bims-cebooc 2025-01-12 papers

bims-cebooc

Biomed News

on Cell biology of oocytes

Issue of 2025–01–12
twelve papers selected by
Gabriele Zaffagnini, Universität zu Köln

Satellite DNA shapes dictate pericentromere packaging in female meiosis.
ERK activation dynamics in maturing oocyte controls embryonic nuclear divisions in Caenorhabditis elegans.
Spatially ordered zygotic genome activation fulfills embryo quality control.
Extended Live Imaging of Female Drosophila melanogaster Germline Stem Cell Niches.
Animal and vegetal materials of mouse oocytes segregate at first zygotic cleavage: a simple mechanism that makes the 2-cell blastomeres differ reciprocally from the start.
SUMO-mediated regulation of H3K4me3 reader SET-26 controls germline development in C. elegans.
Nup107 contributes to the maternal to zygotic transition by preventing the premature nuclear export of pri-miRNA 427.
Deletion of ddx4 Ovary-Specific Transcript Causes Dysfunction of Meiosis and Derepress of DNA Transposons in Zebrafish Ovaries.
Distinct and interdependent functions of three RING proteins regulate recombination during mammalian meiosis.
Genetic gradual reduction of OGT activity unveils the essential role of O-GlcNAc in the mouse embryo.
ZAR1/2-Regulated Epigenetic Modifications are Essential for Age-Associated Oocyte Quality Maintenance and Zygotic Activation.
Oversized cells activate global proteasome-mediated protein degradation to maintain cell size homeostasis.

Nature. 2025 Jan 08.

Satellite DNA shapes dictate pericentromere packaging in female meiosis.

Damian Dudka, Jennine M Dawicki-McKenna, Xueqi Sun, Keagan Beeravolu, Takashi Akera, Michael A Lampson, Ben E Black.

The abundance and sequence of satellite DNA at and around centromeres is evolving rapidly despite the highly conserved and essential process through which the centromere directs chromosome inheritance1-3. The impact of such rapid evolution is unclear. Here we find that sequence-dependent DNA shape dictates packaging of pericentromeric satellites in female meiosis through a conserved DNA-shape-recognizing chromatin architectural protein, high mobility group AT-hook 1 (HMGA1)4,5. Pericentromeric heterochromatin in two closely related mouse species, M. musculus and M. spretus, forms on divergent satellites that differ by both density of narrow DNA minor grooves and HMGA1 recruitment. HMGA1 binds preferentially to M. musculus satellites, and depletion in M. musculus oocytes causes massive stretching of pericentromeric satellites, disruption of kinetochore organization and delays in bipolar spindle assembly. In M. musculus × spretus hybrid oocytes, HMGA1 depletion disproportionately impairs M. musculus pericentromeres and microtubule attachment to their kinetochores. Thus, DNA shape affects both pericentromere packaging and the segregation machinery. We propose that rapid evolution of centromere and pericentromere DNA does not disrupt these essential processes when the satellites adopt DNA shapes recognized by conserved architectural proteins (such as HMGA1). By packaging these satellites, architectural proteins become part of the centromeric and pericentromeric chromatin, suggesting an evolutionary strategy that lowers the cost of megabase-scale satellite expansion.

DOI: https://doi.org/10.1038/s41586-024-08374-0
Cell Rep. 2025 Jan 09. pii: S2211-1247(24)01508-0. [Epub ahead of print]44(1): 115157

ERK activation dynamics in maturing oocyte controls embryonic nuclear divisions in Caenorhabditis elegans.

Han Bit Baek, Debabrata Das, Shin-Yu Chen, Hongyuan Li, Swathi Arur.

  ERK activity oscillates between sustained activation during oocyte formation and transient inactivation during oocyte maturation, fertilization, and early embryogenesis. Consequences of ectopic ERK activity upon oocyte maturation and in early embryogenesis are unknown. We show, in Caenorhabditis elegans, that ectopic ERK activity upon oocyte maturation (metaphase I oocytes) results in embryos with abnormalities in nuclear divisions leading to embryonic death. We uncover that ERK directly phosphorylates Polo-like kinase I (PLK-1), on Serine 404, to inhibit nuclear envelope breakdown (NEBD) in early embryogenesis. The RAS/ERK/PLK-1 pathway poisons zygotic NEBD and inhibits the merging of parental genomes, underlining the importance of turning off ERK prior to embryogenesis. Given the conserved nature of both ERK signaling to oocyte development and PLK1 to embryonic divisions, this work has implications for women undergoing in vitro fertilization (IVF) where ectopic ERK activation during superovulation through hormonal stimulation may diminish oocyte quality and influence zygotic development.

