Explore the vast range of titles available.

During the essential and conserved process of zygotic genome activation (ZGA), chromatin accessibility must increase to promote transcription. Drosophila is a well-established model for defining mechanisms that drive ZGA. Zelda (ZLD) is a key pioneer transcription factor (TF) that promotes ZGA in the Drosophila embryo. However, many genomic loci that contain GA-rich motifs become accessible during ZGA independent of ZLD. Therefore, we hypothesized that other early TFs that function with ZLD have not yet been identified, especially those that are capable of binding to GA-rich motifs such as chromatin-linked adaptor for male-specific lethal (MSL) proteins (CLAMP). Here, we demonstrate that Drosophila embryonic development requires maternal CLAMP to (1) activate zygotic transcription; (2) increase chromatin accessibility at promoters of specific genes that often encode other essential TFs; and (3) enhance chromatin accessibility and facilitate ZLD occupancy at a subset of key embryonic promoters. Thus, CLAMP functions as a pioneer factor that plays a targeted yet essential role in ZGA.

Following fertilization, the genomes of the germ cells are reprogrammed to form the totipotent embryo. Pioneer transcription factors are essential for remodeling the chromatin and driving the initial wave of zygotic gene expression. In Drosophila melanogaster , the pioneer factor Zelda is essential for development through this dramatic period of reprogramming, known as the maternal-to-zygotic transition (MZT). However, it was unknown whether additional pioneer factors were required for this transition. We identified an additional maternally encoded factor required for development through the MZT, GAGA Factor (GAF). GAF is necessary to activate widespread zygotic transcription and to remodel the chromatin accessibility landscape. We demonstrated that Zelda preferentially controls expression of the earliest transcribed genes, while genes expressed during widespread activation are predominantly dependent on GAF. Thus, progression through the MZT requires coordination of multiple pioneer-like factors, and we propose that as development proceeds control is gradually transferred from Zelda to GAF. Most cells in an organism share the exact same genetic information, yet they still adopt distinct identities. This diversity emerges because only a selection of genes is switched on at any given time in a cell. Proteins that latch onto DNA control this specificity by activating certain genes at the right time. However, to perform this role they first need to physically access DNA: this can be difficult as the genetic information is tightly compacted so it can fit in a cell. A group of proteins can help to unpack the genome to uncover the genes that can then be accessed and activated. While these ‘pioneer factors’ can therefore shape the identity of a cell, much remains unknown about how they can work together to do so. For instance, the pioneer factor Zelda is essential in early fruit fly development, as it enables the genetic information of the egg and sperm to undergo dramatic reprogramming and generate a new organism. Yet, it was unclear whether additional helpers were required for this transition. Using this animal system, Gaskill, Gibson et al. identified GAGA Factor as a protein which works with Zelda to open up and reprogram hundreds of different sections along the genome of fruit fly embryos. This tag-team effort started with Zelda being important initially to activate genes; regulation was then handed over for GAGA Factor to continue the process. Without either protein, the embryo died. Getting a glimpse into early genetic events during fly development provides insights that are often applicable to other animals such as fish and mammals. Ultimately, this research may help scientists to understand how things can go wrong in human embryos.

In mammals, their proper development during the early cleavage stages strongly relies on the gene products newly transcribed by zygotic genome activation (ZGA). Long noncoding RNAs (lncRNAs) have been characterized as key regulators of the ZGA process in mice and human. However, the ZGA stage has not yet been identified and epigenetic regulations of the ZGA process remain largely unknown in goats. Here, we show that ZGA occurred at the 8-cell stage in goats. During ZGA, trimethylation of H3K9 was dynamically changed but maintained strong staining in development arrested embryos. Using single-cell RNA sequencing, we identified 800 mRNAs and 250 lncRNAs as candidates of key molecules in goat preimplantation embryos. These mRNAs and lncRNAs were differentially expressed from 4- to 8-cell stage embryos and were strongly enriched in terms of retinoic acid receptor signaling pathway as well as signaling pathway regulating pluripotency of stem cells. In particular, we found that microinjection of siRNA against lnc 137 caused development arrest. Our results are consistent with the notion that lncRNAs play vital roles during ZGA, and the data presented here provide an excellent source for further ZGA lncRNA studies. Summary Sentence We identified 800 mRNAs and 250 long noncoding RNAs as candidates of key molecules in goat zygotic genome activation and found that lnc 137 is essential for goat early development.

