Epigenetic remodeling in preimplantation embryos: cows are not big mice

Dynamic methylation pattern of H19DMR and KvDMR1 in bovine oocytes and preimplantation embryos

PURPOSE

This study aimed to evaluate the epigenetic reprogramming of ICR1 (KvDMR1) and ICR2 (H19DMR) and expression of genes controlled by them as well as those involved in methylation, demethylation, and pluripotency.

METHODS

We collected germinal vesicle (GV) and metaphase II (MII) oocytes, and preimplantation embryos at five stages [zygote, 4-8 cells, 8-16 cells, morula, and expanded blastocysts (ExB)]. DNA methylation was assessed by BiSeq, and the gene expression was evaluated using qPCR.

RESULTS

H19DMR showed an increased DNA methylation from GV to MII oocytes (68.04% and 98.05%, respectively), decreasing in zygotes (85.83%) until morula (61.65%), and ExB (63.63%). H19 and IGF2 showed increased expression in zygotes, which decreased in further stages. KvDMR1 was hypermethylated in both GV (71.82%) and MII (69.43%) and in zygotes (73.70%) up to morula (77.84%), with a loss of methylation at the ExB (36.64%). The zygote had higher expression of most genes, except for CDKN1C and PHLDA2, which were highly expressed in MII and GV oocytes, respectively. DNMTs showed increased expression in oocytes, followed by a reduction in the earliest stages of embryo development. TET1 was downregulated until 4-8-cell and upregulated in 8-16-cell embryos. TET2 and TET3 showed higher expression in oocytes, and a downregulation in MII oocytes and 4-8-cell embryo.

CONCLUSION

We highlighted the heterogeneity in the DNA methylation of H19DMR and KvDMR1 and a dynamic expression pattern of genes controlled by them. The expression of DNMTs and TETs genes was also dynamic owing to epigenetic reprogramming.

Effect of lipotoxicity on mitochondrial function and epigenetic programming during bovine in vitro embryo production

Maternal metabolic disorders may cause lipotoxic effects on the developing oocyte. Understanding the timing at which this might disrupt embryo epigenetic programming and how this is linked with mitochondrial dysfunction is crucial for improving assisted reproductive treatments, but has not been investigated before. Therefore, we used a bovine in vitro model to investigate if pathophysiological palmitic acid (PA) concentrations during in vitro oocyte maturation and in vitro embryo culture alter embryo epigenetic patterns (DNA methylation (5mC) and histone acetylation/methylation (H3K9ac/H3K9me2)) compared to control (CONT) and solvent control (SCONT), at the zygote and morula stage. Secondly, we investigated if these epigenetic alterations are associated with mitochondrial dysfunction and changes in ATP production rate, or altered expression of epigenetic regulatory genes. Compared to SCONT, H3K9ac and H3K9me2 levels were increased in PA-derived zygotes. Also, 5mC and H3K9me2 levels were increased in PA-exposed morulae compared to SCONT. This was associated with complete inhibition of glycolytic ATP production in oocytes, increased mitochondrial membrane potential and complete inhibition of glycolytic ATP production in 4-cell embryos and reduced SOD2 expression in PA-exposed zygotes and morulae. For the first time, epigenetic alterations in metabolically compromised zygotes and morulae have been observed in parallel with mitochondrial dysfunction in the same study.

The mammalian preimplantation embryo: Its role in the environmental programming of postnatal health and performance

During formation of the preimplantation embryo several cellular and molecular milestones take place, making the few cells forming the early embryo vulnerable to environmental stressors than can impair epigenetic reprogramming and controls of gene expression. Although these molecular alterations can result in embryonic death, a significant developmental plasticity is present in the preimplantation embryo that promotes full-term pregnancy. Prenatal epigenetic modifications are inherited during mitosis and can perpetuate specific phenotypes during early postnatal development and adulthood. As such, the preimplantation phase is a developmental window where developmental programming can take place in response to the embryonic microenvironment present in vivo or in vitro. In this review, the relevance of the preimplantation embryo as a developmental stage where offspring health and performance can be programmed is discussed, with emphasis on malnutrition and assisted reproductive technologies; two major environmental insults with important implications for livestock production and human reproductive medicine.

