Dynamics of the epigenetic landscape during the maternal-to-zygotic transition

Transposable elements as instructors of the immune system

Transposable elements (TEs) are mobile repetitive nucleic acid sequences that have been incorporated into the genome through spontaneous integration, accounting for almost 50% of human DNA. Even though most TEs are no longer mobile today, studies have demonstrated that they have important roles in different biological processes, such as ageing, embryonic development, and cancer. TEs influence these processes through various mechanisms, including active transposition of TEs contributing to ongoing evolution, transposon transcription generating RNA or protein, and by influencing gene regulation as enhancers. However, how TEs interact with the immune system remains a largely unexplored field. In this Perspective, we describe how TEs might influence different aspects of the immune system, such as innate immune responses, T cell activation and differentiation, and tissue adaptation. Furthermore, TEs can serve as a source of neoantigens for T cells in antitumour immunity. We suggest that TE biology is an important emerging field of immunology and discuss the potential to harness the TE network therapeutically, for example, to improve immunotherapies for cancer and autoimmune and inflammatory diseases.

The building blocks of embryo models: embryonic and extraembryonic stem cells

The process of a single-celled zygote developing into a complex multicellular organism is precisely regulated at spatial and temporal levels in vivo. However, understanding the mechanisms underlying development, particularly in humans, has been constrained by technical and ethical limitations associated with studying natural embryos. Harnessing the intrinsic ability of embryonic stem cells (ESCs) to self-organize when induced and assembled, researchers have established several embryo models as alternative approaches to studying early development in vitro. Recent studies have revealed the critical role of extraembryonic cells in early development; and many groups have created more sophisticated and precise ESC-derived embryo models by incorporating extraembryonic stem cell lines, such as trophoblast stem cells (TSCs), extraembryonic mesoderm cells (EXMCs), extraembryonic endoderm cells (XENs, in rodents), and hypoblast stem cells (in primates). Here, we summarize the characteristics of existing mouse and human embryonic and extraembryonic stem cells and review recent advancements in developing mouse and human embryo models.

DUX-mediated configuration of p300/CBP drives minor zygotic genome activation independent of its catalytic activity

Maternal-deposited factors initiate zygotic genome activation (ZGA), driving the maternal-to-zygotic transition; however, the coordination between maternal coactivators and transcription factors (TFs) in this process remains unclear. In this study, by profiling the dynamic landscape of p300 during mouse ZGA, we reveal its role in promoting RNA polymerase II (Pol II) pre-configuration at ZGA gene regions and sequentially establishing enhancer activity and regulatory networks. Moreover, p300/CBP-catalyzed acetylation drives Pol II elongation and minor ZGA gene expression by inducing pivotal TFs such as Dux. Remarkably, the supplementation of exogenous Dux rescues ZGA failure and developmental defects caused by the loss of p300/CBP acetylation. DUX functions as a pioneer factor, guiding p300 and Pol II to minor ZGA gene regions and activating them in a manner dependent on the non-catalytic functions of p300/CBP. Together, our findings reveal a mutual dependency between p300/CBP and DUX, highlighting their coordinated role in regulating minor ZGA activation.

Epigenome dynamics in early mammalian embryogenesis

During early embryonic development in mammals, the totipotency of the zygote - which is reprogrammed from the differentiated gametes - transitions to pluripotency by the blastocyst stage, coincident with the first cell fate decision. These changes in cellular potency are accompanied by large-scale alterations in the nucleus, including major transcriptional, epigenetic and architectural remodelling, and the establishment of the DNA replication programme. Advances in low-input genomics and loss-of-function methodologies tailored to the pre-implantation embryo now enable these processes to be studied at an unprecedented level of molecular detail in vivo. Such studies have provided new insights into the genome-wide landscape of epigenetic reprogramming and chromatin dynamics during this fundamental period of pre-implantation development.

The Complexities of Interspecies Somatic Cell Nuclear Transfer: From Biological and Molecular Insights to Future Perspectives

For nearly three decades, interspecies somatic cell nuclear transfer (iSCNT) has been explored as a potential tool for cloning, regenerative medicine, and wildlife conservation. However, developmental inefficiencies remain a major challenge, largely due to persistent barriers in nucleocytoplasmic transport, mitonuclear communication, and epigenome crosstalk. This review synthesized peer-reviewed English articles from PubMed, Web of Science, and Scopus, spanning nearly three decades, using relevant keywords to explore the molecular mechanisms underlying iSCNT inefficiencies and potential improvement strategies. We highlight recent findings deepening the understanding of interspecies barriers in iSCNT, emphasizing their interconnected complexities, including the following: (1) nucleocytoplasmic incompatibility may disrupt nuclear pore complex (NPC) assembly and maturation, impairing the nuclear transport of essential transcription factors (TFs), embryonic genome activation (EGA), and nuclear reprogramming; (2) mitonuclear incompatibility could lead to nuclear and mitochondrial DNA (nDNA-mtDNA) mismatches, affecting electron transport chain (ETC) assembly, oxidative phosphorylation, and energy metabolism; (3) these interrelated incompatibilities can further influence epigenetic regulation, potentially leading to incomplete epigenetic reprogramming in iSCNT embryos. Addressing these challenges requires a multifaceted, species-specific approach that balances multiple incompatibilities rather than isolating a single factor. Gaining insight into the molecular interactions between the donor nucleus and recipient cytoplast, coupled with optimizing strategies tailored to specific pairings, could significantly enhance iSCNT efficiency, ultimately transforming experimental breakthroughs into real-world applications in reproductive biotechnology, regenerative medicine, and species conservation.

The idiosyncrasies of oocytes

Animal oocytes face extreme challenges. They remain dormant in the body for long periods of time. To support offspring development and health, they need to store genetic material and maternal factors stably and at the same time manage cellular damage in a reliable manner. Recent studies have provided new insights on how oocytes cope with such challenges. This review discusses the many unusual or idiosyncratic nature of oocytes and how understanding oocyte biology can help us address issues of reproduction and intergenerational inheritance.

PRMT3 gene expression and methylation levels in arrested embryos: Implications for developmental arrest defects

Embryos generated through in vitro fertilization (IVF) frequently experience developmental arrests or blocks, which significantly reduces the success rate of IVF therapy. Recent studies have shown that the protein arginine methylase 3 (PRMT3) plays a crucial role in the regulating of gene expression during early embryonic development. However, the exact regulatory mechanisms of PRMT3 involved in early embryonic development are still unclear. In this study, we used discarded arrested and polyspermic embryos from IVF for experiments, employing confocal techniques and qRT-PCR to examine PRMT3 expression and changes in H4R3me2a methylation during various stages of early development. Furthermore, PRMT3 was re-expressed in the arrested embryos to observe their subsequent development. Our findings revealed that PRMT3 nucleic acid and protein were significantly lower in arrested embryos than in control embryos (P < 0.05). Additionally, methylation levels of H4R3me2a were significantly lower in arrested embryos (P < 0.05). Re-expression of PRMT3 could partially rescue embryos that are developmentally arrested, and even a few arrested embryos have the potential to develop into morula or blastocysts. In summary, the reduction or deletion of PRMT3 gene in early embryo may lead to developmental arrested defects. Therefore, it is crucial to regulate the expression and functioning of PRMT3 for the proper development of early embryos, and further research is required to investigate potential therapeutic interventions for embryonic development arrest in vitro.

