bims-cebooc 2025-05-18 papers

Issue of 2025–05–18
nine papers selected by
Gabriele Zaffagnini, Universität zu Köln

Nature. 2025 May 14.

Divergent DNA methylation dynamics in marsupial and eutherian embryos.

Bryony J Leeke, Wazeer Varsally, Sugako Ogushi, Jasmin Zohren, Sergio Menchero, Aurélien Courtois, Daniel M Snell, Aurélie Teissandier, Obah Ojarikre, Shantha K Mahadevaiah, Fanny Decarpentrie, Rebecca J Oakey, John L VandeBerg, James M A Turner.

Based on seminal work in placental species (eutherians)1-10, a paradigm of mammalian development has emerged wherein the genome-wide erasure of parental DNA methylation is required for embryogenesis. Whether such DNA methylation reprogramming is, in fact, conserved in other mammals is unknown. Here, to resolve this point, we generated base-resolution DNA methylation maps in gametes, embryos and adult tissues of a marsupial, the opossum Monodelphis domestica, revealing variations from the eutherian-derived model. The difference in DNA methylation level between oocytes and sperm is less pronounced than that in eutherians. Furthermore, unlike the genome of eutherians, that of the opossum remains hypermethylated during the cleavage stages. In the blastocyst, DNA demethylation is transient and modest in the epiblast. However, it is sustained in the trophectoderm, suggesting an evolutionarily conserved function for DNA hypomethylation in the mammalian placenta. Furthermore, unlike that in eutherians, the inactive X chromosome becomes globally DNA hypomethylated during embryogenesis. We identify gamete differentially methylated regions that exhibit distinct fates in the embryo, with some transient, and others retained and that represent candidate imprinted loci. We also reveal a possible mechanism for imprinted X inactivation, through maternal DNA methylation of the Xist-like noncoding RNA RSX11. We conclude that the evolutionarily divergent eutherians and marsupials use DNA demethylation differently during embryogenesis.

DOI: https://doi.org/10.1038/s41586-025-08992-2

Nature. 2025 May 14.

Marsupial embryos lack the epigenetic reset seen in placental mammals.

Keywords: Developmental biology; Epigenetics

DOI: https://doi.org/10.1038/d41586-025-01477-2

Dev Biol. 2025 May 09. pii: S0012-1606(25)00129-0. [Epub ahead of print]524 105-115

Geometric, cell cycle and maternal-to-zygotic transition-associated YAP dynamics during preimplantation embryo development.

Madeleine Chalifoux, Maria Avdeeva, Eszter Posfai.

During the first cell fate decision in mammalian embryos, the inner cell mass cells, which will give rise to the embryo proper and other extraembryonic tissues, segregate from the trophectoderm cells, the precursors of the placenta. Cell fate segregation proceeds in a gradual manner encompassing two rounds of cell division, as well as cell positional and morphological changes. While it is known that the activity of the Hippo signaling pathway and the subcellular localization of its downstream effector YAP dictate lineage specific gene expression, the response of YAP to these dynamic cellular changes remains incompletely understood. Here we address these questions by quantitative live imaging of endogenously tagged YAP while simultaneously monitoring geometric cellular features and cell cycle progression throughout cell fate segregation. We apply a probabilistic model to our dynamic data, providing a quantitative characterization of the mutual effects of YAP and cellular relative exposed area, which has previously been shown to correlate with subcellular YAP localization in fixed samples. Additionally, we study how nuclear YAP levels are influenced by other factors, such as the decreasing pool of maternally provided YAP that is partitioned to daughter cells through cleavage divisions, cell cycle-associated nuclear volume changes, and a delay after divisions in adjusting YAP levels to new cell positions. Interestingly, we find that establishing low nuclear YAP levels required for the inner cell mass fate is largely achieved by passive cell cycle-associated mechanisms. Moreover, contrary to expectations, we find that mechanical perturbations that result in cell and nuclear shape changes do not influence YAP localization in the embryo. Together our work identifies how various inputs are integrated over a dynamic developmental time course to shape the levels of a key molecular determinant of the first cell fate choice.

Keywords: Cell fate; Dynamic bayesian networks; Live imaging; Mouse; Preimplantation; YAP

DOI: https://doi.org/10.1016/j.ydbio.2025.05.006

Adv Sci (Weinh). 2025 May 11. e2504066

Intermediate Filament Protein BFSP1 Maintains Oocyte Asymmetric Division by Modulating Spindle Length.

