scholarly journals High-resolution profiles of gene expression and DNA methylation highlight mitochondrial modifications during early embryonic development

2017 ◽  
Vol 63 (3) ◽  
pp. 247-261 ◽  
Author(s):  
Likun REN ◽  
Chao ZHANG ◽  
Li TAO ◽  
Jing HAO ◽  
Kun TAN ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
High Resolution ◽  
Embryonic Development ◽  
Early Embryonic Development

scholarly journals DNA Methylation Is Correlated with Gene Expression during Diapause Termination of Early Embryonic Development in the Silkworm (Bombyx mori)

2020 ◽  
Vol 21 (2) ◽  
pp. 671 ◽  
Author(s):  
Bing Li ◽  
Pei Hu ◽  
Lin-Bao Zhu ◽  
Ling-Ling You ◽  
Hui-Hua Cao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Embryonic Development ◽  
Bombyx Mori ◽  
Transcription Initiation ◽  
Early Embryonic Development ◽  
Dna Modification ◽  
Promoter Regions ◽  
Short Interspersed Elements ◽  
Silkworm Bombyx Mori

DNA modification is a naturally occurring DNA modification in prokaryotic and eukaryotic organisms and is involved in several biological processes. Although genome-wide methylation has been studied in many insects, the understanding of global and genomic DNA methylation during insect early embryonic development, is lacking especially for insect diapause. In this study, we analyzed the relationship between DNA methylomes and transcriptomes in diapause-destined eggs compared to diapause-terminated eggs in the silkworm, Bombyx mori (B. mori). The results revealed that methylation was sparse in this species, as previously reported. Moreover, methylation levels in diapause-terminated eggs (HCl-treated) were 0.05% higher than in non-treated eggs, mainly due to the contribution of CG methylation sites. Methylation tends to occur in the coding sequences and promoter regions, especially at transcription initiation sites and short interspersed elements. Additionally, 364 methylome- and transcriptome-associated genes were identified, which showed significant differences in methylation and expression levels in diapause-destined eggs when compared with diapause-terminated eggs, and 74% of methylome and transcriptome associated genes showed both hypermethylation and elevated expression. Most importantly, Kyoto Encyclopaedia of Genes and Genomes (KEGG) analyses showed that methylation may be positively associated with Bombyx mori embryonic development, by regulating cell differentiation, metabolism, apoptosis pathways and phosphorylation. Through analyzing the G2/M phase-specific E3 ubiquitin-protein ligase (G2E3), we speculate that methylation may affect embryo diapause by regulating the cell cycle in Bombyx mori. These findings will help unravel potential linkages between DNA methylation and gene expression during early insect embryonic development and insect diapause.

122 SUPPRESSION OF EPIGENETIC MODIFIERS ALTERS THE BOVINE EMBRYONIC DEVELOPMENTAL PROGRAM DURING IN VITRO CULTURE

2014 ◽  
Vol 26 (1) ◽  
pp. 175 ◽  
Author(s):  
M. D. Snyder ◽  
J. H. Pryor ◽  
M. D. Peoples ◽  
G. L. Williamson ◽  
M. C. Golding ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Embryonic Development ◽  
Dna Methyltransferase ◽  
Test Statistic ◽  
Gene Target ◽  
Blastocyst Rate ◽  
Green Fluorescent ◽  
Fluorescent Dextran

