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Histone modifications and DNA methylation in relation to pluripotency and germ layer induction in Xenopus. Overall the genome is hypermethylated, but both H4K4me3 and H3K27me3 emerge in unmethylated CpG islands with different kinetics.
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The earliest steps of embryonic development involve important changes in chromatin and transcription factor networks, which are orchestrated to establish pluripotent cells that will form the embryo. DNA methylation, histone modifications, the pluripotency regulatory network of transcription factors, maternal factors and newly translated proteins al...
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Background
Multicellular organisms require precise gene regulation during ontogeny, and epigenetic modifications, such as DNA methylation and histone modification, facilitate this precise regulation. The conservative reprogramming patterns of DNA methylation in vertebrates have been well described. However, knowledge of how histone modifications ar...
Citations
... Different from the paternal pronucleus, which is rapidly demethylated, methylation levels of the maternal pronucleus are largely maintained during the first stages of embryo development, being gradually demethylated during the second and third cleavage stages 189 . Currently, a hypomethylation state is known to be necessary for the zygote to obtain a pluripotent stem cell state during its development 191 . Evidence indicates that methylation levels are reduced by almost 70% during the first phase of demethylation, and are subsequently reduced to a minimum of 8% after the second demethylation cycle 192,193 . ...
Diets leading to caloric overload are linked to metabolic disorders and reproductive function impairment. Metabolic and hormonal abnormalities stand out as defining features of metabolic disorders, and substantially affect the functionality of the testis. Metabolic disorders induce testicular metabolic dysfunction, chronic inflammation and oxidative stress. The disruption of gastrointestinal, pancreatic, adipose tissue and testicular hormonal regulation induced by metabolic disorders can also contribute to a state of compromised fertility. In this Review, we will delve into the effects of high-fat diets and metabolic disorders on testicular metabolism and spermatogenesis, which are crucial elements for male reproductive function. Moreover, metabolic disorders have been shown to influence the epigenome of male gametes and might have a potential role in transmitting phenotype traits across generations. However, the existing evidence strongly underscores the unmet need to understand the mechanisms responsible for transgenerational paternal inheritance of male reproductive function impairment related to metabolic disorders. This knowledge could be useful for developing targeted interventions to prevent, counteract, and most of all break the perpetuation chain of male reproductive dysfunction associated with metabolic disorders across generations.
... However, culturing embryonic stem cells in serum free media that con-tains two kinase inhibitors-targeting mitogen-activated protein kinase kinase (MEK) and GSK-3β-produces a hypomethylated genome that is thought to recapitulate the naïve pluripotent ground state [446,447]. In the developing mammalian embryo, the zygote genome is hypomethylated, but becomes hypermethylated by the time of implantation (E6.5 and E7.5 in the mouse) [200,448]. A state of hypermethylation of most genes, and hypomethylation of selected promoters, occurred when we mutated Y180 in cancer cells. ...
The title usage of Unde venisti ‘from where have you come’ is from a now dead language (Latin) that foundationally influenced modern English (not the major influence, but an essential formative one). This is an apt analogy for how both the ancient eukaryotic and eumetazoan functions of PGRMC proteins (PGRMC1 and PGRMC2 in mammals) probably influence modern human biology: via a formative trajectory from an evolutionarily foundational fulcrum. There is an arguable probability, although not a certainty, that PGRMC-like proteins were involved in eukaryogenesis. If so, then the proto-eukaryotic ancestral protein is modelled as having initiated the oxygen-induced and CYP450 (Cytochrome P450)-mediated synthesis of sterols in the endoplasmic reticulum to regulate proto-mitochondrial activity and heme homeostasis, as well as having enabled sterol transport between endoplasmic reticulum (ER) and mitochondria membranes involving the actin cytoskeleton, transport of heme from mitochondria, and possibly the regulation/origins of mitosis/meiosis. Later, during animal evolution, the last eumetazoan common ancestor (LEUMCA) acquired PGRMC phosphorylated tyrosines coincidentally with the gastrulation organizer, Netrin/deleted in colorectal carcinoma (DCC) signaling, muscle fibers, synapsed neurons, and neural recovery via a sleep-like process. Modern PGRMC proteins regulate multiple functions, including CYP450-mediated steroidogenesis, membrane trafficking, heme homeostasis, glycolysis/Warburg effect, fatty acid metabolism, mitochondrial regulation, and genomic CpG epigenetic regulation of gene expression. The latter imposes the system of differentiation status-sensitive cell-type specific proteomic complements in multi-tissued descendants of the LEUMCA. This paper attempts to trace PGRMC functions through time, proposing that key functions were involved in early eukaryotes, and were later added upon in the LEUMCA. An accompanying paper considers the implications of this awareness for human health and disease.
