eadr9869

Noninvasive characterization of oocyte deformability in microconstrictions.

Lucie Barbier, Rose Bulteau, Behnam Rezaei, Thomas Panier, Gaëlle Letort, Elsa Labrune, Marie-Hélène Verlhac, Franck Vernerey, Clément Campillo, Marie-Emilie Terret.

Oocytes naturally present mechanical defects that hinder their development after fertilization. Thus, in the context of assisted reproduction, oocyte selection based on their mechanical properties has great potential to improve the quality of the resulting embryos and the success rate of these procedures. However, using mechanical properties as a quantifiable selective criterion requires robust and nondestructive measurement tools. This study developed a constriction-based microfluidic device that monitors the deformation of mouse oocytes under controlled pressure. The device can distinguish mechanically aberrant oocyte groups from healthy control ones. On the basis of a mathematical model, we propose that deformability measurements infer both oocyte tension and elasticity, elasticity being the most discriminating factor in our geometry. Despite force transmission during oocyte deformation, no long-term damage was observed. This noninvasive characterization of mouse oocyte deformability in microconstrictions allows for a substantial advance in assessing the mechanical properties of mammalian oocytes and has potential application as a quantifiable selective criterion in medically assisted reproduction.

DOI: https://doi.org/10.1126/sciadv.adr9869
Histochem Cell Biol. 2025 Feb 17. 163(1): 32

A simple immunohistochemical method for perinatal mammalian ovaries revealed different kinetics of oocyte apoptosis caused by DNA damage and asynapsis.

Hiroshi Kogo, Akiko Iizuka-Kogo, Hanako Yamamoto, Maiko Ikezawa, Yukiko Tajika, Toshiyuki Matsuzaki.

  Oocytes with meiotic defects are assumed to be eliminated by apoptosis in the perinatal period. However, oocyte apoptosis caused by meiotic defects has not been well analyzed, partly because of the great technical demands of tissue sectioning perinatal ovaries. In the present study, we applied a squash method for immunohistochemical analysis of perinatal mouse ovaries as a substitute for tissue sectioning. As a result, we could show different kinetics of apoptosis caused by DMC1- and SPO11-deficiencies, indicating that DNA damage-induced apoptosis precedes asynapsis-induced apoptosis in mouse oocytes. Double-mutant analysis revealed that only asynapsis-induced apoptosis was significantly dependent on HORMAD2. The present method is simple, easy, and able to analyze a sufficient number of oocytes to detect infrequent events in a single specimen, accelerating detailed immunohistochemical analyses of mammalian ovaries during the fetal and perinatal periods.

Keywords:  Asynapsis; DNA damage; Meiotic prophase checkpoints; Oocyte apoptosis; Squash method

DOI:  https://doi.org/10.1007/s00418-025-02358-5
Cell Biol Toxicol. 2025 Feb 20. 41(1): 48

Trps1 regulates mouse zygotic genome activation and preimplantation embryo development via the PDE4D/AKT/CREB signaling pathway.

Xia Jiang, Weiwei Xu, Jiandong Sun, Jianmin Lin, Zihang Lin, Xiuli Lian, Shumin Liao, Shanshan Luo, Yue Liu, Shie Wang.

  Despite zygotic genome activation (ZGA) is crucial for early embryonic development, its regulatory mechanism is still unclear in mammals. In the present study, we demonstrate that TRPS1, a maternal factor, plays an essential role in mouse early embryogenesis by regulating the transition from 2-cell to 4-cell embryos during preimplantation development. The absence of Trps1 could leads to impaired ZGA through AKT/CREB signaling pathway. Furthermore, our findings suggest that TRPS1 may modulate the transcription of Pde4d to influence AKT and CREB phosphorylation. Interestingly, compared to Trps1 knockdown alone, co-injection of Trps1 siRNA and Pde4d mRNA significantly enhances the development rate of 4-cell embryos. Collectively, these results indicate a negative involvement of Trps1 in mouse preimplantation embryo development by targeting the PDE4D/AKT/CREB pathway to regulate ZGA.

Keywords:  AKT/CREB pathway; Phosphodiesterase 4d; Tricho-rhino-phalangeal syndrome 1; Zygotic genome activation

DOI:  https://doi.org/10.1007/s10565-025-09999-1
Genetics. 2025 Feb 21. pii: iyaf024. [Epub ahead of print]

Tudor domain containing protein 5-like (Tdrd5l) identifies a novel germline body and regulates maternal RNAs during oogenesis in Drosophila.

