scholarly journals N6-Methyladenine in Eukaryotic DNA: Tissue Distribution, Early Embryo Development, and Neuronal Toxicity

2021 ◽  
Vol 12 ◽  
Author(s):  
Sara B. Fernandes ◽  
Nathalie Grova ◽  
Sarah Roth ◽  
Radu Corneliu Duca ◽  
Lode Godderis ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Cell Fate ◽  
Embryo Development ◽  
Epigenetic Modification ◽  
Embryonic Stem ◽  
Early Embryo ◽  
Environmental Pollutant ◽  
Female Rats ◽  
Adenine Methylation ◽  
Eukaryotic Dna

DNA methylation is one of the most important epigenetic modifications and is closely related with several biological processes such as regulation of gene transcription and the development of non-malignant diseases. The prevailing dogma states that DNA methylation in eukaryotes occurs essentially through 5-methylcytosine (5mC) but recently adenine methylation was also found to be present in eukaryotes. In mouse embryonic stem cells, 6-methyladenine (6mA) was associated with the repression and silencing of genes, particularly in the X-chromosome, known to play an important role in cell fate determination. Here, we have demonstrated that 6mA is a ubiquitous eukaryotic epigenetic modification that is put in place during epigenetically sensitive periods such as embryogenesis and fetal development. In somatic cells there are clear tissue specificity in 6mA levels, with the highest 6mA levels being observed in the brain. In zebrafish, during the first 120 h of embryo development, from a single pluripotent cell to an almost fully formed individual, 6mA levels steadily increase. An identical pattern was observed over embryonic days 7–21 in the mouse. Furthermore, exposure to a neurotoxic environmental pollutant during the same early life period may led to a decrease in the levels of this modification in female rats. The identification of the periods during which 6mA epigenetic marks are put in place increases our understanding of this mammalian epigenetic modification, and raises the possibility that it may be associated with developmental processes.

microRNA regulation of pluripotent state transition

2020 ◽  
Vol 64 (6) ◽  
pp. 947-954 ◽  
Author(s):  
Shao-Hua Wang ◽  
Chao Zhang ◽  
Yangming Wang
Keyword(s):  
Stem Cells ◽  
Cell Fate ◽  
Embryo Development ◽  
State Transition ◽  
Embryonic Stem ◽  
Short Review ◽  
Early Embryo ◽  
Mammalian Development ◽  
Early Embryo Development ◽  
Pluripotent State

Abstract microRNAs (miRNAs) play essential roles in mouse embryonic stem cells (ESCs) and early embryo development. The exact mechanism by which miRNAs regulate cell fate transition during embryo development is still not clear. Recent studies have identified and captured various pluripotent stem cells (PSCs) that share similar characteristics with cells from different stages of pre- and post-implantation embryos. These PSCs provide valuable models to understand miRNA functions in early mammalian development. In this short review, we will summarize recent work towards understanding the function and mechanism of miRNAs in regulating the transition or conversion between different pluripotent states. In addition, we will highlight unresolved questions and key future directions related to miRNAs in pluripotent state transition. Studies in these areas will further our understanding of miRNA functions in early embryo development, and may lead to practical means to control human PSCs for clinical applications in regenerative medicine.

Nutritional Status Impacts Epigenetic Regulation in Early Embryo Development: A Scoping Review

2021 ◽  
Author(s):  
Shuang Cai ◽  
Shuang Quan ◽  
Guangxin Yang ◽  
Meixia Chen ◽  
Qianhong Ye ◽  
...  
Keyword(s):  
Embryonic Development ◽  
Embryo Development ◽  
Epigenetic Regulation ◽  
Scoping Review ◽  
Epigenetic Modification ◽  
Reproductive Technologies ◽  
Early Embryo ◽  
Epigenetic Modifications ◽  
Nutrition Status ◽  
Early Embryo Development

