bims-cebooc 2025-07-13 papers

Issue of 2025–07–13
eleven papers selected by
Gabriele Zaffagnini, Universität zu Köln

bioRxiv. 2025 Jul 06. pii: 2025.07.06.663377. [Epub ahead of print]

An Epigenomic Roadmap Primes Non-Growing Oocytes for Maturation and Early Embryogenesis.

Mengwen Hu, Yasuhisa Munakata, Yu-Han Yeh, Han Wang, Neil Hunter, Richard M Schultz, Satoshi H Namekawa.

Female reproductive lifespan is defined by long-lived, non-growing oocytes (NGOs) that comprise the ovarian reserve. NGOs are assumed to acquire the epigenetic marks that will define the early embryo only after they exit the ovarian reserve and become activated for growth. Contrary to this dogma, we show that mouse NGOs possess abundant histone modifications that both underlie maintenance of the ovarian reserve and prime the epigenome of growing oocytes for early embryogenesis. As NGOs are established around birth, Polycomb Repressive Complex 1 (PRC1) mediates abundant H2AK119 ubiquitylation and reprograms the H3K27 acetylation landscape, which is essential to maintain the ovarian reserve. Importantly, the PRC1-driven epigenetic state of NGOs provides a blueprint for subsequent generation of a PRC2-catalyzed H3K27 trimethylation profile in growing oocytes that is characterized by broad domains and DNA methylation-independent imprints that are transmitted to the embryo. Thus, Polycomb complexes play pivotal roles in priming the NGO epigenome for oocyte maturation and early embryogenesis.

DOI: https://doi.org/10.1101/2025.07.06.663377

Mol Biol Cell. 2025 Jul 09. mbcE25050218

The lipid droplet protein Jabba promotes actin remodeling downstream of prostaglandin signaling during Drosophila oogenesis.

Jonathon M Thomalla, Michelle S Giedt, Roger P White, Israel J Wipf, Alicia Shipley, Minhao Chen, Michael A Welte, Tina L Tootle.

Growing evidence supports that lipid droplets (LDs) are critical for producing high-quality oocytes. However, the functions of LDs during oocyte development remain largely unknown. Using Drosophila oogenesis as a model, we previously discovered the LD-associated Adipose Triglyceride Lipase (ATGL) promotes actin remodeling necessary for oocyte development by providing the substrate for producing lipid signals termed prostaglandins (PGs). Here we find that Jabba, a LD-associated protein best known for its role in anchoring other proteins to LDs, also promotes PG-dependent actin remodeling. Overexpression of Jabba results in thickened cortical actin and excessive actin bundles, whereas loss of Jabba results in cortical actin breakdown and severely defective actin bundle formation. We find that Jabba regulates actin remodeling in conjunction with PG signaling. However, the lack of a genetic interaction between Jabba and ATGL suggests the Jabba-PG pathway is independent of ATGL. These data are consistent with the model that there are multiple PG signaling pathways promoting actin remodeling. Overexpression of Jabba rescues the actin defects when PG signaling is lost. Together these data lead to the model that PGs produced independently of ATGL positively regulate Jabba to promote actin remodeling necessary for follicle morphogenesis.

DOI: https://doi.org/10.1091/mbc.E25-05-0218

Nat Methods. 2025 Jul 10.

De novo assembly and delivery of synthetic megabase-scale human DNA into mouse early embryos.

Yue Liu, Jianting Zhou, Duo Liu, Xiaoyu Hu, Lin Yang, Xue-Ru Song, Xiao-Dong Jin, Wei Xie, Luhan Yang, Zichuan Liu, Ying-Jin Yuan.

Epigenetic modifications on natural chromosomes are inherited and maintained in a default state, making it challenging to remove intrinsic marks to study the fundamental principles of their establishment and further influence on transcriptional regulation. In this study, we developed SynNICE, a method for assembling and delivering intact, naive, synthetic megabase (Mb)-scale human DNA into early mouse embryos, to study de novo epigenetic regulation. By assembling and delivering a 1.14-Mb human AZFa (hAZFa) locus, we observed the spontaneous incorporation of murine histones and the establishment of DNA methylation at the one-cell stage. Notably, DNA methylation from scratch strongly enriches at repeat sequences without H3K9me3 reinforcement. Furthermore, the transcription of hAZFa initiated at the four-cell stage is regulated by newly established DNA methylation. This method provides a unique platform for exploring de novo epigenomic regulation mechanisms in higher animals.