Caitlin Pozmanter, Leif Benner, Sydney E Kelly, Harrison Curnutte, Laura Emilfork, Mark Van Doren.

  Tudor domain-containing proteins are conserved across the animal kingdom for their function in germline development and fertility. Previously, we demonstrated that Tudor domain-containing protein 5-like (Tdrd5l) plays an important role in the germline where it promotes male identity. However, Tdrd5l is also expressed in both the ovary and testis during later stages of germline development, suggesting that it plays a role in germline differentiation in both sexes. We found that Tdrd5l localizes to a potentially novel germline body and plays a role in post-transcriptional gene regulation. Additionally, embryos laid by Tdrd5l-mutant females exhibited reduced viability and displayed dorsal appendage defects suggesting a failure of proper dorsal-ventral (D/V) patterning. As D/V patterning is dependent on gurken (grk), we examined Grk expression during oogenesis. We observed premature accumulation of Grk protein in nurse cells indicating that translation is no longer properly repressed during mRNA transport to the oocyte. We also observed increased nurse cell accumulation of the cytoplasmic polyadenylation element binding protein Oo18 RNA-Binding Protein (Orb or CPEB), a translational activator of grk. Decreasing orb function was able to partially rescue the Tdrd5l-mutant phenotype, and so defects in Orb are likely a primary cause of the defects in Tdrd5l mutants. Our data indicate that Tdrd5l is important for translational repression of maternal mRNAs such as orb, and possibly others, following their synthesis in the nurse cells and during their transport to the oocyte.

Keywords:  Drosophila; FlyBase; Tdrd5; Tdrd5l; Tudor-domain; germ cell; grk; maternal RNA; orb

DOI:  https://doi.org/10.1093/genetics/iyaf024
Development. 2025 Feb 18. pii: dev.204405. [Epub ahead of print]

Destabilisation of bam transcripts terminates the mitotic phase of Drosophila female germline differentiation.

Tamsin J Samuels, Elizabeth J Torley, Valeriia Nadmitova, Emily L Naden, Phoebe E Blair, Frankjel A Hernandez Frometa, Felipe Karam Teixeira.

  The tight control of the mitotic phase of differentiation is crucial to prevent tumourigenesis while securing tissue homeostasis. In the Drosophila female germline, differentiation involves precisely four mitotic divisions, and accumulating evidence suggests that bag-of-marbles (bam), the initiator of differentiation, is also involved in controlling the number of divisions. To test this hypothesis, we depleted Bam from differentiating cells and found a reduced number of mitotic divisions. We examined the regulation of Bam using RNA imaging methods and found that the bam 3' UTR conveys instability to the transcript in the 8-cell cyst and early 16-cell cyst. We show that the RNA binding protein, Rbp9, is responsible for timing bam mRNA decay. Rbp9 itself is part of a sequential cascade of RNA binding proteins activated downstream of Bam, and we show that it is regulated through a change in transcription start site, driven by Rbfox1. Altogether, we propose a model in which Bam expression at the dawn of differentiation initiates a series of events that eventually terminates the Bam expression domain.

Keywords:  Drosophila; Germline; Post-transcriptional regulation; RNA stability; Stem cells

DOI:  https://doi.org/10.1242/dev.204405
Nucleic Acids Res. 2025 Feb 08. pii: gkaf095. [Epub ahead of print]53(4):

Crossovers are regulated by a conserved and disordered synaptonemal complex domain.

Ana Rita Rodrigues Neves, Ivana Čavka, Tobias Rausch, Simone Köhler.

During meiosis, the number and distribution of crossovers (COs) must be precisely regulated through CO assurance and interference to prevent chromosome missegregation and genomic instability in the progeny. Here we show that this regulation of COs depends on a disordered and conserved domain within the synaptonemal complex (SC). This domain is located at the C-terminus of the central element protein SYP-4 in Caenorhabditis elegans. While not necessary for synapsis, the C-terminus of SYP-4 is crucial for both CO assurance and interference. Although the SYP-4 C-terminus contains many potential phosphorylation sites, we found that phosphorylation is not the primary regulator of CO events. Instead, we discovered that nine conserved phenylalanines are required to recruit a pro-CO factor predicted to be an E3 ligase and regulate the physical properties of the SC. We propose that this conserved and disordered domain plays a crucial role in maintaining the SC in a state that allows transmitting signals to regulate CO formation. While the underlying mechanisms remain to be fully understood, our findings align with existing models suggesting that the SC plays a critical role in determining the number and distribution of COs along chromosomes, thereby safeguarding the genome for future generations.