Abstract Background The Pacific white shrimp (Litopenaeus vannamei) is the most widely farmed shrimp species globally, yet the epigenetic regulation underlying its embryonic development remains largely unexplored. Histone modifications are known to orchestrate gene expression during early development in model organisms, but their role in crustaceans is poorly understood. Results In this study, we present the first comprehensive histone modification landscape during L. vannamei embryogenesis using CUT&Tag (Cleavage Under Targets and Tagmentation). We profiled high-resolution landscapes of four histone marks (H3K4me1, H3K4me3, H3K27ac, H3K27me3) across seven developmental stages from blastula to nauplius, revealing dynamic chromatin state transitions associated with developmental progression. Integration with transcriptomic data uncovered a strong temporal correlation between chromatin states and gene expression, particularly during zygotic genome activation (ZGA). Furthermore, our analysis uncovered key developmental genes associated with critical biological processes such as molting, body segmentation, and neurogenesis, providing novel insights into the epigenetic regulation of these events. Functional annotation of cis-regulatory elements based on histone marks identified candidate enhancers and regulatory loci linked to these key genes. Conclusions Our study provides the first epigenomic framework of shrimp embryogenesis, uncovering chromatin-based regulatory mechanisms during early development. The identification of stage-specific enhancers and active chromatin regions offers valuable resources for functional genomics in crustaceans and sheds light on conserved and divergent aspects of ZGA regulation beyond model systems.

In spite of its essential role in culture media, the precise influence of lactate on early mouse embryonic development remains elusive. Previous studies have implicated lactate accumulation in medium affecting histone acetylation. Recent research has underscored lactate-derived histone lactylation as a novel epigenetic modification in diverse cellular processes and diseases. Our investigation demonstrated that the absence of sodium lactate in the medium resulted in a pronounced 2-cell arrest at the late G2 phase in embryos. RNA-seq analysis revealed that the absence of sodium lactate significantly impaired the maternal-to-zygotic transition (MZT), particularly in zygotic gene activation (ZGA). Investigations were conducted employing Cut&Tag assays targeting the well-studied histone acetylation and lactylation sites, H3K18la and H3K27ac, respectively. The findings revealed a noticeable reduction in H3K18la modification under lactate deficiency, and this alteration showed a significant correlation with changes in gene expression. In contrast, H3K27ac exhibited minimal correlation. These results suggest that lactate may preferentially influence early embryonic development through H3K18la rather than H3K27ac modifications.

Double homeobox genes are unique to eutherian mammals. It has been proposed that the DUXC clade of the double homeobox gene family, which is present in multicopy long tandem arrays, plays an essential role in zygotic genome activation (ZGA). We generated a deletion of the tandem array encoding the DUXC gene of mouse, Double homeobox (Dux), and found it surprisingly to be homozygous viable and fertile. We characterize the embryonic development and ZGA profile of knockout (KO) embryos, finding that zygotic genome activation still occurs, with only modest alterations in 2-cell embryo gene expression, no defect in in vivo preimplantation development, but an increased likelihood of post-implantation developmental failure, leading to correspondingly smaller litter sizes in the KO strain. While all known 2-cell specific Dux target genes are still expressed in the KO, a subset is expressed at lower levels. These include numerous genes involved in methylation, blastocyst development, and trophectoderm/placental development. We propose that rather than driving ZGA, which is a process common throughout the animal kingdom, DUXC genes facilitate a process unique to eutherian mammals, namely the post-implantation development enabled by an invasive placenta. Summary sentence Mouse Dux is not absolutely required for viability or fertility, nor for zygotic genome activation, however the subset of Dux knockout embryos, post-implantation development fails. Graphical Abstract