DOI: https://doi.org/10.1038/s41592-025-02746-8

PLoS Biol. 2025 Jul;23(7): e3003239

H3K4me2 distinguishes a distinct class of enhancers during the maternal-to-zygotic transition.

Matthew D Hurton, Jennifer M Miller, Miler T Lee.

After egg fertilization, an initially silent embryonic genome is transcriptionally activated during the maternal-to-zygotic transition. In zebrafish, maternal vertebrate pluripotency factors Nanog, Pou5f3 (OCT4 homolog), and Sox19b (SOX2 homolog) (NPS) play essential roles in orchestrating embryonic genome activation, acting as "pioneers" that open condensed chromatin and mediate acquisition of activating histone modifications. However, some embryonic gene transcription still occurs in the absence of these factors, suggesting the existence of other mechanisms regulating genome activation. To identify chromatin signatures of these unknown pathways, we profiled the histone modification landscape of zebrafish embryos using CUT&RUN. Our regulatory map revealed two subclasses of enhancers distinguished by presence or absence of H3K4me2. Enhancers lacking H3K4me2 tend to require NPS factors for de novo activation, while enhancers bearing H3K4me2 are epigenetically bookmarked by DNA hypomethylation to recapitulate gamete activity in the embryo, independent of NPS pioneering. Thus, parallel enhancer activation pathways combine to induce transcriptional reprogramming to pluripotency in the early embryo.

DOI: https://doi.org/10.1371/journal.pbio.3003239

bioRxiv. 2025 Jul 02. pii: 2025.07.01.662550. [Epub ahead of print]

MYCBP interacts with Sakura and Otu and is essential for germline stem cell renewal and differentiation and oogenesis.

Azali Azlan, Ryuya Fukunaga.

The self-renewal and differentiation of germline stem cells (GSCs) are tightly regulated during oogenesis. The Drosophila female germline provides a powerful model to study these regulatory mechanisms. We previously identified Sakura (also known as Bourbon/CG14545) as a crucial factor for maintenance and differentiation of GSCs and oogenesis, and demonstrated that Sakura binds to Ovarian Tumor (Otu), another essential regulator of these processes. Here, we identify MYCBP (c-Myc binding protein) as an additional essential component of this regulatory network. We show that MYCBP physically associates with itself, Sakura, and Otu, forming binary and ternary complexes including a MYCBP•Sakura•Otu complex. MYCBP is highly expressed in the ovary, and mycbp null mutant females exhibit rudimentary ovaries with germline-less and tumorous ovarioles, fail to produce eggs, and are completely sterile. Germline-specific depletion of mycbp disrupts Dpp/BMP signaling, causing aberrant expression of bag-of-marbles ( bam ) and leading to defective differentiation and GSC loss. In addition, mycbp is required for female-specific splicing of sex-lethal ( sxl ), a master regulator of sex identity determination. These phenotypes closely resemble those observed those of sakura and otu mutants. Together, our findings reveal that MYCBP functions in concert with Sakura and Otu to coordinate self-renewal and differentiation of GSCs and oogenesis in Drosophila .

DOI: https://doi.org/10.1101/2025.07.01.662550

bioRxiv. 2025 Jul 03. pii: 2025.07.02.662854. [Epub ahead of print]

Nucleation-dependent propagation of Polycomb modifications emerges during the Drosophila maternal to zygotic transition.

Natalie Gonzaga-Saavedra, Eleanor A Degen, Isabella V Soluri, Corinne Croslyn, Shelby A Blythe.

During zygotic genome activation (ZGA) in Drosophila, broad domains of Polycomb-modified chromatin are rapidly established across the genome. Here, we investigate the spatial and temporal dynamics by which Polycomb group (PcG) histone modifications, H3K27me3 and H2Aub, emerge during early embryogenesis. Using ChIP-seq and live imaging of CRISPR-engineered GFP-tagged PcG components, we show that PRC2-dependent H3K27me3 accumulates adjacent to a subset of E(z)-bound prospective Polycomb Response Elements (PREs) beginning in nuclear cycle 14 (NC14), with patterns indicative of nucleation followed by spreading. Surprisingly, PRE-binding factors Pho, Combgap, and GAGA-factor are excluded from interphase nuclei prior to NC10 despite nuclear localization of E(z) throughout early interphases. Loss-of-function studies further demonstrate that GAGA-factor is largely dispensable for PcG domain establishment, whereas the pioneer factor Zelda is required for proper deposition of H3K27me3 and H2Aub at a subset of Polycomb domains. The role of Zelda at Polycomb domains is context-dependent; a large subset of targets requires Zelda not for PcG factor recruitment, but instead to license a loaded PRE to deposit H3K27me3 and H2Aub. Our findings support a model where licensing of PcG domains is an initial step in the regulatory processes governing Polycomb-regulated developmental genes.