ABSTRACTWith the increasing maternal age and the use of assisted reproductive technology in various countries worldwide, the influence of epigenetic modification on embryonic development is increasingly notable and prominent. Epigenetic modification disorders caused by various nutritional imbalance would cause embryonic development abnormalities and even have an indelible impact on health in adulthood. In this scoping review, we summarize the main epigenetic modifications in mammals and the synergies among different epigenetic modifications, especially DNA methylation, histone acetylation, and histone methylation. We performed an in-depth analysis of the regulation of various epigenetic modifications on mammals from zygote formation to cleavage stage and blastocyst stage, and reviewed the modifications of key sites and their potential molecular mechanisms. In addition, we discuss the effects of nutrition (protein, lipids, and one-carbon metabolism) on epigenetic modification in embryos and emphasize the importance of various nutrients in embryonic development and epigenetics during pregnancy. Failures in epigenetic regulation have been implicated in mammalian and human early embryo loss and disease. With the use of reproductive technologies, it is becoming even more important to establish developmentally competent embryos. Therefore, it is essential to evaluate the extent to which embryos are sensitive to these epigenetic modifications and nutrition status. Understanding the epigenetic regulation of early embryo development will help us make better use of reproductive technologies and nutrition regulation to improve reproductive health in mammals.

scholarly journals Stochastic Modeling Reveals Kinetic Heterogeneity in Post-replication DNA Methylation

2019 ◽  
Author(s):  
Luis Busto-Moner ◽  
Julien Morival ◽  
Arjang Fahim ◽  
Zachary Reitz ◽  
Timothy L. Downing ◽  
...  
Keyword(s):  
Mathematical Modeling ◽  
Dna Methylation ◽  
Rate Constants ◽  
Cytosine Methylation ◽  
Temporal Dynamics ◽  
Epigenetic Modification ◽  
Embryonic Stem ◽  
Likelihood Estimation ◽  
Dna Methyltransferases ◽  
Methylation Patterns

AbstractDNA methylation is a heritable epigenetic modification that plays an essential role in mammalian development. Genomic methylation patterns are dynamically maintained, with DNA methyltransferases mediating inheritance of methyl marks onto nascent DNA over cycles of replication. A recently developed experimental technique employing immunoprecipitation of bromodeoxyuridine labeled nascent DNA followed by bisulfite sequencing (Repli-BS) measures post-replication temporal evolution of cytosine methylation, thus enabling genome-wide monitoring of methylation maintenance. In this work, we combine statistical analysis and stochastic mathematical modeling to analyze Repli-BS data from human embryonic stem cells. We estimate site-specific kinetic rate constants for the restoration of methyl marks on >10 million uniquely mapped cytosines within the CpG (cytosine-phosphate-guanine) dinucleotide context across the genome using Maximum Likelihood Estimation. We find that post-replication remethylation rate constants span approximately two orders of magnitude, with half-lives of per-site recovery of steady-state methylation levels ranging from shorter than ten minutes to five hours and longer. Furthermore, we find that kinetic constants of maintenance methylation are correlated among neighboring CpG sites. Stochastic mathematical modeling provides insight to the biological mechanisms underlying the inference results, suggesting that enzyme processivity and/or collaboration can produce the observed kinetic correlations. Our combined statistical/mathematical modeling approach expands the utility of genomic datasets and disentangles heterogeneity in methylation patterns arising from replication-associated temporal dynamics versus stable cell-to-cell differences.

45 Expression patterns of PRDM family genes in porcine pre-implantation embryos

2020 ◽  
Vol 32 (2) ◽  
pp. 148
Author(s):  
K. Farrell ◽  
K. Uh ◽  
K. Lee
Keyword(s):  
Embryo Development ◽  
Internal Control ◽  
Target Genes ◽  
Expression Patterns ◽  
Embryonic Stem ◽  
Germinal Vesicle ◽  
Early Embryo ◽  
Cell Stage ◽  
Early Embryo Development