DOI: https://doi.org/10.1093/nar/gkaf095
Sci Bull (Beijing). 2025 Feb 13. pii: S2095-9273(25)00168-9. [Epub ahead of print]

Dynamic R-loops at centromeres ensure chromosome alignment during oocyte meiotic divisions in mice.

Yinghong Chen, Liying Wang, Qiuxing Zhou, Wei Wei, Huafang Wei, Yanjie Ma, Tingting Han, Shuang Ma, Xiaoming Huang, Meijia Zhang, Fei Gao, Chao Liu, Wei Li.

  R-loops play various roles in many physiological processes, however, their role in meiotic division remains largely unknown. Here we show that R-loops and their regulator RNase H1 are present at centromeres during oocyte meiotic divisions. Proper centromeric R-loops are essential to ensure chromosome alignment in oocytes during metaphase I (MI). Remarkably, both Rnaseh1 knockout and overexpression in oocytes lead to severe spindle assembly defects and chromosome misalignment due to dysregulation of R-loops at centromeres. Furthermore, we find that replication protein A (RPA) is recruited to centromeric R-loops, facilitating the deposition of ataxia telangiectasia-mutated and Rad3-related (ATR) kinase at centromeres by interacting with the ATR-interaction protein (ATRIP). The ATR kinase deposition triggers the activity of CHK1, stimulating the phosphorylation of Aurora B to finally promote proper spindle assembly and chromosome alignment at the equatorial plate. Most importantly, the application of ATR, CHK1, and Aurora B inhibitors could efficiently rescue the defects in spindle assembly and chromosome alignment due to RNase H1 deficiency in oocytes. Overall, our findings uncover a critical role of R-loops during mouse oocyte meiotic divisions, suggesting that dysregulation of R-loops may be associated with female infertility. Additionally, ATR, CHK1, and Aurora B inhibitors may potentially be used to treat some infertile patients.

Keywords:  Centromeres; Oocyte meiotic divisions; R-loops; RNase H1

DOI:  https://doi.org/10.1016/j.scib.2025.02.009
bioRxiv. 2025 Feb 03. pii: 2025.02.01.636045. [Epub ahead of print]

Mitophagy at the oocyte-to-zygote transition promotes species immortality.

Siddharthan Balachandar Thendral, Sasha Bacot, Katherine S Morton, Qiuyi Chi, Isabel W Kenny-Ganzert, Joel N Meyer, David R Sherwood.

The quality of inherited mitochondria determines embryonic viability 1 , metabolic health during adulthood and future generation endurance. The oocyte is the source of all zygotic mitochondria 2 , and mitochondrial health is under strict developmental regulation during early oogenesis 3-5 . Yet, fully developed oocytes exhibit the presence of deleterious mitochondrial DNA (mtDNA) 6,7 and mitochondrial dysfunction from high levels of endogenous reactive oxygen species 8 and exogenous toxicants 9 . How fully developed oocytes prevent transmission of damaged mitochondria to the zygotes is unknown. Here we discover that the onset of oocyte-to-zygote transition (OZT) developmentally triggers a robust and rapid mitophagy event that we term mitophagy at OZT (MOZT). We show that MOZT requires mitochondrial fragmentation, activation of the macroautophagy system and the mitophagy receptor FUNDC1, but not the prevalent mitophagy factors PINK1 and BNIP3. Oocytes upregulate expression of FUNDC1 in response to diverse mitochondrial insults, including mtDNA mutations and damage, uncoupling stress, and mitochondrial dysfunction, thereby promoting selection against damaged mitochondria. Loss of MOZT leads to increased inheritance of deleterious mtDNA and impaired bioenergetic health in the progeny, resulting in diminished embryonic viability and the extinction of descendent populations. Our findings reveal FUNDC1-mediated MOZT as a mechanism that preserves mitochondrial health during the mother-to-offspring transmission and promotes species continuity. These results may explain how mature oocytes from many species harboring mutant mtDNA give rise to healthy embryos with reduced deleterious mtDNA.