DOI: https://doi.org/10.1101/2025.07.02.662854

Front Cell Dev Biol. 2025 ;13 1625914

Investigating SMYD3 role during oocyte maturation in a 3D follicle-enclosed oocyte in vitro model in sheep.

Chiara Camerano Spelta Rapini, Alessia Peserico, Chiara Di Berardino, Giulia Capacchietti, Camila Rojo-Fleming, Andrada-Ioana Damian-Buda, Irem Unalan, Aldo Roberto Boccaccini, Valentina Grossi, Mauro Mattioli, Barbara Barboni.

Background: SMYD3 is a histone methyltransferase known for its dual role in modifying both histone and non-histone proteins. Despite its established involvement in somatic cell function and oncogenesis, its role in mammalian oogenesis and early embryonic development remains unclear. This study aimed to elucidate the function of SMYD3 in regulating oocyte meiotic progression and developmental competence using sheep as a mono-ovulatory model.
Results: Utilizing a 3D follicle-enclosed in vitro maturation (FEO-IVM) system, the study examined the impact of SMYD3 inhibition on oocyte maturation within Early Antral follicles In the absence of human chorionic gonadotropin oocytes remained arrested at the germinal vesicle (GV) stage. Interestingly, treatment with a SMYD3 inhibitor (iSMYD3) alone prompted germinal vesicle breakdown (GVBD) in 67% of oocytes; however, progression to the metaphase II (MII) stage was achieved only when iSMYD3 was combined with hCG, resulting in a 73% maturation rate. Despite this, MII oocytes from the iSMYD3 group exhibited compromised developmental competence, as evidenced by the failure of parthenogenetic embryos to progress beyond the 8-cell stage, contrasting with a 29% success rate in the hCG-only group. At the molecular level, SMYD3 inhibition led to sustained activation of CDC25A within oocytes, facilitating GVBD but impeding the MI-MII transition due to the absence of CDC25A degradation. Moreover, iSMYD3 failed to activate the MAPK1/3 and PDE5A pathways in the somatic compartment, unlike hCG treatment, indicating distinct signaling mechanisms. Additionally, hCG rapidly downregulated SMYD3 expression in follicular walls and cumulus cells, a process independent of meiotic progression but essential for metabolic decoupling between oocytes and cumulus cells. SMYD3 inhibition disrupted this decoupling by preventing hCG-induced gap junction closure, thereby maintaining prolonged intercellular communication.
Conclusion: SMYD3 is identified as a key modulator of oocyte maturation, orchestrating meiotic progression through CDC25A regulation and interacting with hCG-driven somatic signaling. These findings highlight SMYD3 as a critical determinant of late oogenesis and a potential target for enhancing oocyte competence in assisted reproductive technologies.

Keywords: SMYD3; cumulus-oocyte metabolic coupling; follicle-enclosed oocyte in vitro maturation (FEO-IVM); hCG-dependent signaling pathways; ovine oocyte competence

DOI: https://doi.org/10.3389/fcell.2025.1625914

bioRxiv. 2025 Jul 03. pii: 2025.07.01.662614. [Epub ahead of print]

A stress-dependent postembryonic role for the core CPA factor CFIM-1 in germline integrity.

Anson Sathaseevan, Rhea Ahluwalia, Bin Yu, Claudia Makhenko-Tang, Haruka Nishimura, Alexander Leong, Ka Nam Naomi Kwan, W Brent Derry.