Keywords:  C. elegans; CP: Cell biology; CP: Developmental biology; ERK signaling; NEBD; PLK-1; RASopathies; early embryo; meiosis I; oocyte fertilization; oocyte maturation; oocyte-to-embryo transition

DOI:  https://doi.org/10.1016/j.celrep.2024.115157
bioRxiv. 2025 Jan 02. pii: 2024.12.22.629969. [Epub ahead of print]

Spatially ordered zygotic genome activation fulfills embryo quality control.

Wenchao Qian, Hui Chen, Hongju Lee, Matthew C Good.

Early embryo development features autonomous, maternally-driven cell divisions that self- organize the multicellular blastula or blastocyst tissue. Maternal control cedes to the zygote starting with the onset of widespread zygotic genome activation (ZGA), which is essential for subsequent cell fate determination and morphogenesis. Intriguingly, although the onset of ZGA is highly regulated at the level of an embryo, it can be non-homogenous and precisely patterned at the single-cell level. We previously demonstrated a stereotyped spatial and temporal ordering of ZGA in a model vertebrate embryo. Unknown, however, was whether this precise ZGA patterning was required for development. To address this fundamental question, we devised a strategy to spatially control cell divisions in the embryo that perturb blastula embryo organization. We demonstrate the feasibility of spatially inverting the cell size pattern of embryos and find that these inverted embryos undergo a flipped pattern of ZGA. Mispatterned ZGA along the animal-vegetal axis causes embryo apoptosis, revealing that gastrula embryos have a built-in quality control system to sense inappropriate ZGA patterning, including regional defects in transcriptional onset. The quality control response is non-autonomous which may depend on anti-apoptotic signals that repress cell death outside of the animal hemisphere. These results reveal the requirement of properly patterned ZGA for normal development and the existence of an embryo quality control response exquisitely tuned to the spatial and temporal ordering of genome activation and zygotic gene expression.

DOI: https://doi.org/10.1101/2024.12.22.629969
J Vis Exp. 2024 Dec 20.

Extended Live Imaging of Female Drosophila melanogaster Germline Stem Cell Niches.

Helena Sánchez-Gómez, Juan Garrido-Maraver, Patricia Rojas-Ríos.

Live imaging methods allow the analysis of dynamic cellular processes in detail and in real-time. The Drosophila ovary represents an excellent model to explore the dynamics of a myriad of developmental processes, such as cell division, stemness, differentiation, migration, apoptosis, autophagy, cellular adhesion, etc., over time. Recently, we have implemented an extended ex vivo culture and live imaging of the female Drosophila GSC niche. Using a Drosophila line harboring a GFP::Par-1 transgene as an example, this method allows the visualization of the GSCs' asymmetric division within their niche and the description of the changes in the spectrosome morphology along the cell cycle. Here, we present a detailed protocol for the ex vivo culture of Drosophila germaria, enabling prolonged visualization of the female GSC niche. Importantly, this protocol is broadly applicable to live imaging GSCs with multiple fluorescently tagged proteins of interest that are available in stock centers and/or in the Drosophila research community.

DOI: https://doi.org/10.3791/67389
Mol Hum Reprod. 2024 Dec 30. pii: gaae045. [Epub ahead of print]

Animal and vegetal materials of mouse oocytes segregate at first zygotic cleavage: a simple mechanism that makes the 2-cell blastomeres differ reciprocally from the start.

Thomas Nolte, Reza Halabian, Steffen Israel, Yutaka Suzuki, Roberto A Avelar, Daniel Palmer, Georg Fuellen, Wojciech Makalowski, Michele Boiani.

  Recent advances in embryology have shown that the sister blastomeres of 2-cell mouse and human embryos differ reciprocally in potency. An open question is whether the blastomeres became different as opposed to originating as different. Here we wanted to test two conflicting models: one proposing that each blastomere contains both animal and vegetal materials in balanced proportions because the plane of first cleavage runs close to the animal-vegetal axis of the fertilized oocyte; and the other model proposing that each blastomere contains variable proportions of animal and vegetal materials because the plane of the first cleavage can vary depending on the topology of fertilization. Therefore, we imposed the fertilization site in three distinct regions of mouse oocytes (animal pole, vegetal pole, equator) via intracytoplasmic sperm injection (ICSI). After the first zygotic cleavage, the sister blastomeres were dissociated and subjected to single-cell transcriptome analysis, keeping track of the original pair associations. Non-supervised hierarchical clustering revealed that the frequency of correct pair matches varied with the fertilization site (vegetal pole > animal pole > equator), thereby, confuting the first model of balanced partitioning. However, the inter-blastomere differences had similar signatures of gene ontology across the three groups, thereby, also confuting the competing model of variable partitioning. These conflicting observations could be reconciled if animal and vegetal materials segregated at the first cleavage: an event considered improbable and possibly deleterious in mammals. We tested this occurrence by keeping the fertilized oocytes immobilized from the time of ICSI until the first cleavage. Image analysis revealed that cleavage took place preferentially along the short (ie equatorial) diameter of the oocyte, thereby partitioning the animal and vegetal materials into the 2-cell blastomeres. Our results point to a simple mechanism by which the two sister blastomeres start out as different, rather than becoming different.