... Fertilized zebrafish embryos go through a series of rapid cleavages in the first 3 hours post fertilization (hpf) [11]. Initially, a blastodisc of 16 cells forms a syncytium with the yolk cells, and subsequent cleavages produce cells that are no longer connected, as well as cells that are cytoplasmically connected to the yolk cell (yolk syncytial layer; YSL). ...
... The zygotic genome is activated and midblastula transition occurs at the 1000-cell stage at 3 hpf. Afterwards, cell divisions are slower and asynchronous [11][12][13][14]. ...
... New evidence indicates that there is a progressive series of zygotic genome activation events. In addition to regulating morphogenesis, zygotic genome activation induces and maintains pluripotency [11,14]. One important result of zygotic genome activation is the expression of the pluripotency transcriptional gene circuit: sex-determining region Y-box containing gene 2 (sox2), octamer-binding protein 4 (oct4) also known as POU domain class 5 transcription factor 1 (pou5f1, recently renamed pou5f3) in zebrafish, and nanog q50 homeobox [14,[19][20][21][22]. ...
Fetal alcohol spectrum disorder (FASD) results from prenatal ethanol exposure. The zebrafish (Danio rerio) is an outstanding in vivo FASD model. Early development produced the three germ layers and embryonic axes patterning. A critical pluripotency transcriptional gene circuit of sox2, pou5f1 (oct4; recently renamed pou5f3), and nanog maintain potency and self-renewal. Ethanol affects sox2 expression, which functions with pou5f1 to control target gene transcription. Various genes, like elf3, may interact and regulate sox2, and elf3 knockdown affects early development. Downstream of the pluripotency transcriptional circuit, developmental signaling activities regulate morphogenetic cell movements and lineage specification. These activities are also affected by ethanol exposure. Hedgehog signaling is a critical developmental signaling pathway that controls numerous developmental events, including neural axis specification. Sonic hedgehog activities are affected by embryonic ethanol exposure. Activation of sonic hedgehog expression is controlled by TGF-ß family members, Nodal and Bmp, during dorsoventral (DV) embryonic axis establishment. Ethanol may perturb TGF-ß family receptors and signaling activities, including the sonic hedgehog pathway. Significantly, experiments show that activation of sonic hedgehog signaling rescues some embryonic ethanol exposure effects. More research is needed to understand how ethanol affects early developmental signaling and morphogenesis.
... These modifications are also abundant at promoter regions of genes that code for other factors required during development (Lessard and Crabtree, 2010). It is proposed that this bivalent chromatin mark resolves and there is activation of a few genes to regulate stemness while keeping other genes required for development poised for activation during development and cell differentiation (Bernstein et al., 2006;Lessard and Crabtree, 2010;Harikumar and Meshorer, 2015;Paranjpe and Veenstra, 2015). Recent studies have shown that many lineagecommitment genes have the bivalent mark and RNA polymerase II may be stalled at the promoters of these genes. ...
The molecular mechanisms that regulate stem cell pluripotency and differentiation has shown the crucial role that methylation plays in this process. DNA methylation has been shown to be important in the context of developmental pathways, and the role of histone methylation in establishment of the bivalent state of genes is equally important. Recent studies have shed light on the role of RNA methylation changes in stem cell biology. The dynamicity of these methylation changes not only regulates the effective maintenance of pluripotency or differentiation, but also provides an amenable platform for perturbation by cellular stress pathways that are inherent in immune responses such as inflammation or oncogenic programs involving cancer stem cells. We summarize the recent research on the role of methylation dynamics and how it is reset during differentiation and de-differentiation.
... These transcription factors are generally expressed in the early stages of embryonic development, but significantly decreased in most differentiated tissues (Thiagarajan et al., 2014;Li et al., 2020). They interact with a variety of protein complexes to regulate the expression of multiple genes and maintain the pluripotency and self-renewal ability of ES cells (Paranjpe and Veenstra, 2015). However, studies showed that there were differences in the types of genes involved in maintaining cellular pluripotency for different species (Ralston and Rossant, 2010;Robles et al., 2011). ...
Pluripotency is a transient state in early embryos, which is regulated by an interconnected network of pluripotency-related genes. The pluripotent state itself seems to be highly dynamic, which leads to significant differences in the description of induced pluripotent stem cells from different species at the molecular level. With the application of cell reprogramming technology in fish, the establishment of a set of molecular standards for defining pluripotency will be important for the research and potential application of induced pluripotent stem cells in fish. In this study, by BLAST search and expression pattern analysis, we screen out four pluripotent genes (Oct4, Nanog, Tdgf1, and Gdf3) in zebrafish (Danio rerio) and crucian carp (Carassius). These genes were highly expressed in the short period of early embryonic development, but significantly down-regulated after differentiation. Moreover, three genes (Oct4, Nanog and Tdgf1) have been verified that are suitable for identifying the pluripotency of induced pluripotent stem cells in zebrafish and crucian carp. Our study expands the understanding of the pluripotent markers of induced pluripotent stem cells in fish.