Decoding N6-methyladenosine's dynamic role in stem cell fate and early embryo development: insights into RNA-chromatin interactions

N6-methyladenosine (m6A), a reversible and dynamic RNA modification, plays pivotal roles in regulating stem cell pluripotency and early embryogenesis. Disruptions in m6A homeostasis lead to profound developmental defects, impairing processes such as stem cell self-renewal, lineage specification, oocyte maturation, zygotic genome activation, and maternal RNA degradation after fertilization. Beyond its well-recognized roles in mRNA transport, stability, and translation, recent studies have highlighted m6A's critical role in transcriptional regulation through intricate RNA-chromatin interactions, notably involving chromatin-associated regulatory RNAs (carRNAs) and retrotransposon RNAs. This review delves into the dynamic regulatory landscape of m6A, highlighting its critical interplay with chromatin modifications, and explores its broader implications in stem cell biology and early embryonic development.

The maternal-to-zygotic transition: reprogramming of the cytoplasm and nucleus

A fertilized egg is initially transcriptionally silent and relies on maternally provided factors to initiate development. For embryonic development to proceed, the oocyte-inherited cytoplasm and the nuclear chromatin need to be reprogrammed to create a permissive environment for zygotic genome activation (ZGA). During this maternal-to-zygotic transition (MZT), which is conserved in metazoans, transient totipotency is induced and zygotic transcription is initiated to form the blueprint for future development. Recent technological advances have enhanced our understanding of MZT regulation, revealing common themes across species and leading to new fundamental insights about transcription, mRNA decay and translation.

Queering the genome: ethical challenges of epigenome editing in same-sex reproduction

In this article, I explore the ethical dimensions of same-sex reproduction achieved through epigenome editing-an innovative and transformative technique. For the first time, I analyse the potential normativity of this disruptive approach for reproductive purposes, focusing on its implications for lesbian couples seeking genetically related offspring. Epigenome editing offers a compelling solution to the complex ethical challenges posed by traditional gene editing, as it sidesteps genome modifications and potential long-term genetic consequences. The focus of this article is to systematically analyse the bioethical issues related to the use of epigenome editing for same-sex reproduction. I critically assess the ethical acceptability of epigenome editing with reproductive purposes from multiple angles, considering harm perspectives, the comparison of ethical issues related to gene and epigenome editing, and feminist theories. This analysis reveals that epigenome editing emerges as an ethically acceptable means for lesbian couples to have genetically related children. Moreover, the experiments of a reproductive use of epigenome editing discussed in this article transcend bioethics, shedding light on the broader societal implications of same-sex reproduction. It challenges established notions of biological reproduction and prompts a reevaluation of how we define the human embryo, while poses some issues in the context of gender self-identification and family structures. In a world that increasingly values inclusivity and diversity, this article aims to reveal a progressive pathway for reproductive medicine and bioethics, as well as underscores the need for further philosophical research in this emerging and fertile domain.

Uncovering the Fluctuation of Peroxynitrite during Early Embryonic Development Using an Integrative Nanobeacon

Embryonic development is the beginning of life, and various kinds of bioactive molecules are implicated in this crucial process. Especially in its early stage, some important biochemical reactions regulating physiological balance may be resuscitated. Thus, revealing the dynamic changes of bioactive molecules during early embryonic development is crucial to the elucidation of biological phenomena. Peroxynitrite (ONOO-) is a typical signaling molecule in intercellular communication. However, up to now, no work has studied the fluctuation of ONOO- during early embryonic development due to its low content, especially in mammals. Herein, a polymeric nanobeacon that integrates an ONOO--responsive degradable scaffold and a fluorescence amplification module, named IFN, was designed to selectively sense embryonic ONOO- with high sensitivity. By virtue of the specific dye, ONOO- was sensitively detected in the range of 0-4.5 μM with a detection limit of 20.4 nM. From the attractive embryonic results, a sudden increase in ONOO- content after fertilization was observed in a mammalian model, while the level of ONOO- decreased slightly at the four-cell and eight-cell stages, finally reaching an equilibrium throughout the morula and blastocyst stages. This phenomenon is due to the resuscitation of ovotids, the activation of some life events by fertilization, and the subsequent establishment of physiological balance. This work not only suggests that ONOO- plays a positive role in normal embryonic development but also highlights the molecular events occurring at the initial phase of life. Furthermore it opens up new avenues for monitoring chemical changes during mammalian embryonic development.

Examining cellular heterogeneity in human DNA methylation studies: Overview and recommendations

Intersample cellular heterogeneity (ISCH) is one of the largest contributors to DNA methylation (DNAme) variability. It is imperative to account for ISCH to accurately interpret analysis results in epigenome-wide association studies. We compiled this primer based on the current literature to guide researchers through the process of estimating and accounting for ISCH in DNA methylation studies. This primer outlines the procedure of bioinformatic ISCH prediction, including using reference-based and reference-free algorithms. It then follows with descriptions of several methods to account for ISCH in downstream analyses, including robust linear regression and principal-component-analysis-based adjustments. Finally, we outlined three methods for estimating differential DNAme signals in a cell-type-specific manner. Throughout the primer, we provided statistical and biological justification for our recommendations, as well as R code examples for ease of implementation.

m6A RNA methylation dynamics during in vitro maturation of cumulus-oocyte complexes derived from adult or prepubertal sheep

PURPOSE

N6-methyladenosine (m6A) is the most prevalent base epigenetic modification within eukaryotic mRNAs. It participates in post-transcriptional regulation, including maternal RNA maintenance and decay in mouse oocytes and during maternal-to-zygotic transition. The landscape in other mammalian species remains largely unexplored. The present work analyzed m6A dynamics in sheep cumulus oocyte complexes (COCs), during in vitro maturation. To explore potential relationships with oocyte developmental competence, a previously established model consisting of oocytes derived from adult and prepubertal sheep was adopted.

METHODS

m6a dynamics were analyzed in terms of m6A RNA methylation abundance in cumulus cells (CCs) by colorimetric assay and expression of key m6A methylation-related proteins (METTL3, METTL14, METTL16, VIRMA, YTHDC1, YTHDC2, YTHDF2, YTHDF3, ALKBH5, and FTO) in both cumulus cells and oocytes by real-time PCR.

RESULTS

We report the dynamics of m6A in sheep COCs, and reveal alterations in both oocytes and cumulus cells derived from prepubertal donors. These changes were observed in terms of m6A RNA methylation levels and transcript dynamics of several m6A methylation-related proteins. Notably, our study shows that dysregulations occur after IVM.

CONCLUSION

Overall, this work describes for the first time the dynamics of m6A in sheep COCs and uncovers the involvement of m6A RNA methylation in oocyte developmental potential.

Insights on the Shared Genetic Landscape of Neurodevelopmental and Movement Disorders

PURPOSE OF REVIEW

Large-scale studies using hypothesis-free exome sequencing have revealed the strong heritability of neurodevelopmental disorders (NDDs) and their molecular overlap with later-onset, progressive, movement disorders phenotypes. In this review, we focus on the shared genetic landscape of NDDs and movement disorders.

RECENT FINDINGS

Cumulative research has shown that up to 30% of cases labelled as "cerebral palsy" have a monogenic etiology. Causal pathogenic variants are particularly enriched in genes previously associated with adult-onset progressive movement disorders, such as spastic paraplegias, dystonias, and cerebellar ataxias. Biological pathways that have emerged as common culprits are transcriptional regulation, neuritogenesis, and synaptic function. Defects in the same genes can cause neurological dysfunction both during early development and later in life. We highlight the implications of the increasing number of NDD gene etiologies for genetic testing in movement disorders. Finally, we discuss gaps and opportunities in the translation of this knowledge to the bedside.