Establishing proper levels of pluripotency is essential for normal development. The genome of gametes is remodelled upon fertilisation and pluripotency-related genes are expressed in blastocysts. Multiple pluripotency-related genes are involved in the well-orchestrated process; however, detailed mechanistic actions remain elusive. The PRDM family genes are reported to be closely related to the pluripotency. A previous report noted that PRDM14 plays an important role in the maintenance of pluripotency in human embryonic stem cells (ESCs) and potentially murine ESCs; loss of PRDM14 was found to cause abnormalities in genome-wide epigenetic status. Similarly, PRDM15 was found to be a key regulator of pluripotency in mouse ESCs. Structural similarities among the PRDM family suggest that other PRDM family genes may help to establish and maintain pluripotency in embryos. Unfortunately, little is known about the expression profile of PRDM family in porcine embryos. To expand our understanding of the role of PRDM family in porcine embryos, expression patterns of PRDM gene family were investigated using reverse transcription quantitative (RTq)-PCR. Candidate PRDM family genes were selected based on previous RNA-Seq data in porcine oocytes/embryos. To conduct this study, germinal vesicle (GV), MII, zygote, 4-cell, and blastocyst samples were collected. Complementary DNA synthesised from the samples was used for RT-qPCR to analyse the expression pattern of selected PRDM family genes: PRDM2, PRDM4, PRDM6, PRDM14, and PRDM15. The expression of target genes was normalized to the YWHAG level, an internal control. Then, GV stage was used as a control for ΔΔCT analysis. Two technical replications and three biological replications were performed. Analysis of variance was used for statistical analysis and P-values<0.05 were considered significant. There was a significant decrease in PRDM2 expression in 4-cell and blastocyst, PRDM4 expression in 4-cell, and PRDM6 in all stages (MII, zygote, 4-cell, and blastocyst), compared with the GV stage. Because zygotic genome activation occurs at the 4-cell stage in the pig, the significant decrease in gene expression (PRDM2, PRDM4, and PRDM6) indicates they may be maternally originated and involved in the reprogramming process following fertilisation. On the other hand, there was a significant increase in PRDM15 expression in blastocysts and the PRDM14 transcript was only detected in blastocysts in all three biological replicates, suggesting that the genes are most likely involved in pluripotency maintenance, as was found in previous human studies. These results indicate that PRDM family genes are differentially expressed during early embryo development in pigs and may play a role in maintenance of pluripotency. For further study, we intend to evaluate the role of PRDM family genes during early embryo development in pigs.

130. MICROARRAY ANALYSIS OF FOETAL MOUSE BRAIN FOLLOWING INDUCTION OF MITOCHONDRIAL DYSFUNCTION DURING PRE-IMPLANTATION EMBRYO DEVELOPMENT

2009 ◽  
Vol 21 (9) ◽  
pp. 49
Author(s):  
T. Fullston ◽  
M. Mitchell ◽  
S. Wakefield ◽  
A. Filby ◽  
M. Lane
Keyword(s):  
Gene Expression ◽  
Cell Death ◽  
Mitochondrial Dysfunction ◽  
Embryo Development ◽  
Epigenetic Modification ◽  
Gene Array ◽  
Early Embryo ◽  
Cellular Growth ◽  
Early Embryo Development ◽  
Foetal Brain

Environmental stress can disrupt mitochondrial function in the pre-implantation embryo, subsequently hindering embryo viability. Brain tissue is also sensitive to developmental perturbations, and we have previously discovered genes involved in neurological function and epigenetic modification are differentially expressed in blastocysts following mitochondrial dysfunction by amino-oxyacetate (AOA). In this study CBAxC57Bl6 2 cell stage mouse embryos were cultured in 5μM-AOA without pyruvate for 72h to induce mitochondrial dysfunction. Blastocyst stage embryos were then transferred to pseudopregnant recipients and the expression profile of day 18 foetal brains was interrogated using microarray. mRNA from mouse whole brain (4 per treatment) was extracted and analysed using an Affymetrix gene array. Ingenuity Pathway Analysis software identified persistent alterations in gene expression pathways in foetal brain after AOA treatment during embryo culture, that were subsequently confirmed by qPCR. Expression was significantly increased by both array and qPCR (>1.5 fold, p<0.05) for; 1) Eomes (1.9, 2.9 fold respectively), a T-box transcription factor involved in differentiation, cell death and development, 2) Nr4a3 (1.8, 2.2 fold respectively), a steroid hormone receptor and putative transcriptional activator and 3) Nola3 (1.7, 1.9 fold respectively), a small nucleolar ribonucleoprotein involved in rRNA processing. Neurological disease, behavioural disorders, carbohydrate metabolism, cellular growth and proliferation, cell death, DNA replication, recombination and repair pathways also showed altered gene expression (>1.25 fold). qPCR was performed on 28 genes exhibiting the greatest change in expression. 24/28 genes confirmed the array data, and of the 4 genes that did not; two had expression not detected by qPCR (Snhg1, Speer6-ps1), and two contradicted array results (Atp1b3 p=0.05, Stk38l p=0.06). This study links mitochondrial dysfunction during early embryo development and persistent molecular changes in the developing foetal brain. This indicates that insults incurred during early embryo development can cause permanent changes that we predict results from aberrant epigenetic modification.