... Gene expression analysis has defined that differentiation of cell lineages in D. rerio occurs as early as the oblong stage (3.9 h post fertilisation). At ∼512 cells, the blastodisc contains pluripotent cells and the yolk cell might correspond to mammalian primitive endoderm cells (Paranjpe and Veenstra, 2015). Lineage tracing of cells using time-lapse photographic analysis has revealed that marginal cells of the blastoderm remain pluripotent throughout the late blastula to early gastrula stages (Ho and Kimmel, 1993). ...
With the advancement of cutting-edge live imaging technologies, microtubule remodelling has evolved as an integral regulator for the establishment of distinct differentiated cells. However, despite their fundamental role in cell structure and function, microtubules have received less attention when unravelling the regulatory circuitry of pluripotency. Here, we summarise the role of microtubule organisation and microtubule-dependent events required for the formation of pluripotent cells in vivo by deciphering the process of early embryogenesis: from fertilisation to blastocyst. Furthermore, we highlight current advances in elucidating the significance of specific microtubule arrays in in vitro culture systems of pluripotent stem cells and how the microtubule cytoskeleton serves as a highway for the precise intracellular movement of organelles. This Review provides an informed understanding of the intrinsic role of subcellular architecture of pluripotent cells and accentuates their regenerative potential in combination with innovative light-inducible microtubule techniques.
... During this process, cells respond to extracellular signals as dictated by cell-autonomous constraints such as chromatin state and the presence of factors mediating the response. The embryo is transcriptionally quiescent until zygotic genome activation (ZGA; Paranjpe & Veenstra, 2015;Vastenhouw et al, 2019), which gradually occurs during the mid-blastula stage in Xenopus. This is accompanied by slowing down of cell divisions and introduction of cell cycle gap phases. ...
... Chromatin plays a major role in this process, providing the gene-specific permissive or restrictive context for transcription (Perino & Veenstra, 2016;Jambhekar et al, 2019). This involves histone modifications such as the permissive promoter mark H3K4me3 and the repressive Polycomb mark H3K27me3, both of which increase dramatically during early Xenopus development (Bogdanovi c et al, 2012;Paranjpe & Veenstra, 2015;Hontelez et al, 2015). A large majority of genomic loci is decorated with these histone modifications by maternal factors; these loci are collectively referred to as the maternal regulatory space, whereas a relatively small number of promoters requires new embryonic transcription for the acquisition of H3K4me3 or H3K27me3 (Hontelez et al, 2015). ...
During vertebrate gastrulation, mesoderm is induced in pluripotent cells, concomitant with dorsal-ventral patterning and establishing of the dorsal axis. We applied single-cell chromatin accessibility and transcriptome analyses to explore the emergence of cellular heterogeneity during gastrulation in Xenopus tropicalis. Transcriptionally inactive lineage-restricted genes exhibit relatively open chromatin in animal caps, whereas chromatin accessibility in dorsal marginal zone cells more closely reflects transcriptional activity. We characterized single-cell trajectories and identified head and trunk organizer cell clusters in early gastrulae. By integrating chromatin accessibility and transcriptome data, we inferred the activity of transcription factors in single-cell clusters and tested the activity of organizer-expressed transcription factors in animal caps, alone or in combination. The expression profile induced by a combination of Foxb1 and Eomes most closely resembles that observed in the head organizer. Genes induced by Eomes, Otx2, or the Irx3-Otx2 combination are enriched for maternally regulated H3K4me3 modifications, whereas Lhx8-induced genes are marked more frequently by zygotically controlled H3K4me3. Taken together, our results show that transcription factors cooperate in a combinatorial fashion in generally open chromatin to orchestrate zygotic gene expression.
... When blastula embryos were exposed to gamma-rays with low dose (2 and 5 Gy) or about 10% or less of them were irradiated with 50 Gy of carbon-ion microbeam, they hatched normally even though they showed a transient delay of brain development before hatching. In medaka, the pluripotent ability of blastoderm cells has been identified in vitro and in vivo [6][7][8]24] and the loss of about 10% or less of blastoderm cells might be compensated by the remaining non-damaged pluripotent blastoderm cells. In contrast, the loss of about 25% of the blastoderm cells resulted in the lethality before the time of hatching, suggesting that there is an upper limit of proportion of the lost cells to compensate and restore the development of irradiated embryos. ...