Calcium signals shape metabolic control of H3K27ac and H3K18la to regulate EGA

The use of assisted reproductive technologies (ART) has enabled the birth of over 9 million babies; but it is associated with increased risks of negative metabolic outcomes in offspring. Yet, the underlying mechanism remains unknown. Calcium (Ca2+) signals, which initiate embryo development at fertilization, are frequently disrupted in human ART. In mice, abnormal Ca2+ signals at fertilization impair embryo development and adult offspring metabolism. Changes in intracellular Ca2+ drive mitochondrial activity and production of metabolites used by the epigenetic machinery. For example, acetyl-CoA (derived mainly from pyruvate) and lactyl-CoA (derived from lactate) are used for writing H3K27ac and H3K18la marks that orchestrate initiation of development. Using both a genetic mouse model and treatment with ionomycin to raise intracellular Ca2+ of wild-type fertilized eggs, we found that excess Ca2+ at fertilization changes metabolic substrate availability, causing epigenetic changes that impact embryo development and offspring health. Specifically, increased Ca2+ exposure at fertilization led to increased H3K27ac levels and decreased H3K18la levels at the 1-cell (1C) stage, that persisted until the 2-cell (2C) stage. Ultralow input CUT&Tag revealed significant differences in H3K27ac and H3K18la genomic profiles between control and ionomycin groups. In addition, increased Ca2+ exposure resulted in a marked reduction in global transcription at the 1C stage that persisted through the 2C stage due to diminished activity of RNA polymerase I. Excess Ca2+ following fertilization increased pyruvate dehydrogenase activity (enzyme that converts pyruvate to acetyl-CoA) and decreased total lactate levels. Provision of exogenous lactyl-CoA before ionomycin treatment restored H3K18la levels at the 1C and 2C stages and rescued global transcription to control levels. Our findings demonstrate conclusively that Ca2+ dynamics drive metabolic regulation of epigenetic reprogramming at fertilization and alter EGA.

Transposition element MERVL regulates DNA demethylation through TET3 in oxidative-damaged mouse preimplantation embryos

Transposable elements (TEs) comprise approximately half of eukaryotic genomes and significantly contribute to genome plasticity. In this study, we focused on a specific TE, MERVL, which exhibits particular expression during the 2-cell stage and commonly serves as an indicator of embryonic totipotency. However, its precise role in embryo development remains mysterious. We utilized DRUG-seq to investigate the effects of oxidative damage on genes and TEs expression. Our findings revealed that exposure to hydrogen peroxide (H2O2) could induce DNA damage, apoptosis, and incomplete DNA demethylation in embryos, which were potentially associated with MERVL expression. To further explore its function, antisense nucleotides (ASO) targeting MERVL were constructed to knockdown the expression in early embryos. Notably, this knockdown led to the occurrence of DNA damage and apoptosis as early as the 2-cell stage, consequently reducing the number of embryos that could progress to the blastocyst stage. Moreover, we discovered that MERVL exerted an influence on the reprogramming of embryonic DNA methylation. In MERVL-deficient embryos, the activity of the DNA demethylase ten-eleven translocation 3 (TET3) was suppressed, resulting in impaired demethylation when compared to normal development. This impairment might underpin the mechanism that impacts embryonic development. Collectively, our study not only verified the crucial role of MERVL in embryonic development but also probed its regulatory function in DNA methylation reprogramming, thereby laying a solid foundation for further investigations into MERVL's role.

The gain and loss of plasticity during development and evolution

Studies of embryonic plasticity, which were foundational for developmental biology, revealed variation across species and patterns of association with cleavage programs and adult regenerative capacity. Modern molecular and genetic tools now enable a reexamination of these classical experiments in diverse species and have the potential to reveal mechanisms that regulate plasticity over developmental time. This review synthesizes previous work on plasticity in embryos and adults and associated genetic mechanisms, providing a framework to organize data from a wide range of species. Mechanisms that explain how plasticity is lost in mammalian embryos are highlighted and crystallize a proposal for future studies in new research organisms that could identify shared principles for embryonic plasticity and, potentially, its maintenance into adulthood.

Totipotent-like reprogramming: Molecular machineries and chemical manipulations

Embryonic stem cells (ESCs) exhibit remarkable pluripotency, possessing the dual abilities of self-renewal and differentiation into any cell type within the embryonic lineage. Among cultivated mouse ESCs, a subpopulation known as 2-cell-like cells (2CLCs) displays a transcriptomic signature reminiscent of the 2-cell embryonic stage, with the capacity to differentiate into both embryonic and extraembryonic tissues. These 2CLCs have served as an invaluable totipotent-like cell model for deciphering the cellular and molecular mechanisms underlying the establishment of totipotency. Accumulating evidence has indicated that a multitude of regulators including transcription factors, epigenetic modifications, and RNA regulators, exert crucial functions in the reprogramming of ESCs towards 2CLCs. In addition to 2CLCs, alternative totipotent-like cell types can be induced and maintained through the administration of single or combined chemical supplements, offering promising cell resources for regenerative medicine. In this review, we summarize the current advancements in the molecular regulations of 2CLCs and chemical manipulations of totipotent-like cells in mice, providing a foundation for understanding the regulatory networks underlying cell totipotency.

3-Nitropropionic acid exposure inhibits embryo development by disrupting mitochondrial function and inducing oxidative stress

3-Nitropropionic acid (3-NP) is a naturally occurring mycotoxin produced by various fungi and plants. Despite reports on its toxicity, the potential impact of 3-NP exposure on reproductive health remains elusive. To this end, we conducted an in vitro study to investigate the toxic effects of 3-NP on the developmental processes of mouse embryos. Our results suggested that exposure to 50 μM 3-NP resulted in significant pre-implantation developmental arrest , with most embryos arrested at the 2-cell stage, indicating disruption of normal development. Further analysis indicated that 3-NP exposure altered embryonic gene expression, disrupted zygotic genome activation and maternal gene degradation, and inhibited maternal-zygote transition. Moreover, it impaired mitochondrial dysfunction, causing dysfunctional cellular energy metabolism and elevated intracellular oxidative stress, culminating in increased DNA damage. Additionally, 3-NP exposure caused aberrant epigenetic modifications, particularly the upregulation of histone methylation levels, including elevated H3K27me3 and H3K9me3, which are strongly related to gene expression silencing. In summary, this study elucidates the in vitro toxic effects of 3-NP on mouse embryo development and highlights its potential adverse effects on female reproductive health.

Comparative proteomic landscapes elucidate human preimplantation development and failure

Understanding mammalian preimplantation development, particularly in humans, at the proteomic level remains limited. Here, we applied our comprehensive solution of ultrasensitive proteomic technology to measure the proteomic profiles of oocytes and early embryos and identified nearly 8,000 proteins in humans and over 6,300 proteins in mice. We observed distinct proteomic dynamics before and around zygotic genome activation (ZGA) between the two species. Integrative analysis with translatomic data revealed extensive divergence between translation activation and protein accumulation. Multi-omic analysis indicated that ZGA transcripts often contribute to protein accumulation in blastocysts. Using mouse embryos, we identified several transcriptional regulators critical for early development, thereby linking ZGA to the first lineage specification. Furthermore, single-embryo proteomics of poor-quality embryos from over 100 patient couples provided insights into preimplantation development failure. Our study may contribute to reshaping the framework of mammalian preimplantation development and opening avenues for addressing human infertility.

Current status and hotspots of in vitro oocyte maturation: a bibliometric study of the past two decades

PURPOSE

In vitro maturation (IVM) of oocytes is a promising technique among assisted reproductive technologies. Although IVM has been used for many years, its efficiency is still relatively low compared to that of traditional in vitro fertilization (IVF) procedures. Therefore, we aimed to explore the hotspots and frontiers of IVM research over the past two decades and provide direction for IVM advancement.