During early bovine embryogenesis, the regular establishment of DNA methylation and histone modification patterns is essential for proper gene expression and continuation of embryonic development. Epigenome patterns established during this period, if improperly maintained, can lead to developmental anomalies and may partially explain the lower pregnancy rates of in vitro-produced embryos. We hypothesised that the suppression of translation of the genes euchromatic histone-lysine N-methyltransferase 2 (EHMT2), DNA methyltransferase 3A (DNMT3A), absent, small, or homeotic-like (ASH2L), and SET domain, bifurcated 1 (SETDB1) would provide insightful information on the importance of these genes during early embryonic development in an in vitro setting. In order to define the roles of these genes, small interfering RNA (siRNA) targeting the gene of interest were synthesised and target verified in bovine cell culture using quantitative real-time RT-PCR (RT-qPCR). We acquired matured bovine oocytes from commercial suppliers, followed by IVF by standard laboratory procedures. Eighteen hours post IVF, cumulus cells were removed and zygotes separated into 3 different treatment groups: non-injected controls (CNTL), non-targeting siRNA injected controls (siNULL), and injection with siRNA targeting the gene of interest (si “gene target”). Each siRNA was mixed with a green fluorescent dextran at a concentration of 20 μM and ~100 pL injected cytoplasmically. The green fluorescent dextran was used to give visual confirmation that zygotes were indeed injected. Post-injection, fluorescent embryos were separated and cultured in Bovine Evolve (Zentih Biotech) medium supplemented with 4 mg mL–1 of BSA (Probumin, Millipore). Cleavage rates were monitored on Day 2, and only cleaved embryos were cultured further. On Day 8 post-IVF, embryos were morphologically examined and numbers of blastocysts recorded. Mean development rates between siNULL and targeting siRNA were compared using a t-test statistic. Over the course of these experiments the mean blastocyst rate for CNTL zygotes was 34.5% ± 2.6 s.e.m. (n = 1647). None of the zygotes injected with siEHMT2 (n = 1184) or siSETDB1 (n = 361) reached the blastocyst stage and these rates differed from the siNULL rate (21.0% ± 2.5 s.e.m., n = 1587; P < 0.05). Morphologically, embryos from both groups developed to the morula stage before they exhibited fragmentation. Injection of siDNMT3A also resulted in significant loss of viability at the 8-cell stage and few zygotes injected (n = 1057) developed to blastocyst (2.1% ± 0.5 s.e.m.; P < 0.001). Inhibiting gene expression of ASH2L showed little variation in blastocyst rate from our siNULL embryos (31.3% ± 2.0 s.e.m., n = 466 v. 34.8% ± 1.9 s.e.m., n = 418, respectively, P > 0.2). It is unknown at this time if inhibition of ASH2L translation will have effects later in development. Ongoing experiments analysing DNA methylation and histone modifications through immunocytochemistry and global gene expression via RT-qPCR will further explore the establishment and maintenance of these genes in the embryonic epigenome.

4 SUPPRESSION OF ASH2L ALTERS DNA METHYLATION AND HISTONE PATTERNS DURING BOVINE EMBRYONIC DEVELOPMENT

2016 ◽  
Vol 28 (2) ◽  
pp. 131
Author(s):  
M. D. Snyder ◽  
J. H. Pryor ◽  
M. D. Peoples ◽  
G. L. Williamson ◽  
M. C. Golding ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Embryonic Development ◽  
Blastocyst Stage ◽  
Early Embryonic Development ◽  
Standard Laboratory ◽  
Significant Difference ◽  
Commercial Supplier ◽  
Secondary Antibodies ◽  
Laboratory Protocol

Epigenetic patterns established during early bovine embryogenesis via DNA methylation and histone modification patterns are essential for proper gene expression and embryonic development. We have previously discovered that suppression of absent, small, or homeotic-like (ASH2L) with small interfering RNA (siRNA) had no significant effect during in vitro embryo development when compared with its respective control (31.3 ± 2.0% standard error of the mean, n = 466 v. 34.8 ± 1.9%, n = 418). Analysing DNA methylation and histone modifications via immunocytochemistry will further explain the role of ASH2L during embryonic development, specifically at the blastocyst stage. In this experiment, we obtained mature bovine oocytes from a commercial supplier (De Soto Biosciences, Seymour, TN) and preformed IVF following standard laboratory protocol. Eighteen hours after IVF, presumptive zygotes were divided into 3 treatments: noninjected controls, nontargeting siRNA injected controls (siNULL), and injection with siRNA targeting ASH2L (siASH2L). Each embryo was injected with ~100 pL of 20 nM siRNA previously verified to suppress expression of ASH2L by ~79%. Embryos were cultured in Bovine Evolve (Zenith Biotech, Guilford, CT) supplemented with 4 mg mL–1 of BSA (Probumin, Millipore) for 7 days. Blastocysts from each treatment (N = 601) were fixed and prepared for immunocytochemistry following standard laboratory protocol. The following primary antibodies were used to target specific DNA and histone methylation marks: 5mc mAb (Epigentek, Farmingdale, NY), 5hmc pAb, H3K4me3 pAb (Active Motif, Carlsbad, CA), H3K4me2 pAb, H3K9me2–3 mAb, and H3K27me3 mAb (Abcam, Cambridge, MA). Embryos were fluorescently labelled with the following secondary antibodies: Alexa Flour 488 Goat Anti-Rabbit, Alexa 488 Donkey Anti-Goat, and Alexa Flour 594 Goat Anti-Mouse (Invitrogen, Carlsbad, CA). The DNA was stained with Hoechst 33342 (Invitrogen). Fluorescent images were captured using the Zeiss Stallion digital imaging work station. Ratio averages (targeting mark/DNA) were calculated and statistical analysis performed using one-way ANOVA and Tukey’s honestly significant difference to assess treatment effects. The ratio of DNA methylation to total DNA increased in siASH2L as compared with control and siNULL embryos (0.35 ± 0.01, 0.26 ± 0.02, and 0.30 ± 0.01, respectively; P < 0.01). The 5hmC was inversely related to 5mC levels and decreased in siASH2L embryos (0.75 ± 0.01, 0.93 ± 0.02, 0.87 ± 0.02, respectively; P < 0.0001). The H3K4me3 and H3K27me3 are also inversely related with decreased H3K4me3 in siASH2L versus control and siNULL embryos (0.48 ± 0.02, 0.57 ± 0.02, 0.58 ± 0.02, respectively; P < 0.001) and increased H3K27me3 (0.62 ± 0.02, 0.053 ± 0.01, 0.54 ± 0.02, respectively; P < 0.001). No differences were observed in H3K9me2–3 or H3K4me2 labelling across treatments. These results indicate that ASH2L may play a role in DNA methylation by decreasing 5mc and 5hmc conversion, which is a key event during early embryonic development. Suppression of ASH2L also alters global levels of H3H4me3 and H3K27me3, which may lead to transcription aberrations. Further analysis of siASH2L embryos via RNA-seq will help define its role during early embryonic development.