Keywords:  ICSI; animal model; blastomere; embryo development; fertilization; gene expression; oocyte

DOI:  https://doi.org/10.1093/molehr/gaae045
PLoS Biol. 2025 Jan;23(1): e3002980

SUMO-mediated regulation of H3K4me3 reader SET-26 controls germline development in C. elegans.

Cátia A Carvalho, Ulrike Bening Abu-Shach, Asha Raju, Zlata Vershinin, Dan Levy, Mike Boxem, Limor Broday.

Sumoylation is a posttranslational modification essential for multiple cellular functions in eukaryotes. ULP-2 is a conserved SUMO protease required for embryonic development in Caenorhabditis elegans. Here, we revealed that ULP-2 controls germline development by regulating the PHD-SET domain protein, SET-26. Specifically, loss of ULP-2 results in sterility and a progressive elevation of global protein sumoylation. In the germline of ulp-2 null mutant, meiosis is arrested at the diplotene stage and the cells in the proximal germline acquire a somatic fate. Germline RNAseq analysis revealed the down-regulation of numerous germline genes in ulp-2 mutants, whereas somatic gene expression is up-regulated. To determine the key factors that are regulated by ULP-2, we performed a yeast two-hybrid screen and identified the histone methylation reader, SET-26 as a ULP-2 interacting protein. Loss of SET-26 enhanced the sterility of ulp-2 mutant animals. Consistently, SET-26 is sumoylated and its sumoylation levels are regulated by ULP-2. Moreover, we detected a reduction in H3K4 tri-methylation (H3K4me3) histone levels bound to SET-26 in the ulp-2 mutant background suggesting a dependence of this histone reader on balanced sumoylation. Finally, a comparative proteomics screen between WT and ulp-2 loss of activity identified the predicted methyltransferase SET-27 as a ULP-2-dependent SET-26-associated protein. SET-27 knockout genetically interacts with ULP-2 in the germline, but not with SET-26. Taken together, we revealed a SUMO protease/H3K4me3 histone reader axis which is required for the maintenance and regulation of germline development.

DOI: https://doi.org/10.1371/journal.pbio.3002980
Development. 2025 Jan 10. pii: dev.202865. [Epub ahead of print]

Nup107 contributes to the maternal to zygotic transition by preventing the premature nuclear export of pri-miRNA 427.

Valentyna Kostiuk, Rakib Kabir, Kaitlin Levangie, Stefany Empke, Kimberly Morgan, Nick D L Owens, C Patrick Lusk, Mustafa K Khokha.

  Emerging evidence suggests that the nuclear pore complex can have unique compositions and distinct nucleoporin functions in different cells. Here, we show that Nup107, a key component of the NPC scaffold, varies in expression over development: it is expressed at higher levels in the blastula compared to the gastrula suggesting a critical role prior to gastrulation. We find depletion of Nup107 affects the differentiation of the early germ layers leading to an expansion of the ectoderm at the expense of endoderm and mesoderm. By analyzing an RNAseq time course, we observed that depletion of Nup107 affects the maternal-zygotic transition by delaying the degradation of maternal transcripts that occurs as zygotic transcription begins. The transcripts are enriched in miR427 recognition sites, a conserved microRNA that destabilizes maternal transcripts including REST, which encodes a Kruppel-type zinc finger transcription factor that we demonstrate is critical for ectodermal cell fates. Mechanistically, we show that Nup107 is required to prevent the premature export of pri-miR427 transcript before processing. Nup107 depletion leads to the reduced production of mature miR427 and maternal transcript stabilization. We conclude that high levels of Nup107 in the early embryo are critical for the nuclear retention and subsequent processing of pri-miR427 transcripts that is required for timely maternal RNA clearance to enable gastrulation.