DOI: https://doi.org/10.1101/2025.02.01.636045
Biol Reprod. 2025 Feb 21. pii: ioaf035. [Epub ahead of print]

Disruption of oocyte SUMOylation impacts critical regulatory processes during folliculogenesis in mice.

Zian Liao, Tessa E Steenwinkel, Bruno Moscoso, Ernesto Salas, Bethany K Patton, Amanda Rodriguez, Anna Malovannaya, Stephanie A Pangas.

  The conjugation of small ubiquitin-like modifiers (SUMO) to target proteins, known as SUMOylation, plays a crucial role in regulating protein homeostasis, activity, interaction with other proteins, and subcellular localization. Loss of SUMOylation in non-growing oocytes by conditional deletion of the E2 sumo conjugating enzyme, Ube2i, at the primordial follicle stage leads to female sterility due to complex changes in oocyte development, including altered folliculogenesis, defective meiotic progression, and premature loss of the ovarian reserve. In this study, proteomics was used to compare control and Ube2i conditional knockout ovaries during the first wave of folliculogenesis to identify key differences that may drive the premature follicle loss phenotype. Data are available via ProteomeXchange with identifier PXD055913. Label-free mass spectrometry results showed that 238 proteins were significantly altered more than 2-fold (P < 0.05). Proteins upregulated in the Ube2i conditional knockout ovaries included those involved in mRNA splicing and WNT signaling, while those downregulated were related to metabolism, mitochondria, and the maternal effect proteins NLRP2 and NLRP9B. The majority of differentially expressed proteins showed no change by transcriptome analysis, indicating protein level regulation and revealing potential SUMOylation targets with necessary roles in oocyte and follicle development.

Keywords:  folliculogenesis; infertility; ovary; post-translational protein modification; proteomics; sumoylation

DOI:  https://doi.org/10.1093/biolre/ioaf035
Elife. 2025 Feb 18. pii: RP102409. [Epub ahead of print]13

The conserved ATPase PCH-2 controls the number and distribution of crossovers by antagonizing their formation in Caenorhabditis elegans.

Bhumil Patel, Maryke Grobler, Alberto Herrera, Elias Logari, Valery Ortiz, Needhi Bhalla.

  Meiotic crossover recombination is essential for both accurate chromosome segregation and the generation of new haplotypes for natural selection to act upon. This requirement is known as crossover assurance and is one example of crossover control. While the conserved role of the ATPase, PCH-2, during meiotic prophase has been enigmatic, a universal phenotype when pch-2 or its orthologs are mutated is a change in the number and distribution of meiotic crossovers. Here, we show that PCH-2 controls the number and distribution of crossovers by antagonizing their formation. This antagonism produces different effects at different stages of meiotic prophase: early in meiotic prophase, PCH-2 prevents double-strand breaks from becoming crossover-eligible intermediates, limiting crossover formation at sites of initial double-strand break formation and homolog interactions. Later in meiotic prophase, PCH-2 winnows the number of crossover-eligible intermediates, contributing to the designation of crossovers and ultimately, crossover assurance. We also demonstrate that PCH-2 accomplishes this regulation through the meiotic HORMAD, HIM-3. Our data strongly support a model in which PCH-2's conserved role is to remodel meiotic HORMADs throughout meiotic prophase to destabilize crossover-eligible precursors and coordinate meiotic recombination with synapsis, ensuring the progressive implementation of meiotic recombination and explaining its function in the pachytene checkpoint and crossover control.

Keywords:  C. elegans; cell biology; checkpoint; chromosomes; crossover; gene expression; meiosis; recombination; synapsis; synaptonemal complex

DOI:  https://doi.org/10.7554/eLife.102409
PLoS Biol. 2025 Feb 18. 23(2): e3003045

Gap junctions allow transfer of metabolites between germ cells and somatic cells to promote germ cell growth in the Drosophila ovary.

Caroline Vachias, Camille Tourlonias, Louis Grelée, Nathalie Gueguen, Yoan Renaud, Parvathy Venugopal, Graziella Richard, Pierre Pouchin, Emilie Brasset, Vincent Mirouse.