scholarly journals Revealing the bovine embryo transcript profiles during early in vivo embryonic development

Reproduction ◽  
2009 ◽  
Vol 138 (1) ◽  
pp. 95-105 ◽  
Author(s):  
Maud Vallée ◽  
Isabelle Dufort ◽  
Stéphanie Desrosiers ◽  
Aurélie Labbe ◽  
Catherine Gravel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Embryonic Development ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Current Knowledge ◽  
Mrna Level ◽  
Early Embryonic Development ◽  
Bovine Embryo ◽  
Rna Content

Gene expression profiling is proving to be a powerful approach for the identification of molecular mechanisms underlying complex cellular functions such as the dynamic early embryonic development. The objective of this study was to perform a transcript abundance profiling analysis of bovine early embryonic development in vivo using a bovine developmental array. The molecular description of the first week of life at the mRNA level is particularly challenging when considering the important fluctuations in RNA content that occur between developmental stages. Accounting for the different intrinsic RNA content between developmental stages was achieved by restricting the reaction time during the global amplification steps and by using spiked controls and reference samples. Analysis based on intensity values revealed that most of the transcripts on the array were present at some point during in vivo bovine early embryonic development, while the varying number of genes detected in each developmental stage confirmed the dynamic profile of gene expression occurring during embryonic development. Pair-wise comparison of gene expression showed a marked difference between oocytes and blastocysts profiles, and principal component analysis revealed that the majority of the transcripts could be regrouped into three main clusters representing distinct RNA abundance profiles. Overall, these data provide a detailed temporal profile of the abundance of mRNAs revealing the richness of signaling processes in early mammalian development. Results presented here provide better knowledge of bovine in vivo embryonic development and contribute to the progression of our current knowledge regarding the first week of life in mammals.

The requirement for protein kinase C delta (PRKCD) during preimplantation bovine embryo development

2016 ◽  
Vol 28 (4) ◽  
pp. 482 ◽  
Author(s):  
Qi-En Yang ◽  
Manabu Ozawa ◽  
Kun Zhang ◽  
Sally E. Johnson ◽  
Alan D. Ealy
Keyword(s):  
Gene Expression ◽  
Protein Kinase C ◽  
Protein Kinase ◽  
Embryonic Development ◽  
Embryo Development ◽  
Early Embryonic Development ◽  
Bovine Embryo ◽  
Bovine Embryos ◽  
Cell Stage ◽  
Kinase C