Keywords:  Germ layers patterning; Maternal to zygotic transition; MiR427; MicroRNA; Nuclear transport; Nucleoporins

DOI:  https://doi.org/10.1242/dev.202865
Biology (Basel). 2024 Dec 16. pii: 1055. [Epub ahead of print]13(12):

Deletion of ddx4 Ovary-Specific Transcript Causes Dysfunction of Meiosis and Derepress of DNA Transposons in Zebrafish Ovaries.

Yuanyuan Chen, Xing Lin, Jing Dai, Yifan Bai, Fei Liu, Daji Luo.

  Alternative splicing of ddx4 (DEAD-box helicase 4), a key germline marker gene, has been reported to generate sex-specific transcripts in zebrafish gonads. The biological functions and regulatory mechanisms of the ddx4 ovary-specific transcript (ddx4-L) during oogenesis remain unclear. In this study, we found that ddx4-L mutants, in which ddx4-L was specifically deleted, had enlarged ovaries but laid fewer eggs, along with having a lower fertilization rate compared to WT controls. RNA-seq analysis was performed to detect the changes in gene expression between WT and ddx4-L mutant ovaries. A total of 524 upregulated and 610 downregulated DEGs were identified. GO and GSEA enrichment analyses showed that genes involved in fertilization and reproduction biological processes were significantly downregulated. More specifically, we observed a remarkable reduction in Sycp1, a core component of synaptonemal complex, in ddx4-L mutant ovaries at both the mRNA and protein levels. In addition, the expressions of transposon elements, as well as the events of alternative splicing, alternative polyadenylation, and RNA editing, were analyzed based on the RNA-seq data. We found that the deletion of ddx4-L resulted in derepression of DNA transposons in zebrafish ovaries, possibly causing genome instability. In conclusion, our work demonstrates that the ovary-specific ddx4 transcript plays important roles in oocyte meiosis and DNA transposon repression, which extends our understanding of the biological functions and regulatory mechanisms of sex-specific alternative splicing in zebrafish oogenesis and reproduction.

Keywords:  ddx4 (vasa); meiosis; ovary; transposon repression; zebrafish

DOI:  https://doi.org/10.3390/biology13121055
Proc Natl Acad Sci U S A. 2025 Jan 14. 122(2): e2412961121

Distinct and interdependent functions of three RING proteins regulate recombination during mammalian meiosis.

Masaru Ito, Yan Yun, Dhananjaya S Kulkarni, Sunkyung Lee, Sumit Sandhu, Briana Nuñez, Linya Hu, Kevin Lee, Nelly Lim, Rachel M Hirota, Rowan Prendergast, Cynthia Huang, Ivy Huang, Neil Hunter.

  During meiosis, each pair of homologous chromosomes becomes connected by at least one crossover, as required for accurate segregation, and adjacent crossovers are widely separated thereby limiting total numbers. In coarsening models, this crossover patterning results from nascent recombination sites competing to accrue a limiting pro-crossover RING-domain protein (COR) that diffuses between synapsed chromosomes. Here, we delineate the localization dynamics of three mammalian CORs in the mouse and determine their interdependencies. RNF212, HEI10, and the newest member RNF212B show divergent spatiotemporal dynamics along synapsed chromosomes, including profound differences in spermatocytes and oocytes, that are not easily reconciled by elementary coarsening models. Contrasting mutant phenotypes and genetic requirements indicate that RNF212B, RNF212, and HEI10 play distinct but interdependent functions in regulating meiotic recombination and coordinating the events of meiotic prophase-I by integrating signals from DNA breaks, homolog synapsis, the cell-cycle, and incipient crossover sites.

Keywords:  crossover; gamete; meiosis; reproduction; ubiquitin

DOI:  https://doi.org/10.1073/pnas.2412961121
PLoS Genet. 2025 Jan;21(1): e1011507

Genetic gradual reduction of OGT activity unveils the essential role of O-GlcNAc in the mouse embryo.

Sara Formichetti, Agnieszka Sadowska, Michela Ascolani, Julia Hansen, Kerstin Ganter, Christophe Lancrin, Neil Humphreys, Mathieu Boulard.

The reversible glycosylation of nuclear and cytoplasmic proteins (O-GlcNAcylation) is catalyzed by a single enzyme, namely O-GlcNAc transferase (OGT). The mammalian Ogt gene is X-linked, and it is essential for embryonic development and for the viability of proliferating cells. We perturbed OGT's function in vivo by creating a murine allelic series of four single amino acid substitutions, reducing OGT's catalytic activity to a range of degrees. The severity of the embryonic lethality was proportional to the extent of impairment of OGT's catalysis, demonstrating that the O-GlcNAc modification itself is required for early development. We identified hypomorphic Ogt alleles that perturb O-GlcNAc homeostasis while being compatible with embryogenesis. The analysis of the transcriptomes of the mutant embryos at different developmental stages suggested a sexually-dimorphic developmental delay caused by the decrease in O-GlcNAc. Furthermore, a mild reduction of OGT's enzymatic activity was sufficient to loosen the silencing of endogenous retroviruses in vivo.