scholarly journals Lysine Deprivation during Maternal Consumption of Low-Protein Diets Could Adversely Affect Early Embryo Development and Health in Adulthood

2020 ◽  
Vol 17 (15) ◽  
pp. 5462
Author(s):  
Lon J. Van Winkle ◽  
Vasiliy Galat ◽  
Philip M. Iannaccone
Keyword(s):  
Embryo Development ◽  
Embryonic Stem ◽  
Early Embryo ◽  
Mammalian Embryo ◽  
Early Embryo Development ◽  
Low Protein ◽  
Glutamate Production ◽  
The Mean ◽  
Hes Cells ◽  
Protein Diets

The conversion of lysine to glutamate is needed for signaling in all plants and animals. In mouse embryonic stem (mES) cells, and probably their progenitors, endogenous glutamate production and signaling help maintain cellular pluripotency and proliferation, although the source of glutamate is yet to be determined. If the source of glutamate is lysine, then lysine deprivation caused by maternal low-protein diets could alter early embryo development and, consequently, the health of the offspring in adulthood. For these reasons, we measured three pertinent variables in human embryonic stem (hES) cells as a model for the inner cell masses of human blastocysts. We found that RNA encoding the alpha-aminoadipic semialdehyde synthase enzyme, which regulates glutamate production from lysine, was highly expressed in hES cells. Moreover, the mean amount of lysine consumed by hES cells was 50% greater than the mean amount of glutamate they produced, indicating that lysine is likely converted to glutamate in these cells. Finally, hES cells expressed RNA encoding at least two glutamate receptors. Since this may also be the case for hES progenitor cells in blastocysts, further studies are warranted to verify the presence of this signaling process in hES cells and to determine whether lysine deprivation alters early mammalian embryo development.

scholarly journals AtNSE1 and AtNSE3 are required for embryo pattern formation and maintenance of cell viability during Arabidopsis embryogenesis

2019 ◽  
Vol 70 (21) ◽  
pp. 6229-6244
Author(s):  
Gang Li ◽  
Wenxuan Zou ◽  
Liufang Jian ◽  
Jie Qian ◽  
Jie Zhao
Keyword(s):  
Cell Death ◽  
Cell Viability ◽  
Cell Fate ◽  
Embryo Development ◽  
Higher Plants ◽  
Early Embryo ◽  
Embryo Cell ◽  
Early Embryogenesis ◽  
Embryo Abortion ◽  
Cell Fate Decisions

Abstract Embryogenesis is an essential process during seed development in higher plants. It has previously been shown that mutation of the Arabidopsis non-SMC element genes AtNSE1 or AtNSE3 leads to early embryo abortion, and their proteins can interact with each other directly. However, the crucial regions of these proteins in this interaction and how the proteins are cytologically involved in Arabidopsis embryo development are unknown. In this study, we found that the C-terminal including the Ring-like motif of AtNSE1 can interact with the N-terminal of AtNSE3, and only the Ring-like motif is essential for binding with three α motifs of AtNSE2 (homologous to AtMMS21). Using genetic assays and by analysing molecular markers of cell fate decisions (STM, WOX5, and WOX8) in mutant nse1 and nse3 embryos, we found that AtNSE1 and AtNSE3 work non-redundantly in early embryo development, and that differentiation of the apical meristem and the hypophysis fails in the mutants, which have disrupted auxin transportation and responses. However, the upper cells of the suspensor in the mutants seem to have proper embryo cell identity. Cytological examination showed that cell death occurred from the early embryo stage, and that vacuolar programmed cell death and necrosis in the nse1 and nse3 mutant embryos led to ovule abortion. Thus, AtNSE1 and AtNSE3 are essential for maintaining cell viability and growth during early embryogenesis. Our results improve our understanding of the functions of SMC5/6 complex in early embryogenesis in Arabidopsis.

scholarly journals Deadly decisions: the role of genes regulating programmed cell death in human preimplantation embryo development