Yu Li, Hanwen Zhang, Wenjun Zeng, Yilong Miao, Shaochen Sun, Yu Zhang, Bo Xiong.

The cytoskeleton is composed of microtubules, microfilaments, and intermediate filaments in cells. While the functions of microtubules and microfilaments have been well elucidated, the roles of intermediate filaments and associated proteins remain largely unknown, especially in meiosis. BFSP1 is an intermediate filament protein mainly expressed in the eye lens to play important roles in the development of congenital cataract. Here, we document that BFSP1 functions as a spindle regulator to drive the oocyte asymmetric division. Specifically, we found that BFSP1 distributed on the spindle apparatus during oocyte meiotic maturation. Depletion of BFSP1 resulted in symmetric division of oocytes, accompanied by the formation of elongated spindles at metaphase I and anaphase/telophase I stages. In addition, immunoprecipitation combined with mass spectrometry analysis identified MAP1B, a microtubule-associated protein, as an interacting partner of BFSP1. Depletion or mutation of MAP1B phenocopied the meiotic defects observed in BFSP1-depleted oocytes, and expression of exogenous MAP1B-EGFP in BFSP1-depleted oocytes recovered the spindle length and asymmetric division. We further determined that BFSP1 recruited molecular chaperone HSP90α on the spindle to stabilize MAP1B, thereby controlling the spindle length. To sum up, our findings reveal a unique meiotic role for BFSP1 in the regulation of spindle dynamics and oocyte asymmetric division.

Keywords: BFSP1; asymmetric division; intermediate filament protein; oocyte meiosis; spindle length

DOI: https://doi.org/10.1002/advs.202504066

Hum Reprod. 2025 May 13. pii: deaf086. [Epub ahead of print]

Single-cell proteomics analysis of human oocytes during GV-to-MI transition.

Zeling Zhang, Lei Luo, Shiwei Fan, Shun Bai, Bo Xu.

STUDY QUESTION: Which proteins are involved in the transition of human oocytes from the germinal vesicle (GV) to metaphase I (MI) phase?
SUMMARY ANSWER: A total of 2369 proteins were identified, including 149 with significantly differential expression, 79 with upregulated expression in MI oocytes and 70 with downregulated expression.
WHAT IS KNOWN ALREADY: During oocyte maturation, maternal proteins and RNA are stored to support early embryo development. However, GV oocytes matured in vitro have a lower chance of developing into blastocysts than MI oocytes. Therefore, identifying key differentially expressed proteins between the GV and MI stages can provide a better understanding of human oocyte development and maturation mechanisms and improve the utilization of oocytes.
STUDY DESIGN, SIZE, DURATION: In total, 16 oocytes at the GV and MI stages were collected from female patients who underwent ovulation induction due to male factor infertility requiring embryo retrieval for ICSI. Differential proteins were identified in 16 oocytes using liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis, and the expression of several differential proteins was verified by immunofluorescence (IF). RNA interference was employed to identify the functions of specific proteins during oocyte maturation.
PARTICIPANTS/MATERIALS, SETTING, METHODS: 16 immature human oocytes discarded during ICSI cycles (eight GV oocytes and eight MI oocytes) were collected from 10 female patients. Two cohorts of oocytes underwent zona pellucida removal, lysis, and enzymatic digestion prior to peptide detection using LC-MS/MS methodology. Peptide detection outcomes were subjected to differential protein screening and functional annotation employing distinct analytical algorithms and datasets. To corroborate the sequencing findings, proteins exhibiting notable differential expression were authenticated via IF. Concerning protein functionality, siRNA was introduced during the GV phase, and oocyte maturation was evaluated through observation of polar body extrusion, alongside assessment of siRNA interference efficacy via IF analysis.
MAIN RESULTS AND THE ROLE OF CHANCE: A total of 2369 proteins were identified, including 149 with significantly differential expression, 79 with upregulated expression in MI oocytes and 70 with downregulated expression. Gene ontology functional annotation and functional analysis revealed that these differentially expressed proteins are involved mainly in organic matter and cell metabolism, biological regulation, primary metabolism, nitrogen compound metabolism, and other biological processes. Kyoto Encyclopedia of Genes and Genomes analysis revealed that the differentially expressed genes were involved mainly in the following pathways: transport and catabolism, signal transduction, protein folding, and energy and amino acid metabolism. The differentially expressed proteins included actin-related protein 2 (ACTR2), NADH: Ubiquinone Oxidoreductase Core Subunit S1 (NDUFS1), Tubulin Gamma Complex Component 3 (TUBGCP3), Heat Shock Protein Family B (Small) Member 1 (HSPB1), and Eukaryotic Translation Initiation Factor 3 Subunit B, which are involved mainly in mitochondrial function, cell division, and signal transduction. ACTR2, HSPB1, NDUFS1, and TUBGCP3 were selected for IF staining, and the difference in fluorescence intensity between GV and MI oocytes was consistent with the sequencing results. Three pairs of primers were designed for each gene corresponding to the top 10 differentially upregulated and downregulated proteins (with siRNAs successfully designed for eight upregulated and seven downregulated proteins) to study their function, and the results revealed that the protein expression of TUBGCP3 was downregulated after RNA interference.
LARGE SCALE DATA: See supplementary tables.
LIMITATIONS, REASONS FOR CAUTION: Although we have identified some differentially expressed proteins during the transition from human oocyte GV to MI stage, their crucial roles in oocyte maturation remain elusive. To elucidate the functions of these proteins in oocyte maturation, we have generated conditional knockout mice targeting selected proteins.
WIDER IMPLICATIONS OF THE FINDINGS: We conducted single-cell level analysis to identify differentially expressed proteins between the human oocyte GV and MI stages. Our objective is to ascertain the potential of supplementing these proteins in the in vitro maturation culture medium to augment both oocyte maturation rates and quality.
STUDY FUNDING/COMPETING INTEREST(S): This research was supported by the National Natural Science Foundation of China (82171599 and 82471657, B.X., 82301871, L.L.); China Postdoctoral Science Foundation (2024M763169, S.B.); and the National Key Research and Development Project of China (2029YFA0802600, B.X.). None of the authors has any conflict of interest to declare.
TRIAL REGISTRATION NUMBER: N/A.