DOI: https://doi.org/10.1371/journal.pgen.1011507
Adv Sci (Weinh). 2025 Jan 04. e2410305

ZAR1/2-Regulated Epigenetic Modifications are Essential for Age-Associated Oocyte Quality Maintenance and Zygotic Activation.

Yan Rong, Yu-Ke Wu, Yingyan Chen, Qing Liu, Leilei Ai, Yun-Wen Wu, Yezhang Zhu, Yin-Li Zhang, Chengkan Liu, Yerong Ma, Xiaomei Tong, Jiamin Jin, Xiaoxuan Li, Yan Zhou, Shu-Yan Ji, Songying Zhang, Heng-Yu Fan.

  The developmental competence and epigenetic progression of oocytes gradually become dysregulated with increasing maternal age. However, the mechanisms underlying age-related epigenetic regulation in oocytes remain poorly understood. Zygote arrest proteins 1 and 2 (ZAR1/2) are two maternal factors with partially redundant roles in maintaining oocyte quality, mainly known by regulating mRNA stability. In addition to this known function, it is found that ZAR1/2 is required for oocyte epigenetic maturation and zygotic reprogramming. Zar1/2-deleted oocytes exhibited reduced levels of multiple histone modifications and of the expression of corresponding histone modifiers, along with over-condensed chromatin, leading to compromised minor zygotic genome activation and deficient embryo development following fertilization. Cytoplasmic ZAR1/2 participated in intranuclear epigenetic maturation by binding the transcripts encoding histone modifiers and regulating their stability and translational activity. Moreover, oocytes from aged mice exhibited similar histone-modification deficiencies as the Zar1/2-deleted oocytes. ZAR1/2 mRNA and protein levels are downregulated in oocytes from mice and women with advanced ages, suggesting ZAR1/2 as regulators of epigenetic changes with reproductive aging. This study presents a new nucleo-cytoplasmic interaction mechanism that is involved in preventing oocyte epigenetic aging. Further, ZAR1/2 represents potential gene targets for diagnosis and clinical interventions in age-associated deficiencies in oocyte and embryo development.

Keywords:  histone modifications; maternal factor; oocyte epigenetic maturation; oocyte‐to‐embryo transition; reproductive aging

DOI:  https://doi.org/10.1002/advs.202410305
Elife. 2025 Jan 10. pii: e75393. [Epub ahead of print]14

Oversized cells activate global proteasome-mediated protein degradation to maintain cell size homeostasis.

Shixuan Liu, Ceryl Tan, Chloe Melo-Gavin, Miriam B Ginzberg, Ron Blutrich, Nish Patel, Michael Rape, Kevin G Mark, Ran Kafri.

  Proliferating animal cells maintain a stable size distribution over generations despite fluctuations in cell growth and division size. Previously, we showed that cell size control involves both cell size checkpoints, which delay cell cycle progression in small cells, and size-dependent regulation of mass accumulation rates (Ginzberg et al., 2018). While we previously identified the p38 MAPK pathway as a key regulator of the mammalian cell size checkpoint (S. Liu et al., 2018), the mechanism of size-dependent growth rate regulation has remained elusive. Here, we quantified global rates of protein synthesis and degradation in cells of varying sizes, both under unperturbed conditions and in response to perturbations that trigger size-dependent compensatory growth slowdown. We found that protein synthesis rates scale proportionally with cell size across cell cycle stages and experimental conditions. In contrast, oversized cells that undergo compensatory growth slowdown exhibit a superlinear increase in proteasome-mediated protein degradation, with accelerated protein turnover per unit mass, suggesting activation of the proteasomal degradation pathway. Both nascent and long-lived proteins contribute to the elevated protein degradation during compensatory growth slowdown, with long-lived proteins playing a crucial role at the G1/S transition. Notably, large G1/S cells exhibit particularly high efficiency in protein degradation, surpassing that of similarly sized or larger cells in S and G2, coinciding with the timing of the most stringent size control in animal cells. These results collectively suggest that oversized cells reduce their growth efficiency by activating global proteasome-mediated protein degradation to promote cell size homeostasis.

Keywords:  cell biology; human

DOI:  https://doi.org/10.7554/eLife.75393