Reproduction ◽  
2004 ◽  
Vol 128 (3) ◽  
pp. 281-291 ◽  
Author(s):  
Andrea Jurisicova ◽  
Beth M Acton
Keyword(s):  
Gene Expression ◽  
Cell Death ◽  
Cell Fate ◽  
Embryo Development ◽  
Preimplantation Embryo ◽  
Culture Media ◽  
Culture Conditions ◽  
Early Embryo ◽  
Preimplantation Embryo Development

Human preimplantation embryo development is prone to high rates of early embryo wastage, particularly under currentin vitroculture conditions. There are many possible underlying causes for embryo demise, including DNA damage, poor embryo metabolism and the effect of suboptimal culture media, all of which could result in an imbalance in gene expression and the failed execution of basic embryonic decisions. In view of the complex interactions involved in embryo development, a thorough understanding of these parameters is essential to improving embryo quality. An increasing body of evidence indicates that cell fate (i.e. survival/differentiation or death) is determined by the outcome of specific intracellular interactions between pro- and anti-apoptotic proteins, many of which are expressed during oocyte and preimplantation embryo development. The recent availability of mutant mice lacking expression of various genes involved in the regulation of cell survival has enabled rapid progress towards identifying those molecules that are functionally important for normal oocyte and preimplantation embryo development. In this review we will discuss the current understanding of the regulation of cell death gene expression during preimplantation embryo development, with a focus on human embryology and a discussion of animal models where appropriate.

scholarly journals DNA methylation presents distinct binding sites for human transcription factors

eLife ◽  
2013 ◽  
Vol 2 ◽  
Author(s):  
Shaohui Hu ◽  
Jun Wan ◽  
Yijing Su ◽  
Qifeng Song ◽  
Yaxue Zeng ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Epigenetic Modification ◽  
Specific Binding ◽  
Protein Microarray ◽  
Embryonic Stem ◽  
Underlying Mechanism ◽  
Binding Activity ◽  
Site Directed Mutagenesis ◽  
Promoter Regions

DNA methylation, especially CpG methylation at promoter regions, has been generally considered as a potent epigenetic modification that prohibits transcription factor (TF) recruitment, resulting in transcription suppression. Here, we used a protein microarray-based approach to systematically survey the entire human TF family and found numerous purified TFs with methylated CpG (mCpG)-dependent DNA-binding activities. Interestingly, some TFs exhibit specific binding activity to methylated and unmethylated DNA motifs of distinct sequences. To elucidate the underlying mechanism, we focused on Kruppel-like factor 4 (KLF4), and decoupled its mCpG- and CpG-binding activities via site-directed mutagenesis. Furthermore, KLF4 binds specific methylated or unmethylated motifs in human embryonic stem cells in vivo. Our study suggests that mCpG-dependent TF binding activity is a widespread phenomenon and provides a new framework to understand the role and mechanism of TFs in epigenetic regulation of gene transcription.

DNA methylation in the vertebrate germline: balancing memory and erasure

2019 ◽  
Vol 63 (6) ◽  
pp. 649-661 ◽  
Author(s):  
Oscar Ortega-Recalde ◽  
Timothy Alexander Hore
Keyword(s):  
Dna Methylation ◽  
Cytosine Methylation ◽  
Epigenetic Modification ◽  
Epigenetic Inheritance ◽  
Direct Consequence ◽  
Early Embryo ◽  
Germline Development ◽  
Evolutionary Mechanisms ◽  
Information Module ◽  
Methylation Patterns

Abstract Cytosine methylation is a DNA modification that is critical for vertebrate development and provides a plastic yet stable information module in addition to the DNA code. DNA methylation memory establishment, maintenance and erasure is carefully balanced by molecular machinery highly conserved among vertebrates. In mammals, extensive erasure of epigenetic marks, including 5-methylcytosine (5mC), is a hallmark of early embryo and germline development. Conversely, global cytosine methylation patterns are preserved in at least some non-mammalian vertebrates over comparable developmental windows. The evolutionary mechanisms which drove this divergence are unknown, nevertheless a direct consequence of retaining epigenetic memory in the form of 5mC is the enhanced potential for transgenerational epigenetic inheritance (TEI). Given that DNA methylation dynamics remains underexplored in most vertebrate lineages, the extent of information transferred to offspring by epigenetic modification might be underestimated.

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