Keywords: assisted reproductive technology; germinal vesicle; metaphase I; oocyte maturation; single-cell proteomics

DOI: https://doi.org/10.1093/humrep/deaf086

G3 (Bethesda). 2025 May 13. pii: jkaf104. [Epub ahead of print]

The Drosophila nucleoporin ELYS is required for parental chromosome arrangement at fertilization.

Kazuyuki Hirai, Hiroki Sakamoto, Yoko Keira, Mika Ozaki, Kanta Yamazoe, Hiroyuki O Ishikawa, Yoshihiro H Inoue, Kyoichi Sawamura.

One key aspect of fertilization is the unification of the maternal and paternal genomes driven by the first mitotic spindle. However, little is known about the mechanisms that underlie the formation of a bipolar spindle that interacts with the two discrete chromosome sets in juxtaposition. We here show that, in Drosophila, the maternally provided ELYS-an evolutionarily conserved subunit of the nuclear pore complex-localizes to female and male pronuclei and then redistributes to the interior of the spindle and the resulting zygotic nuclei. Both Elys loss-of-function mutations and ELYS overexpression in the female germline were associated with maternal-effect lethality. Our cytological studies of fertilized eggs revealed that ELYS is primarily involved in the apposition of female and male pronuclei, potentially impacting the parental genome configuration of the first mitotic spindle. We propose that pronuclear apposition is essential for centrosome localization at the emergent pronuclear junction to promote bipolar spindle formation for the first mitosis. In addition, we discuss the possible involvement of ELYS in interspecific hybrid incompatibility.

Keywords: centrosomes; early embryos; maternal effects; pronuclear apposition; spindle bipolarity; the first mitosis; zygotes

DOI: https://doi.org/10.1093/g3journal/jkaf104

Dev Biol. 2025 May 13. pii: S0012-1606(25)00135-6. [Epub ahead of print]

Coilin-containing nuclear biomolecular condensates in zebra finch Taeniopygia guttata growing oocytes.

Svetlana Galkina, Kseniia Matveeva, Olga Takki, Valeriia Volodkina, Maria Kulak, Julia Shalutina, Elena Gaginskaya.