METHODS

The articles and reviews related to IVM in the Web of Science Core Collection (WoSCC) were retrieved on June 03, 2024. Three bibliometric tools, VOSviewer 1.6.18 (2010), CiteSpace 6.1. R6 (2006), and Bibliometrix R package 4.1.0 (2017), were used to generate network maps and explore knowledge frontiers and trends. To uncover the latest research advancements and frontiers in the IVM field, we conducted an analysis of the entire IVM field, including all species. Given our focus on human IVM developments, we identified the leading countries, institutions, authors, and journals driving progress in human IVM.

RESULTS

A total of 5150 publications about IVM and 1534 publications in the specific context of human IVM were retrieved from the WoSCC. The number of publications on both overall IVM and human IVM fields has increased steadily. In human IVM, the United States (USA) and McGill University were the most prolific country and institution, respectively. Human Reproduction was both the most published in and the most cited journal in human IVM. Seang Lin, Tan was the most productive author, and Ri-Cheng, Chian's papers were the most cited in human IVM. Furthermore, five hotspot topics were summarized, namely, culture system, supplementation, cooperation in the ovarian follicle, gene expression, and oocyte cryopreservation.

CONCLUSIONS

Further studies could concentrate on the following topics: (1) the mechanisms involved in oocyte maturation in vivo and in vitro, especially in energy metabolism and intercellular communications; (2) the establishment of IVM culture systems, including standardization of the biphasic IVM culture system and supplementation; (3) the genetic differences between oocytes matured in vivo and in vitro; and (4) the mechanism of cryopreservation-inflicted damage and solutions to this challenge. For human IVM, it is necessary to precisely assess the developmental stages of oocytes and adjust the IVM process accordingly to develop tailored culture media. Concurrently, clinical trials are essential for evaluating the effectiveness and safety of IVM.

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

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

One carbon metabolism supplementation in maturation medium but not embryo culture medium improves the yield of blastocysts from bovine oocytes

Optimizing oocyte maturation and embryo culture media could enhance in vitro embryo production. The purpose of the present study was to investigate the role of supplementing one carbon metabolism (OCM) substrates and its cofactors (Cystine, Zinc, Betaine, B2, B3, B6, B12 and 5-methyltetrahydrofolate) in maturation and/or embryo culture media on the rate of blastocyst formation and pregnancy outcomes following the transfer of the resulting blastocysts in bovines. In the first experiment, 2537 bovine oocytes were recovered from slaughterhouse ovaries and then matured either in conventional maturation medium (IVM) or IVM supplemented with OCM substrates (Sup-IVM). After in vitro fertilization, the putative zygotes from each treatment (IVM or Sup-IVM) were cultured in the media either without (IVM/IVC or Sup-IVM/IVC) or with (IVM/Sup-IVC or Sup-IVM/Sup-IVC) OCM supplementation. The blastocyst rate, assessed on day 8, was significantly increased in Sup-IVM/IVC group (34.90 ± 2.52) as compared to IVM/IVC (17.06 ± 1.69; P = 0.0001) and Sup-IVM/Sup-IVC (20.29 ± 2.75; P = 0.004) and non-significantly as compared to IVM/Sup-IVC (24.86 ± 5.37). In the second experiment, non-matured bovine oocytes were collected by transvaginal ovum pick up after FSH stimulation, randomly allocated into IVM/IVC (n = 275) and Sup-IVM/IVC (n = 260) and the blastocysts achieved at day 7 were transferred in recipient cattle. The blastocyst rate was significantly higher in Sup-IVM/IVC group (38.85%) as compared to the IVM/IVC group (23.64%; P < 0.0001). After single embryo transfer, the supplemented blastocysts were at least as competent as non-supplemented ones with a non-significantly higher (20% vs. 14%) pregnancy rate and the advantage of several good quality blastocysts available for future use. In conclusion, optimizing the maturation medium with OCM substrates and its cofactors could enhance the formation of viable blastocysts with the potential to increase the cumulative birth rate in cattle.

Herpesviruses mimic zygotic genome activation to promote viral replication

Zygotic genome activation (ZGA) is crucial for maternal to zygotic transition at the 2-8-cell stage in order to overcome silencing of genes and enable transcription from the zygotic genome. In humans, ZGA is induced by DUX4, a pioneer factor that drives expression of downstream germline-specific genes and retroelements. Here we show that herpesviruses from all subfamilies, papillomaviruses and Merkel cell polyomavirus actively induce DUX4 expression to promote viral transcription and replication. Analysis of single-cell sequencing data sets from patients shows that viral DUX4 activation is of relevance in vivo. Herpes-simplex virus 1 (HSV-1) immediate early proteins directly induce expression of DUX4 and its target genes, which mimics zygotic genome activation. Upon HSV-1 infection, DUX4 directly binds to the viral genome and promotes viral transcription. DUX4 is functionally required for infection, since genetic depletion by CRISPR/Cas9 as well as degradation of DUX4 by nanobody constructs abrogates HSV-1 replication. Our results show that DNA viruses including herpesviruses mimic an embryonic-like transcriptional program that prevents epigenetic silencing of the viral genome and facilitates herpesviral gene expression.

LncRNA XLOC-040580 targeted by TPRA1 coordinate zygotic genome activation during porcine embryonic development

Long noncoding RNAs (lncRNAs) are crucial in porcine preimplantation embryonic development, yet their regulatory role during zygote genome activation (ZGA) is poorly understood. We analyzed transcriptome data from porcine fetal fibroblasts (PEF), induced pluripotent stem cells (iPS), and preimplantation embryos, identifying ZGA-specific lncRNAs like XLOC-040580, and further predicted its potentially interacting genes TPRA1 and BCL2L1 via co-expression network. XLOC-040580 was knocked down by siRNA microinjection and the expression of ZGA-related genes was detected by qRT-PCR. After microinjecting siRNA targeting TPRA1 and BCL2L1 at the one-cell stage, we counted the blastocyst development rate. The blastocyst development rate was consistent with the results from si-XLOC-040580 after si-TPRA1. Through dual-luciferase reporter assays, we found that XLOC-040580 was a downstream target of TPRA1. To further elucidate the mechanism of XLOC-040580, Single-cell mRNA sequencing after XLOC-040580 knockdown revealed its regulatory network involved in embryonic developmental defects. Transcriptome analysis revealed that XLOC-040580 was specifically expressed during zygote activation. Knockdown of XLOC-040580 decreased the blastocyst development rate and reduced both the total blastocyst cell number and TE cell number. TPRA1 and BCL2L1 were specifically co-expressed with XLOC-040580 during ZGA stage, and TPRA1 could interact with the promoter region of XLOC-040580 and regulate its expression. Knockdown of TPRA1 or XLOC-040580 blocked porcine embryonic development by affecting the expression of ZGA-related genes. We found and validated that lncRNA XLOC-040580 played a key role in the ZGA process, which was regulated by TPRA1. These results implied that the functional axis of TPRA1-XLOC-040580-downstream genes involved in ZGA-related functions also coordinated early embryonic development in porcine.