Background The transcriptional changes around zygotic genome activation (ZGA) in preimplantation embryos are critical for studying mechanisms of embryonic developmental arrest and searching for key transcription factors. However, studies on the transcription profile of porcine ZGA are limited. Results In this study, we performed RNA sequencing in porcine in vivo developed (IVV) and somatic cell nuclear transfer (SCNT) embryo at different stages and compared the transcriptional activity of porcine embryos with mouse, bovine and human embryos. The results showed that the transcriptome map of the early porcine embryos was significantly changed at the 4-cell stage, and 5821 differentially expressed genes (DEGs) in SCNT embryos failed to be reprogrammed or activated during ZGA, which mainly enrichment to metabolic pathways. c-MYC was identified as the highest expressed transcription factor during ZGA. By treating with 10,058-F4, an inhibitor of c-MYC , the cleavage rate (38.33 ± 3.4%) and blastocyst rate (23.33 ± 4.3%) of porcine embryos were significantly lower than those of the control group (50.82 ± 2.7% and 34.43 ± 1.9%). Cross-species analysis of transcriptome during ZGA showed that pigs and bovines had the highest similarity coefficient in biological processes. KEGG pathway analysis indicated that there were 10 co-shared pathways in the four species. Conclusions Our results reveal that embryos with impaired developmental competence may be arrested at an early stage of development. c-MYC helps promote ZGA and preimplantation embryonic development in pigs. Pigs and bovines have the highest coefficient of similarity in biological processes during ZGA. This study provides an important reference for further studying the reprogramming regulatory mechanism of porcine embryos during ZGA.

In early mammalian embryos, the genome is transcriptionally quiescent until the zygotic genome activation （ZGA） which occurs 2-3 days after fertilization. Despite a long-standing effort, maternal transcription factors regulating this crucial developmental event remain largely elusive. Here, using maternal and paternal mouse models of Yapl deletion, we show that maternally accumulated yes-associated protein （YAP） in oocyte is essential for ZGA. Maternal Yapl-knoekout embryos exhibit a prolonged two-cell stage and develop into the four-cell stage at a much slower pace than the wild-type controls. Transcriptome analyses identify YAP target genes in early blastomeres; two of which, Rp113 and Rrm2, are required to mediate maternal YAP＇s effect in conferring developmental competence on preim- plantation embryos. Furthermore, the physiological YAP activator, lysophosphatidic acid, can substantially improve early development of wild-type, but not maternal Yapl-knockout embryos in both oviduct and culture. These obser- vations provide insights into the mechanisms of ZGA, and suggest potentials of YAP activators in improving the de- velopmental competence of cultured embryos in assisted human reproduction and animal biotechnology.

The rhesus macaque is one of the closest evolutionary relatives to humans, making the study of alternative splicing (AS) during its early embryonic development highly valuable for understanding human embryogenesis and related diseases. However, systematic studies in this context remain limited. Here, a comprehensive bioinformatic analysis of AS was performed using RNA-seq data spanning early rhesus macaque embryogenesis. We identified multiple previously unannotated zygotic genome activation (ZGA) genes, thereby refining the rhesus macaque ZGA gene repertoire. The landscape of AS and differential AS events (DASEs) across early stages was characterized, revealing dynamic and stage-specific regulation, with a marked increase in AS events from the 8-cell to morula stages. In addition, weighted gene co-expression network analysis identified 35 key splicing factors (SFs) involved in regulating early rhesus macaque embryonic development. Finally, we calculated the correlation between differentially expressed SFs and DASEs during the ZGA process, and identified potential regulatory relationships between several SFs (TRA2B, IGF2BP1, HNRNPAB, and MATR3) and specific DASEs. Collectively, this study provides the first systematic analysis of AS dynamics and regulation in early rhesus macaque embryogenesis, highlighting its critical role in development and offering a valuable reference for understanding AS in early human embryos.

At the early developmental stage, embryos are susceptible to environmental factors, which modulate development trajectories. In our study, we examined how different incubation temperatures (35 °C, 37 °C, and 39 °C) in vitro during the first embryonic cleavage affect the morphology, cell division rate, and DNA methylation in two-, four-, and eight-cell embryos and the viability of these two-cell embryos transferred to recipient females. Embryos kept at 35 °C for the first 24 h after in vitro fertilization in two- and four-cell embryos at 37 °C showed enhanced variability in the size of blastomeres and DNA 5mC level among blastomeres, as compared to the groups kept at 37 °C and 39 °C. This was associated with the highest rate of embryo death in four- and eight-cell embryos and the highest viability of newborns. In contrast, incubation at 39 °C did not significantly impact developmental dynamics and viability in vitro but led to a notably higher rate of gestation failure compared to other groups. The indicators of the 37 °C group fell within an intermediate range. Therefore, we conclude that a decrease in temperature during zygotic genome activation (ZGA) highlights the adaptive potential of embryos during their initial cleavages, while an increase in temperature does not show clear effects on their fate.