In most animals, oocyte growth is accompanied by genome activation, an increase in nuclear volume, and the formation of various biomolecular condensates (BioMCs) through multivalent interactions involving intrinsically disordered protein regions (IDRs) and phase separation. In this study, we characterize specific nuclear biomolecular condensates (NBioMCs) detectable by light microscopy in the oocytes of the zebra finch (Taeniopygia guttata, Passeriformes, Aves), a model species in genomics and neurobiology. We identified a nucleolus in oocytes at the early diplotene stage and observed numerous NBioMCs that tested positive for coilin in oocytes at the lampbrush stage, a period of active transcription. The coilin-positive NBioMCs may be freely distributed within the nucleus or associated with chromosome centromeres. They share characteristics with several known nuclear structures, including nucleoli (due to the presence of fibrillarin and nucleolin), Cajal bodies (marked by coilin and scaRNA2), interchromatin granule clusters (containing SRSF2), and centromeric protein bodies (CPBs) described in other avian species (exhibiting centromeric localization when chromosome-associated and containing STAG2 and SMC5). However, their specific function in zebra finch oocytes remains unclear and requires further investigation.

Keywords: Cajal bodies; birds; lampbrush chromosomes; nuclear biomolecular condensates; oogenesis

DOI: https://doi.org/10.1016/j.ydbio.2025.05.012

Dev Biol. 2025 May 08. pii: S0012-1606(25)00120-4. [Epub ahead of print]

Anna B Zike, Madison G Abel, Sophie A Fleck, Emily D DeWitt, Lesley N Weaver.

Adult tissue function is dependent on intrinsic factors that mediate stem cell self-renewal and proliferation in response to changes in physiology and the environment. The estrogen-related receptor (ERR) subfamily of orphan nuclear receptors are major transcriptional regulators of metabolism and animal physiology. In mammals, ERRs (NR3B1, NR3B2, NR3B3) have roles in regulating mitochondrial biosynthesis, lipid metabolism, as well as stem cell maintenance. The sole Drosophila ERR ortholog promotes larval growth by establishing a metabolic state during the latter half of embryogenesis. In addition, ERR is required in adult Drosophila males to coordinate glycolytic metabolism with lipid synthesis and within the testis to regulate spermatogenesis gene expression and fertility. Despite extensive work characterizing the role of ERR in Drosophila metabolism, whether ERR has a conserved requirement in regulating stem cell behavior has been understudied. To determine whether ERR regulates stem cell activity in Drosophila, we used the established adult female germline stem cell (GSC) lineage as a model. We found that whole-body ERR knockout in adult females using conditional heat shock-driven FLP-FRT recombination significantly decreases GSC number and glycolytic enzyme expression in GSCs. In addition, we found that ERR activity is required cell-autonomously in the adult female germline for maintenance of GSCs; whereas ERR regulation of GSCs is independent of its activity in adult female adipocytes. Our results highlight an ancient and conserved role for ERRs in the regulation of stem cell self-renewal.

Keywords: NR3B1; NR3B2; NR3B3; nuclear receptor; oogenesis

DOI: https://doi.org/10.1016/j.ydbio.2025.05.005

Development. 2025 May 01. pii: dev204696. [Epub ahead of print]152(9):

Emerging roles for the nucleolus in development and stem cells.

Bryony J Leeke, Imke Staffhorst, Michelle Percharde.

The nucleolus is a membrane-less subnuclear compartment known for its role in ribosome biogenesis. However, emerging evidence suggests that nucleolar function extends beyond ribosome production and is particularly important during mammalian development. Nucleoli are dynamically reprogrammed post-fertilisation: totipotent early mouse embryos display non-canonical, immature nucleolar precursor bodies, and their remodelling to mature nucleoli is essential for the totipotency-to-pluripotency transition. Mounting evidence also links nucleolar disruption to various pathologies, including embryonic lethality in mouse mutants for nucleolar factors, human developmental disorders and observations of nucleolar changes in disease states. As well as its role in ribogenesis, new findings point to the nucleolus as an essential regulator of genome organisation and heterochromatin formation. This Review summarises the varied roles of nucleoli in development, primarily in mammals, highlighting the importance of nucleolar chromatin for genome regulation, and introduces new techniques for exploring nucleolar function.

Keywords: Development; ESCs; Heterochromatin; NADs; Nuclear architecture; Nucleoli

DOI: https://doi.org/10.1242/dev.204696