Polycomb function in early mouse development

Epigenetic factors are crucial for ensuring proper chromatin dynamics during the initial stages of embryo development. Among these factors, the Polycomb group (PcG) of proteins plays a key role in establishing correct transcriptional programmes during mouse embryogenesis. PcG proteins are classified into two complexes: Polycomb repressive complex 1 (PRC1) and PRC2. Both complexes decorate histone proteins with distinct post-translational modifications (PTMs) that are predictive of a silent transcriptional chromatin state. In recent years, a critical adaptation of the classical techniques to analyse chromatin profiles and to study biochemical interactions at low-input resolution has allowed us to deeply explore PcG molecular mechanisms in the very early stages of mouse embryo development- from fertilisation to gastrulation, and from zygotic genome activation (ZGA) to specific lineages differentiation. These advancements provide a foundation for a deeper understanding of the fundamental role Polycomb complexes play in early development and have elucidated the mechanistic dynamics of PRC1 and PRC2. In this review, we discuss the functions and molecular mechanisms of both PRC1 and PRC2 during early mouse embryo development, integrating new studies with existing knowledge. Furthermore, we highlight the molecular functionality of Polycomb complexes from ZGA through gastrulation, with a particular focus on non-canonical imprinted and bivalent genes, and Hox cluster regulation.

Rise and SINE: roles of transcription factors and retrotransposons in zygotic genome activation

In sexually reproducing organisms, life begins with the fusion of transcriptionally silent gametes, the oocyte and sperm. Although initiation of transcription in the embryo, known as zygotic genome activation (ZGA), is universally required for development, the transcription factors regulating this process are poorly conserved. In this Perspective, we discuss recent insights into the mechanisms of ZGA in totipotent mammalian embryos, namely ZGA regulation by several transcription factors, including by orphan nuclear receptors (OrphNRs) such as the pioneer transcription factor NR5A2, and by factors of the DUX, TPRX and OBOX families. We performed a meta-analysis and compiled a list of pan-ZGA genes, and found that most of these genes are indeed targets of the above transcription factors. Remarkably, more than a third of these ZGA genes appear to be regulated both by OrphNRs such as NR5A2 and by OBOX proteins, whose motifs co-occur in SINE B1 retrotransposable elements, which are enriched near ZGA genes. We propose that ZGA in mice is activated by recruitment of multiple transcription factors to SINE B1 elements that function as enhancers, and discuss a potential relevance of this mechanism to Alu retrotransposable elements in human ZGA.

Shedding light on DNA methylation and its clinical implications: the impact of long-read-based nanopore technology

DNA methylation is an essential epigenetic mechanism for regulation of gene expression, through which many physiological (X-chromosome inactivation, genetic imprinting, chromatin structure and miRNA regulation, genome defense, silencing of transposable elements) and pathological processes (cancer and repetitive sequences-associated diseases) are regulated. Nanopore sequencing has emerged as a novel technique that can analyze long strands of DNA (long-read sequencing) without chemically treating the DNA. Interestingly, nanopore sequencing can also extract epigenetic status of the nucleotides (including both 5-Methylcytosine and 5-hydroxyMethylcytosine), and a large variety of bioinformatic tools have been developed for improving its detection properties. Out of all genomic regions, long read sequencing provides advantages in studying repetitive elements, which are difficult to characterize through other sequencing methods. Transposable elements are repetitive regions of the genome that are silenced and usually display high levels of DNA methylation. Their demethylation and activation have been observed in many cancers. Due to their repetitive nature, it is challenging to accurately estimate DNA methylation levels within transposable elements using short sequencing technologies. The advantage to sequence native DNA (without PCR amplification biases or harsh bisulfite treatment) and long and ultra long reads coupled with epigenetic states of the DNA allows to accurately estimate DNA methylation levels in transposable elements. This is a big step forward for epigenomic studies, and unsolved questions regarding gene expression and transposable elements silencing through DNA methylation can now be answered.

Zscan4 mediates ubiquitination and degradation of the corepressor complex to promote chromatin accessibility in 2C-like cells

Zygotic genome activation occurs in two-cell (2C) embryos, and a 2C-like state is also activated in sporadic (~1%) naïve embryonic stem cells in mice. Elevated chromatin accessibility is critical for the 2C-like state to occur, yet the underlying molecular mechanisms remain elusive. Zscan4 exhibits burst expression in 2C embryos and 2C-like cells. Here, we show that Zscan4 mediates chromatin remodeling to promote the chromatin accessibility for achieving the 2C-like state. Through coimmunoprecipitation/mass spectrometry, we identified that Zscan4 interacts with the corepressors Kap1/Trim28, Lsd1, and Hdac1, also with H3K9me3 modifiers Suv39h1/2, to transiently form a repressive chromatin complex. Then, Zscan4 mediates the degradation of these chromatin repressors by recruiting Trim25 as an E3 ligase, enabling the ubiquitination of Lsd1, Hdac1, and Suv39h1/2. Degradation of the chromatin repressors promotes the chromatin accessibility for activation of the 2C-like state. These findings reveal the molecular insights into the roles of Zscan4 in promoting full activation of the 2C-like state.

HIRA and dPCIF1 coordinately establish totipotent chromatin and control orderly ZGA in Drosophila embryos

Early embryos undergo profound changes in their genomic architecture to establish the totipotent state, enabling pioneer factors to access chromatin and drive zygotic genome activation (ZGA). However, the mechanisms by which the totipotent state is established and properly interpreted by pioneer factors to allow orderly ZGA remain unknown. Here, we identify the H3.3-specific chaperone HIRA as a factor involving establishing totipotent-state chromatin in Drosophila early embryos. Through cophase separation with HIRA, the pioneer factor GAGA factor (GAF) efficiently binds to H3.3-marked nucleosomes to activate major-wave zygotic genes. Importantly, dPCIF1, a chromatin-associated protein, antagonized the GAF-HIRA interaction by competitively binding to HIRA, thereby restricting GAF on earlier chromatin and avoiding premature ZGA. Hence, the coordinated action of HIRA and dPCIF1 ensures sequential ZGA from the minor to major wave in early embryos. This study provides insights into understanding how a totipotent state is established and properly controlled during ZGA.

Population size interacts with reproductive longevity to shape the germline mutation rate

Mutation rates vary across the tree of life by many orders of magnitude, with lower mutation rates in species that reproduce quickly and maintain large effective population sizes. A compelling explanation for this trend is that large effective population sizes facilitate selection against weakly deleterious "mutator alleles" such as variants that interfere with the molecular efficacy of DNA repair. However, in multicellular organisms, the relationship of the mutation rate to DNA repair efficacy is complicated by variation in reproductive age. Long generation times leave more time for mutations to accrue each generation, and late reproduction likely amplifies the fitness consequences of any DNA repair defect that creates extra mutations in the sperm or eggs. Here, we present theoretical and empirical evidence that a long generation time amplifies the strength of selection for low mutation rates in the spermatocytes and oocytes. This leads to the counterintuitive prediction that the species with the highest germline mutation rates per generation are also the species with most effective mechanisms for DNA proofreading and repair in their germ cells. In contrast, species with different generation times accumulate similar mutation loads during embryonic development. Our results parallel recent findings that the longest-lived species have the lowest mutation rates in adult somatic tissues, potentially due to selection to keep the lifetime mutation load below a harmful threshold.

Epigenetic Explorations of Neurological Disorders, the Identification Methods, and Therapeutic Avenues

Neurodegenerative disorders are major health concerns globally, especially in aging societies. The exploration of brain epigenomes, which consist of multiple forms of DNA methylation and covalent histone modifications, offers new and unanticipated perspective into the mechanisms of aging and neurodegenerative diseases. Initially, chromatin defects in the brain were thought to be static abnormalities from early development associated with rare genetic syndromes. However, it is now evident that mutations and the dysregulation of the epigenetic machinery extend across a broader spectrum, encompassing adult-onset neurodegenerative diseases. Hence, it is crucial to develop methodologies that can enhance epigenetic research. Several approaches have been created to investigate alterations in epigenetics on a spectrum of scales-ranging from low to high-with a particular focus on detecting DNA methylation and histone modifications. This article explores the burgeoning realm of neuroepigenetics, emphasizing its role in enhancing our mechanistic comprehension of neurodegenerative disorders and elucidating the predominant techniques employed for detecting modifications in the epigenome. Additionally, we ponder the potential influence of these advancements on shaping future therapeutic approaches.

