Reciprocal zebrafish-medaka hybrids reveal maternal control of zygotic genome activation timing

After fertilization, the sperm and egg contribute unequally to the newly formed zygote. While the sperm contributes mainly paternal DNA, the egg provides both maternal DNA and the bulk of the future embryonic cytoplasm. Most embryonic processes (like the onset of zygotic transcription) depend on maternally-provided cytoplasmic components, and it is largely unclear whether paternal components besides the centrosome play a role in the regulation of early embryogenesis. Here we report a reciprocal zebrafish-medaka hybrid system as a powerful tool to investigate paternal vs. maternal influence during early development. By combining expression of zebrafish Bouncer on the medaka egg with artificial egg activation, we demonstrate the in vitro generation of paternal zebrafish x maternal medaka (reripes) hybrids. These hybrids complement the previously established paternal medaka x maternal zebrafish (latio) hybrids (Herberg et al., 2018). As proof of concept, we investigated maternal vs. paternal control of zygotic genome activation (ZGA) timing using this reciprocal hybrid system. RNA-seq analysis of the purebred fish species and hybrids revealed that the onset of ZGA is primarily governed by the egg. Overall, our study establishes the reciprocal zebrafish-medaka hybrid system as a versatile tool to dissect parental control mechanisms during early development.

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CLAMP regulates Zygotic Genome Activation in Drosophila embryos

Genetics ◽

10.1093/genetics/iyab107 ◽

2021 ◽

Author(s):

Megan M Colonnetta ◽

Juan E Abrahante ◽

Paul Schedl ◽

Daryl M Gohl ◽

Girish Deshpande

Keyword(s):

Temporal Dynamics ◽

Embryonic Patterning ◽

Zygotic Genome Activation ◽

Promoter Sequences ◽

Genome Wide ◽

Zygotic Transcription ◽

Pioneer Factor ◽

Genome Activation ◽

Drosophila Embryos ◽

Zygotic Genome

Abstract Embryonic patterning is critically dependent on zygotic genome activation (ZGA). In Drosophila melanogaster embryos, the pioneer factor Zelda directs ZGA, possibly in conjunction with other factors. Here we have explored novel involvement of Chromatin-Linked Adapter for MSL Proteins (CLAMP) during ZGA. CLAMP binds thousands of sites genome-wide throughout early embryogenesis. Interestingly, CLAMP relocates to target promoter sequences across the genome when ZGA is initiated. Although there is a considerable overlap between CLAMP and Zelda binding sites, the proteins display distinct temporal dynamics. To assess whether CLAMP occupancy affects gene expression, we analyzed transcriptomes of embryos zygotically compromised for either clamp or zelda and found that transcript levels of many zygotically-activated genes are similarly affected. Importantly, compromising either clamp or zelda disrupted the expression of critical segmentation and sex determination genes bound by CLAMP (and Zelda). Furthermore, clamp knockdown embryos recapitulate other phenotypes observed in Zelda-depleted embryos, including nuclear division defects, centrosome aberrations, and a disorganized actomyosin network. Based on these data, we propose that CLAMP acts in concert with Zelda to regulate early zygotic transcription.

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Maternal Dppa2 and Dppa4 are dispensable for zygotic genome activation but important for offspring survival

Development ◽

10.1242/dev.200191 ◽

2021 ◽

Vol 148 (24) ◽

Author(s):

Oana Kubinyecz ◽

Fatima Santos ◽

Deborah Drage ◽

Wolf Reik ◽

Melanie A. Eckersley-Maslin

Keyword(s):