Protein kinase C (PKC) delta (PRKCD) is a member of the novel PKC subfamily that regulates gene expression in bovine trophoblast cells. Additional functions for PRKCD in early embryonic development in cattle have not been fully explored. The objectives of this study were to describe the expression profile of PRKCD mRNA in bovine embryos and to examine its biological roles during bovine embryo development. Both PRKCD mRNA and protein are present throughout early embryo development and increases in mRNA abundance are evident at morula and blastocyst stages. Phosphorylation patterns are consistent with detection of enzymatically active PRKCD in bovine embryos. Exposure to a pharmacological inhibitor (rottlerin) during early embryonic development prevented development beyond the eight- to 16-cell stage. Treatment at or after the 16-cell stage reduced blastocyst development rates, total blastomere numbers and inner cell mass-to-trophoblast cell ratio. Exposure to the inhibitor also decreased basal interferon tau (IFNT) transcript abundance and abolished fibroblast growth factor-2 induction of IFNT expression. Furthermore, trophoblast adhesion and proliferation was compromised in hatched blastocysts. These observations provide novel insights into PRKCD mRNA expression profiles in bovine embryos and provide evidence for PRKCD-dependent regulation of embryonic development, gene expression and post-hatching events.

Changes in DNA methylation during mouse embryonic development in relation to X-chromosome activity and imprinting

1990 ◽  
Vol 326 (1235) ◽  
pp. 299-312 ◽  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Embryonic Development ◽  
X Chromosome ◽  
De Novo ◽  
Germ Line ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Chromatin Configuration ◽  
Methylation Patterns

Changing DNA methylation patterns during embryonic development are discussed in relation to differential gene expression, changes in X-chromosome activity and genomic imprinting. Sperm DNA is more methylated than oocyte DNA, both overall and for specific sequences. The methylation difference between the gametes could be one of the mechanisms (along with chromatin structure) regulating initial differences in expression of parental alleles in early development. There is a loss of methylation during development from the morula to the blastocyst and a marked decrease in methylase activity. De novo methylation becomes apparent around the time of implantation and occurs to a lesser extent in extra-embryonic tissue DNA. In embryonic DNA, de novo methylation begins at the time of random X-chromosome inactivation but it continues to occur after X-chromosome inactivation and may be a mechanism that irreversibly fixes specific patterns of gene expression and X-chromosome inactivity in the female. The germ line is probably delineated before extensive de novo methylation and hence escapes this process. The marked undermethylation of the germ line DNA may be a prerequisite for X-chromosome reactivation. The process underlying reactivation and removal of parent-specific patterns of gene expression may be changes in chromatin configuration associated with meiosis and a general reprogramming of the germ line to developmental totipotency.

scholarly journals DNA methylation and miRNA-1296 act in concert to mediate spatiotemporal expression of KPNA7 during bovine oocyte and early embryonic development

2019 ◽  
Author(s):  
Lei Wang ◽  
Jacqelyn M. Hand ◽  
Liyuan Fu ◽  
George W. Smith ◽  
Jianbo Yao
Keyword(s):  
Dna Methylation ◽  
Embryonic Development ◽  
Early Stage ◽  
Early Embryonic Development ◽  
Hek293 Cells ◽  
Proximal Promoter ◽  
Pcr Analysis ◽  
Coding Region ◽  
Cell Stage ◽  
Cpg Sites

Abstract Background Epigenetic regulation of oocyte-specific maternal factors is essential for oocyte and early embryonic development. KPNA7 is an oocyte-specific maternal factor, which controls transportation of nuclear proteins important for early embryonic development. To elucidate the epigenetic mechanisms involved in the controlled expression of KPNA7, both DNA methylation associated transcriptional silencing and miRNA-mediated mRNA degradation of KPNA7 were examined. Results Comparison of DNA methylation profiles at the proximal promoter of KPNA7 gene between oocyte and 6 different somatic tissues identified 3 oocyte-specific differentially methylated CpG sites. Expression of KPNA7 mRNA was reintroduced in bovine kidney-derived CCL2 cells after treatment with the methylation inhibitor, 5-aza-2-deoxycytidine (5-Aza). Analysis of the promoter region of KPNA7 gene in CCL2 cells treated with 5-Aza showed a lighter methylation rate in all the CpG sites. Bioinformatic analysis predicted 4 miRNA-1296 binding sites in the coding region of KPNA7 mRNA. Ectopic co-expression of miRNA-1296 and KPNA7 in HEK293 cells led to reduced expression of KPNA7 protein. Quantitative real time PCR analysis revealed that miRNA-1296 is expressed in oocytes and early stage embryos, and the expression reaches a peak level in 8-cell stage embryos, coincident with the time of embryonic genome activation and the start of declining of KPNA7 expression. Conclusions These results suggest that DNA methylation may account for oocyte-specific expression of KPNA7, and miRNA-1296 targeting the coding region of KPNA7 is a potential mechanism for KPNA7 transcript degradation during the maternal-to-zygotic transition.

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