Screening of functional maternal-specific chromatin regulators in early embryonic development of zebrafish

The early stages of embryonic development rely on maternal products for proper regulation. However, screening for functional maternal-specific factors is challenging due to the time- and labor-intensive nature of traditional approaches. Here, we combine a computational pipeline and F0 null mutant technology to screen for functional maternal-specific chromatin regulators in zebrafish embryogenesis and identify Mcm3l, Mcm6l, and Npm2a as playing essential roles in DNA replication and cell division. Our results contribute to understanding the molecular mechanisms underlying early embryo development and highlight the importance of maternal-specific chromatin regulators in this critical stage.

5-Formylcytosine is an activating epigenetic mark for RNA Pol III during zygotic reprogramming

5-Methylcytosine (5mC) is an established epigenetic mark in vertebrate genomic DNA, but whether its oxidation intermediates formed during TET-mediated DNA demethylation possess an instructive role of their own that is also physiologically relevant remains unresolved. Here, we reveal a 5-formylcytosine (5fC) nuclear chromocenter, which transiently forms during zygotic genome activation (ZGA) in Xenopus and mouse embryos. We identify this chromocenter as the perinucleolar compartment, a structure associated with RNA Pol III transcription. In Xenopus embryos, 5fC is highly enriched on Pol III target genes activated at ZGA, notably at oocyte-type tandem arrayed tRNA genes. By manipulating Tet and Tdg enzymes, we show that 5fC is required as a regulatory mark to promote Pol III recruitment as well as tRNA expression. Concordantly, 5fC modification of a tRNA transgene enhances its expression in vivo. The results establish 5fC as an activating epigenetic mark during zygotic reprogramming of Pol III gene expression.

The subcortical maternal complex modulates the cell cycle during early mammalian embryogenesis via 14-3-3

The subcortical maternal complex (SCMC) is essential for safeguarding female fertility in mammals. Assembled in oocytes, the SCMC maintains the cleavage of early embryos, but the underlying mechanism remains unclear. Here, we report that 14-3-3, a multifunctional protein, is a component of the SCMC. By resolving the structure of the 14-3-3-containing SCMC, we discover that phosphorylation of TLE6 contributes to the recruitment of 14-3-3. Mechanistically, during maternal-to-embryo transition, the SCMC stabilizes 14-3-3 protein and contributes to the proper control of CDC25B, thus ensuring the activation of the maturation-promoting factor and mitotic entry in mouse zygotes. Notably, the SCMC establishes a conserved molecular link with 14-3-3 and CDC25B in human oocytes/embryos. This study discloses the molecular mechanism through which the SCMC regulates the cell cycle in early embryos and elucidates the function of the SCMC in mammalian early embryogenesis.

Somatic mosaicism in schizophrenia brains reveals prenatal mutational processes

Germline mutations modulate the risk of developing schizophrenia (SCZ). Much less is known about the role of mosaic somatic mutations in the context of SCZ. Deep (239×) whole-genome sequencing (WGS) of brain neurons from 61 SCZ cases and 25 controls postmortem identified mutations occurring during prenatal neurogenesis. SCZ cases showed increased somatic variants in open chromatin, with increased mosaic CpG transversions (CpG>GpG) and T>G mutations at transcription factor binding sites (TFBSs) overlapping open chromatin, a result not seen in controls. Some of these variants alter gene expression, including SCZ risk genes and genes involved in neurodevelopment. Although these mutational processes can reflect a difference in factors indirectly involved in disease, increased somatic mutations at developmental TFBSs could also potentially contribute to SCZ.

The emerging H3K9me3 chromatin landscape during zebrafish embryogenesis

The structural organization of eukaryotic genomes is contingent upon the fractionation of DNA into transcriptionally permissive euchromatin and repressive heterochromatin. However, we have a limited understanding of how these distinct states are first established during animal embryogenesis. Histone 3 lysine 9 trimethylation (H3K9me3) is critical to heterochromatin formation, and bulk establishment of this mark is thought to help drive large-scale remodeling of an initially naive chromatin state during animal embryogenesis. However, a detailed understanding of this process is lacking. Here, we leverage CUT&RUN to define the emerging H3K9me3 landscape of the zebrafish embryo with high sensitivity and temporal resolution. Despite the prevalence of DNA transposons in the zebrafish genome, we found that LTR transposons are preferentially targeted for embryonic H3K9me3 deposition, with different families exhibiting distinct establishment timelines. High signal-to-noise ratios afforded by CUT&RUN revealed new, emerging sites of low-amplitude H3K9me3 that initiated before the major wave of zygotic genome activation (ZGA). Early sites of establishment predominated at specific subsets of transposons and were particularly enriched for transposon sequences with maternal piRNAs and pericentromeric localization. Notably, the number of H3K9me3 enriched sites increased linearly across blastula development, while quantitative comparison revealed a >10-fold genome-wide increase in H3K9me3 signal at established sites over just 30 min at the onset of major ZGA. Continued maturation of the H3K9me3 landscape was observed beyond the initial wave of bulk establishment.

Inhibition of neddylation disturbs zygotic genome activation through histone modification change and leads to early development arrest in mouse embryos

Post-translational modification and fine-tuned protein turnover are of great importance in mammalian early embryo development. Apart from the classic protein degradation promoting ubiquitination, new forms of ubiquitination-like modification are yet to be fully understood. Here, we demonstrate the function and potential mechanisms of one ubiquitination-like modification, neddylation, in mouse preimplantation embryo development. Treated with specific inhibitors, zygotes showed a dramatically decreased cleavage rate and almost all failed to enter the 4-cell stage. Transcriptional profiling showed genes were differentially expressed in pathways involving cell fate determination and cell differentiation, including several down-regulated zygotic genome activation (ZGA) marker genes. A decreased level of phosphorylated RNA polymerase II was detected, indicating impaired gene transcription inside the embryo cell nucleus. Proteomic data showed that differentially expressed proteins were enriched in histone modifications. We confirmed the lowered in methyltransferase (KMT2D) expression and a decrease in histone H3K4me3. At the same time, acetyltransferase (CBP/p300) reduced, while deacetylase (HDAC6) increased, resulting in an attenuation in histone H3K27ac. Additionally, we observed the up-regulation in YAP1 and RPL13 activities, indicating potential abnormalities in the downstream response of Hippo signaling pathway. In summary, we found that inhibition of neddylation induced epigenetic changes in early embryos and led to abnormalities in related downstream signaling pathways. This study sheds light upon new forms of ubiquitination regulating mammalian embryonic development and may contribute to further investigation of female infertility pathology.

New insights into oocyte cytoplasmic lattice-associated proteins

Oocyte maturation and preimplantation embryo development are critical to successful pregnancy outcomes and the correct establishment and maintenance of genomic imprinting. Thanks to novel technologies and omics studies in human patients and mouse models, the importance of the proteins associated with the cytoplasmic lattices (CPLs), highly abundant structures found in the cytoplasm of mammalian oocytes and preimplantation embryos, in the maternal to zygotic transition is becoming increasingly evident. This review highlights the recent discoveries on the role of these proteins in protein storage and other oocyte cytoplasmic processes, epigenetic reprogramming, and zygotic genome activation (ZGA). A better comprehension of these events may significantly improve clinical diagnosis and pave the way for targeted interventions aiming to correct or mitigate female fertility issues and genomic imprinting disorders.