Null Allele ◽

Embryonic Stem ◽

Offspring Survival ◽

Zygotic Genome Activation ◽

Molecular Events ◽

Genome Activation ◽

Mitotic Chromatin ◽

Zygotic Genome

ABSTRACT Zygotic genome activation (ZGA) represents the initiation of transcription following fertilisation. Despite its importance, we know little of the molecular events that initiate mammalian ZGA in vivo. Recent in vitro studies in mouse embryonic stem cells have revealed developmental pluripotency associated 2 and 4 (Dppa2/4) as key regulators of ZGA-associated transcription. However, their roles in initiating ZGA in vivo remain unexplored. We reveal that Dppa2/4 proteins are present in the nucleus at all stages of preimplantation development and associate with mitotic chromatin. We generated conditional single and double maternal knockout mouse models to deplete maternal stores of Dppa2/4. Importantly, Dppa2/4 maternal knockout mice were fertile when mated with wild-type males. Immunofluorescence and transcriptome analyses of two-cell embryos revealed that, although ZGA took place, there were subtle defects in embryos that lacked maternal Dppa2/4. Strikingly, heterozygous offspring that inherited the null allele maternally had higher preweaning lethality than those that inherited the null allele paternally. Together, our results show that although Dppa2/4 are dispensable for ZGA transcription, maternal stores have an important role in offspring survival, potentially via epigenetic priming of developmental genes.

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Whole-Transcriptome Sequencing-Based Analysis of DAZL and Its Interacting Genes during Germ Cells Specification and Zygotic Genome Activation in Chickens

International Journal of Molecular Sciences ◽

10.3390/ijms21218170 ◽

2020 ◽

Vol 21 (21) ◽

pp. 8170

Author(s):

Deivendran Rengaraj ◽

Sohyoung Won ◽

Jong Won Han ◽

DongAhn Yoo ◽

Heebal Kim ◽

...

Keyword(s):

Germ Cells ◽

Transcriptome Sequencing ◽

Germ Plasm ◽

Prediction Method ◽

Zygotic Genome Activation ◽

Zygotic Transcription ◽

Whole Transcriptome Sequencing ◽

Genome Activation ◽

Whole Transcriptome ◽

Zygotic Genome

The deleted in azoospermia like (DAZL) is required for germ cells development and maintenance. In chickens, the mRNA and protein of DAZL, a representative maternally inherited germ plasm factor, are detected in the germ plasm of oocyte, zygote, and all stages of the intrauterine embryos. However, it is still insufficient to explain the origin and specification process of chicken germ cells, because the stage at which the zygotic transcription of DAZL occurs and the stage at which the maternal DAZL RNA/protein clears have not yet been fully identified. Moreover, a comprehensive understanding of the expression of DAZL interacting genes during the germ cells specification and development and zygotic genome activation (ZGA) is lacking in chickens. In this study, we identified a set of DAZL interacting genes in chickens using in silico prediction method. Then, we analyzed the whole-transcriptome sequencing (WTS)-based expression of DAZL and its interacting genes in the chicken oocyte, zygote, and Eyal-Giladi and Kochav (EGK) stage embryos (EGK.I to EGK.X). In the results, DAZL transcripts are increased in the zygote (onset of transcription), maintained the increased level until EGK.VI, and decreased from EGK.VIII (possible clearance of maternal RNAs). Among the DAZL interacting genes, most of them are increased either at 1st ZGA or 2nd ZGA, indicating their involvement in germ cells specification and development.

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Expression of eukaryotic elongation initiation factor 1A differentially marks zygotic genome activation in biparental and parthenogenetic porcine embryos and correlates with in vitro developmental potential

Reproduction Fertility and Development ◽

10.1071/rd08072 ◽

2008 ◽

Vol 20 (7) ◽

pp. 818 ◽

Cited By ~ 14

Author(s):

Luca Magnani ◽

Christine M. Johnson ◽

Ryan A. Cabot

Keyword(s):

Expression Profile ◽

Initiation Factor ◽

In Vitro Fertilisation ◽

Zygotic Genome Activation ◽

Cell Stage ◽

Developmental Potential ◽

Genome Activation ◽

Parthenogenetic Embryos ◽

Zygotic Genome

Zygotic genome activation (ZGA) is a major event during cleavage development. In vitro manipulation of mammalian embryos (including embryo culture) can result in developmental arrest around the time of ZGA. Eukaryotic elongation initiation factor 1A (eIF1A) has been used as a marker for ZGA in some mammalian species. We hypothesised expression of eIF1A can be used to assess ZGA in the pig; we also hypothesised that the expression profile of eIF1A can be used to assess developmental potential in vitro. The aims of the present study were to determine the expression pattern of eIF1A during porcine cleavage development and to assess its expression levels in embryos of different quality. We used a real-time reverse transcription–polymerase chain reaction assay to quantify eIF1A transcripts at different time points during cleavage development in porcine embryos produced by parthenogenetic activation (PA) and in vitro fertilisation (IVF). We found that eIF1A is activated at the two-cell stage in IVF embryos and at the four-cell stage in PA embryos. We showed that the increase in transcript levels observed in parthenogenetic embryos is dependent on de novo transcription. We found altered levels of eIF1A transcripts in parthenogenetic embryos that presented as either two- or eight-cell embryos 48 h after activation compared with four-cell embryos at the same time point. Our work supports the hypothesis that eIF1A is a marker of porcine ZGA and its expression profile can be used to assess embryo quality.