Post-transcriptional processing of pre-mRNAs generates a diversity of 3' UTR transcript isoforms that can vary in their function and stability. The differential enrichment of transcript isoforms has been implicated in diseases ranging from cancer to neurodevelopmental disorders. However, the post-embryonic developmental roles of the core ensemble of cleavage and polyadenylation (CPA) factors that mediate these post-transcriptional changes remain poorly characterized. Here, we report a stress- dependent role for the core CPA factor CFIM-1 in germline integrity in Caenorhabditis elegans. Total loss-of-function of cfim-1 elicits a temperature-sensitive sterile phenotype in hermaphrodites. These changes in brood size are accompanied by broad sperm, oocyte and germline morphology defects. Surveying the transcriptome of cfim-1(lf) worms, we uncover changes in transcript isoform abundance for dozens of genes with known functions related to the development and maintenance of these structures, consistent with a model in which post-transcriptional regulation of target genes via cfim- 1 is crucial to the development and maintenance of germline integrity. Our findings collectively define a novel post-embryonic role for a core CPA factor in tissue-specific development.

DOI: https://doi.org/10.1101/2025.07.01.662614

Proc Natl Acad Sci U S A. 2025 Jul 15. 122(28): e2504361122

WT1 directs normal progesterone receptor-chromatin binding essential for uterine receptivity at peri-implantation.

Zhangli Ni, Chuanhui Guo, Xiaojing Liu, Gaizhen Li, Yedong Tang, Han Cai, Weiyu Huang, Fei Gao, Zhaowei Tu, Chao Wang, Haibin Wang, Shuangbo Kong, Haili Bao.

Progesterone receptor (PR)-mediated progesterone (P4) signaling plays a crucial role in the establishment of uterine receptivity which is the prerequisite for successful embryo implantation in mammals. However, detailed molecular mechanisms underlying PR-chromatin binding and transcriptional activity in the uterus remain largely elusive. Here, combining the P4-administrated ovariectomized mouse model and PR-chromatin immunoprecipitation sequencing, we identified transcription factor WT1 as a potential cooperator of PR in the uterus. WT1 was specifically expressed in uterine stromal cells. Uterine deletion of Wt1 resulted in implantation failure due to attenuated P4 responsiveness in stromal cells and aberrant uterine receptivity. Mechanistically, WT1 physically interacted with PR in stromal cells, and exhibited genome-wide co-occupancy with PR. Furthermore, WT1 was indispensable for directing PR onto the chromatin via corecruitment and tethering manners, and facilitated PR to activate the transcription of target genes that were critical for uterine receptivity. Collectively, our study provided substantial evidence that WT1 served as a functional partner of PR in uterine stromal cells, thus guaranteeing P4 responsiveness conducive to uterine receptivity.

Keywords: WT1; progesterone receptor; uterine receptivity

DOI: https://doi.org/10.1073/pnas.2504361122

Hum Reprod. 2025 Jul 10. pii: deaf139. [Epub ahead of print]

Pathogenic variants in DLGAP5 cause female infertility characterized by oocyte maturation arrest and embryonic arrest.