Protein Modifications During Early Embryo Development

BACKGROUND

Infertility is a global reproductive health burden. Assisted reproductive technologies (ARTs) have been widely used to help patients become pregnant. Few embryos develop to the blastocyst stage with ARTs, leading to relatively low live birth rates. Protein modifications play crucial roles in nearly every aspect of cell biology, including reproductive processes. The aim of this study was to explore the characteristics of protein modifications during embryonic development.

METHODS

Proteomic data from humans and mice were acquired from the integrated proteome resources (iProX) of ProteomeXchange (PXD024267) and a tandem mass tag (TMT)-mass spectrometry dataset. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were applied for functional annotation. Protein-protein interactions (PPIs) of the modification-related genes were revealed by the STRING database. Modified proteins during mouse embryogenesis were visualized through heatmaps of hierarchically clustering using k-means.

RESULTS

We identified modification-related proteins in human embryo development and characterized them through heatmaps, GO analysis, KEGG analysis, and PPI network analysis. We found that the 4-cell stage to the 8-cell stage might be the demarcation period for modification-related protein expression patterns during embryo development. Using quantitative mass spectrometry, we elucidated the methylation, acetylation, and ubiquitination events that occur during mouse embryogenesis to validate our findings in human embryonic development to some extent.

CONCLUSIONS

The results of our study suggest that the posttranslational modifications (PTMs) of human preimplantation embryos might exhibit the same trends as those in mice to exert synergistic and fine-tuned regulatory effects during embryonic development.

Kick-starting the zygotic genome: licensors, specifiers, and beyond

Zygotic genome activation (ZGA), the first transcription event following fertilization, kickstarts the embryonic program that takes over the control of early development from the maternal products. How ZGA occurs, especially in mammals, is poorly understood due to the limited amount of research materials. With the rapid development of single-cell and low-input technologies, remarkable progress made in the past decade has unveiled dramatic transitions of the epigenomes, transcriptomes, proteomes, and metabolomes associated with ZGA. Moreover, functional investigations are yielding insights into the key regulators of ZGA, among which two major classes of players are emerging: licensors and specifiers. Licensors would control the permission of transcription and its timing during ZGA. Accumulating evidence suggests that such licensors of ZGA include regulators of the transcription apparatus and nuclear gatekeepers. Specifiers would instruct the activation of specific genes during ZGA. These specifiers include key transcription factors present at this stage, often facilitated by epigenetic regulators. Based on data primarily from mammals but also results from other species, we discuss in this review how recent research sheds light on the molecular regulation of ZGA and its executors, including the licensors and specifiers.

Transcriptome analysis of the effects of high temperature on zygotic genome activation in porcine embryos

Damage to the development of porcine gametes and embryos caused by high temperatures (HT) is one of the main reasons for the decline in the economic benefits of the livestock industry. Zygotic genome activation (ZGA) marks the beginning of gene expression programs in mammalian pre-implantation embryos. In pigs, ZGA occurs at the 4-cell (4 C) stage, indicating that correct gene expression at this stage plays an important regulatory role in embryonic development. However, the effect of the HT environment on early porcine embryonic development and the RNA expression profile of ZGA remain unclear. In this study, we compared the RNA transcription patterns of porcine 4 C embryos under normal and HT conditions using RNA-seq and identified 326 differentially expressed genes (DEGs). These changes were mainly related to DNA polymerase activity, DNA replication, and nucleotidyltransferase activity. In addition, entries for reverse transcription and endonuclease activity were enriched, indicating that ZGA interfered under HT conditions. Further comparison of the experimental results with the porcine ZGA gene revealed 39 ZGA genes among the DEGs. KEGG and GSEA analysis showed that the oxidative phosphorylation pathway was significantly enriched and signaling pathways related to energy metabolism were significantly downregulated. We also found that NDUFA6 and CDKN1A were located at the center of the protein-protein interaction network diagram of the DEGs. In summary, HT conditions affect mitochondrial function and oxidative phosphorylation levels, and lead to changes in the expression pattern of ZGA in early porcine embryos, with its hub genes NDUFA6 and CDKN1A.

The role of epigenetics in women's reproductive health: the impact of environmental factors

This paper explores the significant role of epigenetics in women's reproductive health, focusing on the impact of environmental factors. It highlights the crucial link between epigenetic modifications-such as DNA methylation and histones post-translational modifications-and reproductive health issues, including infertility and pregnancy complications. The paper reviews the influence of pollutants like PM2.5, heavy metals, and endocrine disruptors on gene expression through epigenetic mechanisms, emphasizing the need for understanding how dietary, lifestyle choices, and exposure to chemicals affect gene expression and reproductive health. Future research directions include deeper investigation into epigenetics in female reproductive health and leveraging gene editing to mitigate epigenetic changes for improving IVF success rates and managing reproductive disorders.

Variants in NLRP2 and ZFP36L2, non-core components of the human subcortical maternal complex, cause female infertility with embryonic development arrest

The subcortical maternal complex (SCMC), which is vital in oocyte maturation and embryogenesis, consists of core proteins (NLRP5, TLE6, OOEP), non-core proteins (PADI6, KHDC3L, NLRP2, NLRP7), and other unknown proteins that are encoded by maternal effect genes. Some variants of SCMC genes have been linked to female infertility characterized by embryonic development arrest. However, so far, the candidate non-core SCMC components associated with embryonic development need further exploration and the pathogenic variants that have been identified are still limited. In this study, we discovered two novel variants [p.(Ala131Val) and p.(Met326Val)] of NLRP2 in patients with primary infertility displaying embryonic development arrest from large families. In vitro studies using 293T cells and mouse oocytes, respectively, showed that these variants significantly decreased protein expression and caused the phenotype of embryonic development arrest. Additionally, we combined the 'DevOmics' database with the whole exome sequence data of our cohort and screened out a new candidate non-core SCMC gene ZFP36L2. Its variants [p.(Ala241Pro) and p.(Pro291dup)] were found to be responsible for embryonic development arrest. Co-immunoprecipitation experiments in 293T cells, used to demonstrate the interaction between proteins, verified that ZFP36L2 is one of the human SCMC components, and microinjection of ZFP36L2 complementary RNA variants into mouse oocytes affected embryonic development. Furthermore, the ZFP36L2 variants were associated with disrupted stability of its target mRNAs, which resulted in aberrant H3K4me3 and H3K9me3 levels. These disruptions decreased oocyte quality and further developmental potential. Overall, this is the first report of ZFP36L2 as a non-core component of the human SCMC and we found four novel pathogenic variants in the NLRP2 and ZFP36L2 genes in 4 of 161 patients that caused human embryonic development arrest. These findings contribute to the genetic diagnosis of female infertility and provide new insights into the physiological function of SCMC in female reproduction.

Epigenetic aging in major depressive disorder: Clocks, mechanisms and therapeutic perspectives

Depression, a chronic mental disorder characterized by persistent sadness, loss of interest, and difficulty in daily tasks, impacts millions globally with varying treatment options. Antidepressants, despite their long half-life and minimal effectiveness, leave half of patients undertreated, highlighting the need for new therapies to enhance well-being. Epigenetics, which studies genetic changes in gene expression or cellular phenotype without altering the underlying Deoxyribonucleic Acid (DNA) sequence, is explored in this article. This article delves into the intricate relationship between epigenetic mechanisms and depression, shedding light on how environmental stressors, early-life adversity, and genetic predispositions shape gene expression patterns associated with depression. We have also discussed Histone Deacetylase (HDAC) inhibitors, which enhance cognitive function and mood regulation in depression. Non-coding RNAs, (ncRNAs) such as Long Non-Coding RNAs (lncRNAs) and micro RNA (miRNAs), are highlighted as potential biomarkers for detecting and monitoring major depressive disorder (MDD). This article also emphasizes the reversible nature of epigenetic modifications and their influence on neuronal growth processes, underscoring the dynamic interplay between genetics, environment, and epigenetics in depression development. It explores the therapeutic potential of targeting epigenetic pathways in treating clinical depression. Additionally, it examines clinical findings related to epigenetic clocks and their role in studying depression and biological aging.