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CLAMP and Zelda function together to promote Drosophila zygotic genome activation

eLife ◽

10.7554/elife.69937 ◽

2021 ◽

Vol 10 ◽

Author(s):

Jingyue Duan ◽

Leila Rieder ◽

Megan M Colonnetta ◽

Annie Huang ◽

Mary Mckenney ◽

...

Keyword(s):

Transcription Factor ◽

Embryonic Development ◽

Essential Role ◽

Chromatin Accessibility ◽

Zygotic Genome Activation ◽

Zygotic Transcription ◽

Pioneer Factor ◽

Pioneer Transcription Factor ◽

Genome Activation ◽

Zygotic Genome

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 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; 3) enhance chromatin accessibility and facilitate ZLD occupancy at a subset of key embryonic promoters. Thus, CLAMP functions as a pioneer factor which plays a targeted yet essential role in ZGA.

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Transposable Element Dynamics and Regulation during Zygotic Genome Activation in Mammalian Embryos and Embryonic Stem Cell Model Systems

Stem Cells International ◽

10.1155/2021/1624669 ◽

2021 ◽

Vol 2021 ◽

pp. 1-17

Author(s):

Yixuan Low ◽

Dennis Eng Kiat Tan ◽

Zhenhua Hu ◽

Shawn Ying Xuan Tan ◽

Wee-Wei Tee

Keyword(s):

Cell Model ◽

Embryonic Stem ◽

Model Systems ◽

Specific Class ◽

Mammalian Development ◽

Zygotic Genome Activation ◽

Somatic Tissues ◽

Genome Activation ◽

Zygotic Genome

Transposable elements (TEs) are mobile genetic sequences capable of duplicating and reintegrating at new regions within the genome. A growing body of evidence has demonstrated that these elements play important roles in host genome evolution, despite being traditionally viewed as parasitic elements. To prevent ectopic activation of TE transposition and transcription, they are epigenetically silenced in most somatic tissues. Intriguingly, a specific class of TEs—retrotransposons—is transiently expressed at discrete phases during mammalian development and has been linked to the establishment of totipotency during zygotic genome activation (ZGA). While mechanisms controlling TE regulation in somatic tissues have been extensively studied, the significance underlying the unique transcriptional reactivation of retrotransposons during ZGA is only beginning to be uncovered. In this review, we summarize the expression dynamics of key retrotransposons during ZGA, focusing on findings from in vivo totipotent embryos and in vitro totipotent-like embryonic stem cells (ESCs). We then dissect the functions of retrotransposons and discuss how their transcriptional activities are finetuned during early stages of mammalian development.

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Pou5f3, SoxB1 and Nanog remodel chromatin on High Nucleosome Affinity Regions at Zygotic Genome Activation

10.1101/344168 ◽

2018 ◽

Cited By ~ 1

Author(s):

Marina Veil ◽

Lev Yampolsky ◽

Björn Grüning ◽

Daria Onichtchouk

Keyword(s):