STUDY QUESTION: Can new genetic factors responsible for oocyte defects be identified in infertile women, especially for those with spindle assembly defects?
SUMMARY ANSWER: We identified homozygous and compound heterozygous variants of DLGAP5 in three infertile individuals from two independent families.
WHAT IS KNOWN ALREADY: Some genes have been found to be responsible for female infertility with oocyte maturation defects. During mitosis, DLGAP5 is involved in promoting microtubule polymerization and spindle formation.
STUDY DESIGN, SIZE, DURATION: The DLGAP5 variants were identified by whole-exome sequencing in a cohort of 3627 female infertility patients diagnosed with oocyte maturation defects or embryonic development problems, and all participants were recruited from 2015 to 2023. Thirty-six hours after cell transfection, the expression levels of wild-type (WT) and mutant DLGAP5 were evaluated by western blot (n = 3 biological replicates). Human germinal vesicle (GV) oocytes retrieved from assisted reproductive procedure were introduced for cRNA (n = 3-5 oocytes per group) and antibody injection (n = 10-15 oocytes per group). Knock-in (KI) mouse model was generated by CRISPR-Cas9 and genotyping was performed at postnatal Days 10-15. Sexually mature females (6-10 weeks old) were used for fertility test (n = 6 mice per group, lasts 6-8 months), western blot (n = 3 biological replicates), IVF (n = 3 biological replicates), embryos collection (n = 3 biological replicates), immunofluorescence (n = 3 biological replicates), RNA-sequencing (RNA-seq, n = 3 biological replicates), and other functional assays between 2019 and 2023.
PARTICIPANTS/MATERIALS, SETTING, METHODS: The DLGAP5 variants were identified by whole-exome sequencing and further confirmed by Sanger sequencing. Western blot was used to detect the expression of mutant DLGAP5 in HEK-293T cells after transfection. cRNA injection and immunofluorescence were performed to view the location of DLGAP5 in human oocytes. Knockdown of DLGAP5 by Trim-Away in human oocytes was conducted to observe the effect of DLGAP5 on spindle assembly and oocyte maturation. Then, Dlgap5 KI mice were constructed to mimic the phenotype of the affected individuals. After phenotypic assessment, western blot, IVF, assessment of embryonic development, chromosome counting, RNA-seq, and quantitative real-time PCR were performed to elucidate the pathological mechanism of DLGAP5 variants.
MAIN RESULTS AND THE ROLE OF CHANCE: We identified homozygous nonsense DLGAP5 variant (NM_014750.5, c.431delA (p.Lys144Argfs*55)) in two affected sisters from family 1 and compound heterozygous variants (c.C847G (p.Pro283Ala) and c. C1202G (p.Thr401Ser)) in one infertile individual in family 2. p. Lys144Argfs*55 led to protein degradation (P < 0.0001) and p. Pro283Ala resulted in a significant decrease in protein level (P = 0.0021). DLGAP5 was located on the spindle and mutant did not alter its location. Knockdown of DLGAP5 in human oocytes impaired spindle assembly and led to oocyte maturation arrest (P = 0.0055). Homozygous (HO) Dlgap5 KI female mice showed reduced fertility (P < 0.0001) due to embryonic arrest at the 4-cell stage (P < 0.0001) and a low blastocyst formation rate (P < 0.0001). RNA-seq data of 4-cell embryos showed that differentially expressed genes (DEGs) were involved in cell cycle regulation, checkpoint control, and TGF-β signaling pathways, which may account for the embryonic development arrest.
LARGE SCALE DATA: N/A.
LIMITATIONS, REASONS FOR CAUTION: Due to phenotypic differences between different DLGAP5 variants, more cases are needed to expand our understanding of the function of DLGAP5 in female infertility. Although RNA-seq data have shown the potential impact of DLGAP5 on cell cycle, embryonic development, and regulation of TGF-β signaling, more experiments are still requested to demonstrate the more direct role of DLGAP5 in oocyte and embryonic development.
WIDER IMPLICATIONS OF THE FINDINGS: Our findings elucidated the role of DLGAP5 in human oocyte spindle assembly and the effects of the corresponding variants in the pathogenesis of oocyte maturation arrest, and these findings suggest that DLGAP5 is a novel maker for genetic counseling.
STUDY FUNDING/COMPETING INTEREST(S): This work was supported by the National Key Research and Development Program of China (2024YFC2706600), the National Natural Science Foundation of China (82325021, 82288102, 32130029, 82371662, 82171643, 82201767, 82422033), the National Key Research and Development Program of China (2022YFC2702300), the New Cornerstone Science Foundation through the XPLORER PRIZE, L.W. is a SANS Exploration Scholar, and the Fund of Fudan University and Cao'ejiang Basic Research (24FCB01). None of the authors declare any conflict of interest.
TRIAL REGISTRATION NUMBER: N/A.

Keywords: DLGAP5 ; TGF-β; cell cycle; embryonic development; knock-in (KI); oocyte maturation arrest (OMA); signaling pathway; variant

DOI: https://doi.org/10.1093/humrep/deaf139

Genes Dev. 2025 Jul 10.

Studying ovarian aging and its health impacts: modern tools and approaches.

Bérénice A Benayoun, Alison Kochersberger, Jennifer L Garrison.

Ovarian aging is a critical yet understudied driver of systemic aging in female bodies, with profound implications for female health and longevity. Despite its significance, we still know little about ovarian aging and its systemic effects on aging trajectories. With new efforts over the past few years, interest in the field has been growing and there is momentum to address these questions. This review highlights the importance of leveraging modern tools and approaches to better understand ovarian aging and its impact on health span. Specifically, we believe it will be useful for both aging researchers looking to go into research on ovarian aging and reproductive researchers looking to adopt more modern toolkit. We focus on menopause-a key marker of ovarian aging-as a lens through which to examine the current state of the field, identify limitations in existing research, and outline goals for future progress. By emphasizing cutting-edge techniques and emerging models, we seek to illuminate new pathways for research that could lead to improved strategies for managing ovarian aging and enhancing overall female health.

Keywords: biomarkers; menopause; ovarian aging

DOI: https://doi.org/10.1101/gad.352732.125