Efficiency of the zinc chelator 1,10-phenanthroline for assisted oocyte activation following ICSI in pigs

Context In vitro embryo production in pigs is an important tool for advancing biomedical research. Intracytoplasmic sperm injection (ICSI) circumvents the polyspermy problems associated with conventional IVF in porcine. However, the suboptimal efficiency for ICSI in pigs requires new strategies to increase blastocyst formation rates. Aim To investigate novel methods for assisted activation using the zinc chelator 1,10-phenanthroline (PHEN), and to improve embryo developmental competence and quality of ICSI porcine blastocyst. Methods ICSI embryos were treated with PHEN after or before sperm injection, recording pronuclear formation, blastocyst rate and the expression of SMARCA4, OCT4, SOX2 and CDX2. Key results Neither electrical nor PHEN significantly improves pronuclear formation rates before or after ICSI. Following in vitro culture to the blastocyst stage, no significant differences were observed in developmental rates among the groups. Moreover, the use of PHEN did not alter the total cell number or the expression of OCT4, SOX2 and CDX2 in pig ICSI blastocysts. Conclusions Assisted oocyte activation with PHEN does not affect the preimplantation development of ICSI-derived pig embryos. Implications These results hold significance in refining and advancing the application of assisted oocyte activation techniques. They offer insights into addressing fertility issues and propelling advancements in human and animal reproductive medicine.

GATAD2B is required for pre-implantation embryonic development by regulating zygotic genome activation

Major zygotic genome activation (ZGA) occurs at the late 2-cell stage and involves the activation of thousands of genes, supporting early embryonic development. The reasons underlying the regulation of ZGA are not clear. Acetylation modifications of histone tails promote transcriptional activation, and the maternal deletion of H4K16ac leads to failure in ZGA. GATAD2B is one of the core subunits of the nucleosome remodelling and histone deacetylation (NuRD) complex. Our research has shown that GATAD2B exhibits specific nucleus localization and high protein expression from the late 2-cell stage to the 8-cell stage. This intriguing phenomenon prompted us to investigate the relationship between GATAD2B and the ZGA. We discovered a distinctive pattern of GATAD2B, starting from the late 2-cell stage with nuclear localization. GATAD2B depletion resulted in defective embryonic development, including increased DNA damage at morula, decreased blastocyst formation rate, and abnormal differentiation of ICM/TE lineages. Consistent with the delay during the cleavage stage, the transcriptome analysis of the 2-cell embryo revealed inhibition of the cell cycle G2/M phase transition pathway. Furthermore, the GATAD2B proteomic data provided clear evidence of a certain association between GATAD2B and molecules involved in the cell cycle pathway. As hypothesized, GATAD2B-deficient 2-cell embryos exhibited abnormalities in ZGA during the maternal-to-embryonic transition, with lower expression of the major ZGA marker MERVL. Overall, our results demonstrate that GATAD2B is essential for early embryonic development, in part through facilitating ZGA.

Intergenerational metabolism-disrupting effects of maternal exposure to plasticizer acetyl tributyl citrate (ATBC)

Environmental chemicals and pollutants are increasingly recognized for their potential transgenerational effects. Acetyl tributyl citrate (ATBC), a widely used plasticizer substituting di-(2-ethylhexyl) phthalate (DEHP), was identified as an inducer of lipogenesis in male mice by our previous research. This study aimed to investigate the impact of ATBC exposure on the metabolic homeostasis of female mice and simultaneously evaluate its intergenerational effects. Female C57BL/6J mice were orally exposed to ATBC (0.01 or 1 μg/kg/day) for 10 weeks before mating with unexposed male mice. The resulting F1 female mice were bred with unexposed males to generate F2 offspring. Our results indicated that 10-week ATBC exposure disrupted glucose metabolism homeostasis and the reproductive system in F0 female mice. In F1 female mice, elevated liver lipid levels and mild insulin resistance were observed. In the F2 generation, maternal ATBC exposure resulted in increased weight gain, elevated liver triglycerides, and higher fasting blood glucose levels, primarily in F2 male mice. These findings suggest that maternal ATBC exposure may exert intergenerational disturbing effects on glucose metabolism across generations of mice. Further investigation is needed to evaluate the health risks associated with ATBC exposure.

Expression pattern of ATG4C and its effect on early embryonic development of porcine oocytes

Autophagy is essential for oocyte maturation and preimplantation embryo development. ATG4C, a member of the ATG4 family, plays a crucial role in the autophagy process. The effect of ATG4C on the early embryonic development in pig has not been studied. In this study, the expression patterns of ATG4C were explored using qRT-PCR and immunofluorescence staining. Different concentrations of serum were added to in vitro maturation (IVM) medium to investigate its effects on oocyte maturation and embryonic development. Finally, the developmental potential of parthenogenetic embryos was detected by downregulating ATG4C in MII stage oocytes under 0 % serum condition. The results revealed that ATG4C was highly expressed in porcine oocytes matured in vitro and in parthenogenetic embryos. Compared with the 10 % serum group, the cumulus cell expansion, first polar body (PB1) extrusion rate, and subsequent developmental competence of embryos were reduced in the 0 % and 5 % serum groups. The mRNA levels of LC3, ATG5, BECLIN1, TFAM, PGC1α, and PINK1 were significantly increased (P < 0.05) in the 0 % serum group. ATG4C was significantly upregulated in the embryos at the 1-cell, 2-cell, 8-cell, and 16-cell stages in the 0 % serum group (P < 0.05). Compared with the negative control group, downregulation of ATG4C significantly decreased the 4-cell, 8-cell, and blastocyst rates (P < 0.05), and the expression of genes related to autophagy, mitochondria, and zygotic genome activation (ZGA) was significantly decreased (P < 0.05). The relative fluorescence intensity of LC3 and mitochondrial content in the ATG4C siRNA group was significantly reduced (P < 0.05). Collectively, the results indicate that ATG4C is highly expressed in porcine oocytes matured in vitro and in early embryos, and inhibition of ATG4C effects embryonic developmental competence by decreasing autophagy, mitochondrial content, and ZGA under serum-free condition.

RNA m6A modification regulates cell fate transition between pluripotent stem cells and 2-cell-like cells

N6-methyladenosine (m6A) exerts essential roles in early embryos, especially in the maternal-to-zygotic transition stage. However, the landscape and roles of RNA m6A modification during the transition between pluripotent stem cells and 2-cell-like (2C-like) cells remain elusive. Here, we utilised ultralow-input RNA m6A immunoprecipitation to depict the dynamic picture of transcriptome-wide m6A modifications during 2C-like transitions. We found that RNA m6A modification was preferentially enriched in zygotic genome activation (ZGA) transcripts and MERVL with high expression levels in 2C-like cells. During the exit of the 2C-like state, m6A facilitated the silencing of ZGA genes and MERVL. Notably, inhibition of m6A methyltransferase METTL3 and m6A reader protein IGF2BP2 is capable of significantly delaying 2C-like state exit and expanding 2C-like cells population. Together, our study reveals the critical roles of RNA m6A modification in the transition between 2C-like and pluripotent states, facilitating the study of totipotency and cell fate decision in the future.