Nucleosome Occupancy ◽

Open Chromatin ◽

Zygotic Genome Activation ◽

Chromatin Dynamics ◽

Cell Cycles ◽

Dna Shape ◽

Genome Activation ◽

Zygotic Genome

AbstractThe zebrafish embryo is mostly transcriptionally quiescent during the first 10 cell cycles, until the main wave of Zygotic Genome Activation (ZGA) occurs, accompanied by fast chromatin remodeling. At ZGA, homologs of mammalian stem cell transcription factors (TFs) Pou5f3, Nanog and Sox19b bind to thousands of developmental enhancers to initiate transcription. So far, how these TFs influence chromatin dynamics at ZGA has remained unresolved. To address this question, we analyzed nucleosome positions in wild-type and Maternal-Zygotic (MZ) mutants for pou5f3 and nanog by MNase-seq. We show that Nanog, Sox19b and Pou5f3 bind to the High Nucleosome Affinity Regions (HNARs). HNARs are spanning over 600 bp, featuring high in vivo and predicted in vitro nucleosome occupancy and high predicted propeller twist DNA shape value. We suggest a two-step nucleosome destabilization-depletion model, where the same intrinsic DNA properties of HNAR promote both high nucleosome occupancy and differential binding of TFs. In the first step, already prior to ZGA, Pou5f3 and Nanog destabilize nucleosomes on HNAR centers genome-wide. In the second step, post-ZGA, Nanog, Pou5f3 and SoxB1 maintain open chromatin state on the subset of HNARs, acting synergistically. Nanog binds to the HNAR center, while the Pou5f3 stabilizes the flanks. The HNAR model will provide a useful tool for genome regulatory studies in the variety of biological systems.

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DPPA2 and DPPA4 are dispensable for mouse zygotic genome activation and preimplantation development

Development ◽

10.1242/dev.200178 ◽

2021 ◽

Author(s):

Zhiyuan Chen ◽

Zhenfei Xie ◽

Yi Zhang

Keyword(s):

De Novo ◽

Genetic Manipulation ◽

Embryonic Stem ◽

Preimplantation Development ◽

Dependent Manner ◽

Maternal Factors ◽

Zygotic Genome Activation ◽

Genome Activation ◽

Zygotic Genome

How maternal factors in oocytes initiate zygotic genome activation (ZGA) remains elusive in mammals, partly due to the challenge of de novo identification of key factors using scarce materials. The 2-cell (2C) embryo like cells has been widely used as an in vitro model to understand mouse ZGA and totipotency given its expression of a group of 2C embryo-specific genes and its simplicity for genetic manipulation. Recent studies indicate that DPPA2 and DPPA4 are required for establishing the 2C-like state in mouse embryonic stem cells (ESCs) in a DUX-dependent manner. These results suggest that DPPA2 and DPPA4 are essential maternal factors that regulate Dux and ZGA in embryos. By analyzing maternal knockout and maternal-zygotic knockout embryos, we unexpectedly found that DPPA2 and DPPA4 are dispensable for Dux activation, ZGA, and preimplantation development. Our study suggests that 2C-like cells do not fully recapitulate 2-cell embryos in terms of 2C-gene regulation and cautions should be taken when studying ZGA and totipotency using 2C-like cells as the model system.

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Maternal Dppa2 and Dppa4 are dispensable for zygotic genome activation but important for offspring survival

10.1101/2021.09.13.460183 ◽

2021 ◽

Author(s):

Oana Kubinyecz ◽

Fatima Santos ◽

Deborah Drage ◽

Wolf Reik ◽

Melanie A Eckersley-Maslin

Keyword(s):

Null Allele ◽

Embryonic Stem ◽

Offspring Survival ◽

Zygotic Genome Activation ◽

Molecular Events ◽

Genome Activation ◽

Mitotic Chromatin ◽

Zygotic Genome

Zygotic Genome Activation (ZGA) represents the initiation of transcription following fertilisation. Despite its importance in shifting developmental control from primarily maternal stores in the oocyte to the embryo proper, we know little of the molecular events that initiate ZGA in vivo. Recent in vitro studies in mouse embryonic stem cells (ESCs) have revealed Developmental Pluripotency Associated 2 and 4 (Dppa2/4) as key regulators of ZGA-associated transcription. However, their roles in initiating ZGA in vivo remain unexplored. We reveal Dppa2/4 proteins are present in the nucleus at all stages of preimplantation development and associate with mitotic chromatin. We generated single and double maternal knockout mouse models to deplete maternal stores of Dppa2/4. Importantly, while fertile, Dppa2/4 maternal knockout mice had reduced litter sizes, indicating decreased offspring survival. Immunofluorescence and transcriptome analyses of 2-cell embryos revealed while ZGA took place there were subtle defects in embryos lacking maternal Dppa2/4. Strikingly, heterozygous offspring that inherited the null allele maternally had higher preweaning lethality than those that inherited the null allele paternally. Together our results show that while Dppa2/4 are dispensable for ZGA transcription, maternal stores have an important role in offspring survival, potentially via epigenetic priming of developmental genes.

Download Full-text