Gap junctions allow the exchange of small molecules between cells. How this function could be used to promote cell growth is not yet fully understood. During Drosophila ovarian follicle development, germ cells, which are surrounded by epithelial somatic cells, undergo massive growth. We found that this growth depends on gap junctions between these cell populations, with a requirement for Innexin4 and Innexin2, in the germ cells and the somatic cells, respectively. Translatomic analyses revealed that somatic cells express enzymes and transporters involved in amino acid metabolism that are absent in germ cells. Among them, we identified a putative amino acid transporter required for germline growth. Its ectopic expression in the germline can partially compensate for its absence or the one of Innexin2 in somatic cells. Moreover, affecting either gap junctions or the import of some amino acids in somatic cells induces P-bodies in the germ cells, a feature usually associated with an arrest of translation. Finally, in somatic cells, innexin2 expression and gap junction assembly are regulated by the insulin receptor/PI3K kinase pathway, linking the growth of the two tissues. Overall, these results support the view that metabolic transfer through gap junction promotes cell growth and illustrate how such a mechanism can be integrated into a developmental program, coupling growth control by extrinsic systemic signals with the intrinsic coordination between cell populations.

DOI: https://doi.org/10.1371/journal.pbio.3003045
Nat Commun. 2025 Feb 19. 16(1): 1772

AI-based approach to dissect the variability of mouse stem cell-derived embryo models.

Paolo Caldarelli, Luca Deininger, Shi Zhao, Pallavi Panda, Changhuei Yang, Ralf Mikut, Magdalena Zernicka-Goetz.

Recent advances in stem cell-derived embryo models have transformed developmental biology, offering insights into embryogenesis without the constraints of natural embryos. However, variability in their development challenges research standardization. To address this, we use deep learning to enhance the reproducibility of selecting stem cell-derived embryo models. Through live imaging and AI-based models, we classify 900 mouse post-implantation stem cell-derived embryo-like structures (ETiX-embryos) into normal and abnormal categories. Our best-performing model achieves 88% accuracy at 90 h post-cell seeding and 65% accuracy at the initial cell-seeding stage, forecasting developmental trajectories. Our analysis reveals that normally developed ETiX-embryos have higher cell counts and distinct morphological features such as larger size and more compact shape. Perturbation experiments increasing initial cell numbers further supported this finding by improving normal development outcomes. This study demonstrates deep learning's utility in improving embryo model selection and reveals critical features of ETiX-embryo self-organization, advancing consistency in this evolving field.

DOI: https://doi.org/10.1038/s41467-025-56908-5
Elife. 2025 Feb 19. pii: RP87742. [Epub ahead of print]12

SMARCAD1 and TOPBP1 contribute to heterochromatin maintenance at the transition from the 2C-like to the pluripotent state.

Ruben Sebastian-Perez, Shoma Nakagawa, Xiaochuan Tu, Sergi Aranda, Martina Pesaresi, Pablo Aurelio Gomez-Garcia, Marc Alcoverro-Bertran, Jose Luis Gomez-Vazquez, Davide Carnevali, Eva Borràs, Eduard Sabidó, Laura Martin, Malka Nissim-Rafinia, Eran Meshorer, Maria Victoria Neguembor, Luciano Di Croce, Maria Pia Cosma.

  Chromocenters are established after the 2-cell (2C) stage during mouse embryonic development, but the factors that mediate chromocenter formation remain largely unknown. To identify regulators of 2C heterochromatin establishment in mice, we generated an inducible system to convert embryonic stem cells (ESCs) to 2C-like cells. This conversion is marked by a global reorganization and dispersion of H3K9me3-heterochromatin foci, which are then reversibly formed upon re-entry into pluripotency. By profiling the chromatin-bound proteome (chromatome) through genome capture of ESCs transitioning to 2C-like cells, we uncover chromatin regulators involved in de novo heterochromatin formation. We identified TOPBP1 and investigated its binding partner SMARCAD1. SMARCAD1 and TOPBP1 associate with H3K9me3-heterochromatin in ESCs. Interestingly, the nuclear localization of SMARCAD1 is lost in 2C-like cells. SMARCAD1 or TOPBP1 depletion in mouse embryos leads to developmental arrest, reduction of H3K9me3, and remodeling of heterochromatin foci. Collectively, our findings contribute to comprehending the maintenance of chromocenters during early development.

Keywords:  2C-like cells; chromatin; developmental biology; embryonic stem cells; mouse; proteomics; regenerative medicine; stem cells

DOI:  https://doi.org/10.7554/eLife.87742