... Previous studies in medaka demonstrated that the time point of the start of zygotic gene transcription, mid-blastula transition (MBT), was around stage 11 [31,32]. In zebrafish and Xenopus, the embryos before MBT lack the ability to arrest cell cycle progression by checkpoint and they acquire the ability to perform apoptosis after MBT [24,[33][34][35][36][37]. Our transcriptome analysis in medaka supports these findings, since the genes related with apoptotic induction, cell proliferation, DNA repair and cell cycle arrest might not fully function in the irradiated blastula at 4 h after the irradiation (Table 1 and Dataset S1), which provides the evidence that blastoderm cells do not arrest cell cycle even when they are severely damaged by exposure to high-dose IR. ...
It has been widely accepted that prenatal exposure to ionizing radiation (IR) can affect embryonic and fetal development in mammals, depending on dose and gestational age of the exposure, however, the precise machinery underlying the IR-induced disturbance of embryonic development is still remained elusive. In this study, we examined the effects of gamma-ray irradiation on blastula embryos of medaka and found transient delay of brain development even when they hatched normally with low dose irradiation (2 and 5 Gy). In contrast, irradiation of higher dose of gamma-rays (10 Gy) killed the embryos with malformations before hatching. We then conducted targeted irradiation of blastoderm with a collimated carbon-ion microbeam. When a part (about 4, 10 and 25%) of blastoderm cells were injured by lethal dose (50 Gy) of carbon-ion microbeam irradiation, loss of about 10% or less of blastoderm cells induced only the transient delay of brain development and the embryos hatched normally, whereas embryos with about 25% of their blastoderm cells were irradiated stopped development at neurula stage and died. These findings strongly suggest that the developmental disturbance in the IR irradiated embryos is determined by the proportion of severely injured cells in the blastoderm.
... The key feature of CSCs is their capacity for self-renewal and asymmetric cell division, similar to normal stem cells. Pluripotency transcription factors (TFs), such as Nanog, Oct4 and Sox2, are known to form an interaction network with essential roles in the maintenance of pluripotency both in embryonic stem cells [61] and during embryonic development [62,63], as well as in the reprogramming of somatic cells to pluripotent stem cells [64]. Consistent with the CSC hypothesis, pluripotency factors are also overexpressed in CSCs [65]. ...
Ovarian cancer is the most lethal gynecological malignancy due to its late detection and high recurrence rate. Resistance to conventional platinum-based therapies and metastasis are attributed to a population of cells within tumors called cancer stem cells, which possess stem-like features and are able to recapitulate new tumors. Recent studies have deepened the understanding of the biology of ovarian cancer stem cells and their special properties and have identified multiple markers and signaling pathways responsible for their self-renewal abilities. Targeting cancer stem cells represents the most promising strategy for overcoming therapy resistance and reducing mortality in ovarian cancer, but further efforts must be made to improve our understanding of the mechanisms involved in therapy resistance. In this review, we summarize our current knowledge about ovarian cancer stem cells, their involvement in metastasis and their interactions with the tumor microenvironment; we also discuss the therapeutic approaches that are being developed to target them to prevent tumor relapse.
... Injection of sox2 mRNA partially rescues ethanol-induced epiboly, gastrulation and gene expression defects. Sox2 plays a critical role in pluiripotency and embryogenesis 32,33 . The pluripotency transcriptional circuit, which includes Sox2, regulates pre-gastrulation events in the zebrafish embryos 27,29 . ...
Ethanol exposure during prenatal development causes fetal alcohol spectrum disorder (FASD), the most frequent preventable birth defect and neurodevelopmental disability syndrome. The molecular targets of ethanol toxicity during development are poorly understood. Developmental stages surrounding gastrulation are very sensitive to ethanol exposure. To understand the effects of ethanol on early transcripts during embryogenesis, we treated zebrafish embryos with ethanol during pre-gastrulation period and examined the transcripts by Affymetrix GeneChip microarray before gastrulation. We identified 521 significantly dysregulated genes, including 61 transcription factors in ethanol-exposed embryos. Sox2, the key regulator of pluripotency and early development was significantly reduced. Functional annotation analysis showed enrichment in transcription regulation, embryonic axes patterning, and signaling pathways, including Wnt, Notch and retinoic acid. We identified all potential genomic targets of 25 dysregulated transcription factors and compared their interactions with the ethanol-dysregulated genes. This analysis predicted that Sox2 targeted a large number of ethanol-dysregulated genes. A gene regulatory network analysis showed that many of the dysregulated genes are targeted by multiple transcription factors. Injection of sox2 mRNA partially rescued ethanol-induced gene expression, epiboly and gastrulation defects. Additional studies of this ethanol dysregulated network may identify therapeutic targets that coordinately regulate early development.