Unraveling the Consequences of Oxygen Imbalance on Early Embryo Development: Exploring Mitigation Strategies

Although well-established and adopted by commercial laboratories, the in vitro embryo production system still requires refinements to achieve its highest efficiency. Early embryonic development is a dynamic event, demanding suitable conditions to provide a high number of embryos with quality and competence. The first step to obtaining an optimized in vitro environment is to know the embryonic metabolism and energy request throughout the different stages of development. Oxygen plays a crucial role in several key biological processes necessary to sustain and complete embryonic development. Nonetheless, there is still controversy regarding the optimal in vitro atmospheric concentrations during culture. Herein, we discuss the impact of oxygen tension on the viability of in vitro-produced embryos during early development. The importance of oxygen tension is addressed as its roles regarding essential embryonic traits, including embryo production rates, embryonic cell viability, gene expression profile, epigenetic regulation, and post-cryopreservation survival. Finally, we highlight the damage caused by in vitro unbalanced oxygen tensions and strategies to mitigate the harmful effects.

Histone remodeling reflects conserved mechanisms of bovine and human preimplantation development

How histone modifications regulate changes in gene expression during preimplantation development in any species remains poorly understood. Using CUT&Tag to overcome limiting amounts of biological material, we profiled two activating (H3K4me3 and H3K27ac) and two repressive (H3K9me3 and H3K27me3) marks in bovine oocytes, 2-, 4-, and 8-cell embryos, morula, blastocysts, inner cell mass, and trophectoderm. In oocytes, broad bivalent domains mark developmental genes, and prior to embryonic genome activation (EGA), H3K9me3 and H3K27me3 co-occupy gene bodies, suggesting a global mechanism for transcription repression. During EGA, chromatin accessibility is established before canonical H3K4me3 and H3K27ac signatures. Embryonic transcription is required for this remodeling, indicating that maternally provided products alone are insufficient for reprogramming. Last, H3K27me3 plays a major role in restriction of cellular potency, as blastocyst lineages are defined by differential polycomb repression and transcription factor activity. Notably, inferred regulators of EGA and blastocyst formation strongly resemble those described in humans, as opposed to mice. These similarities suggest that cattle are a better model than rodents to investigate the molecular basis of human preimplantation development.

Micro-vibration results in vitro-derived bovine blastocysts with greater cryotolerance, epigenetic abnormalities, and a massive transcriptional change

Much effort has been employed to improve the quality of embryos obtained by in vitro production (IVP) given the relevance of this technology to current livestock systems. In this context, dynamic IVP systems have proved beneficial to the embryo once they mimic fluid flows and mechanical forces resulting from the movement of ciliated cells and muscle contraction in the reproductive tract. In the present study, we sought to confirm these initial findings as well as assess potential molecular consequences to the embryo by applying micro-vibration (45 Hz for 5 s once per 60 min) during both oocyte maturation and embryo culture in cattle. As a result, micro-vibration led to lower incidence of apoptosis in blastocysts following vitrification-thawing. Further analyses revealed epigenetic and transcriptional changes in blastocysts derived from the micro-vibration treatment, with a total of 502 differentially expressed genes. Enrichment analyses linked differentially expressed genes to 'Oxidative phosphorylation', 'Cytokine-cytokine receptor interaction', and 'Signaling pathways regulating pluripotency of stem cells'. Yet, a meta-analysis indicated that the transcriptional changes induced by micro-vibration were not toward that of in vivo-derived embryos. In conclusion, micro-vibration increases the cryoresistance of bovine embryos, but caution should be taken given the unclear consequences of epigenetic and transcriptional abnormalities induced by the treatment.

Bovine In Vitro Oocyte Maturation and Embryo Production Used as a Model for Testing Endocrine Disrupting Chemicals Eliciting Female Reproductive Toxicity With Diethylstilbestrol as a Showcase Compound

Endocrine disrupting chemicals (EDCs) can interfere with normal hormonal action and regulation. Exposure of women to EDCs has been associated with adverse reproductive health outcomes. The assays currently used to identify EDCs that elicit female reproductive toxicity lack screening tests that address effects on the maturation of oocytes, a process that enables them to be fertilized and develop into embryos. Here, a screening method employing the bovine model of in vitro oocyte maturation and embryo production is described. Endpoints explored address important events in oocyte maturation and developmental competence acquisition. To test the method, the effects of the known human EDC diethylstilbestrol (DES; an estrogen receptor agonist) were evaluated in a range of concentrations (10^–9 M, 10^–7 M, 10^–5 M). Bovine oocytes were exposed to DES during in vitro maturation (IVM) or embryos were exposed during in vitro embryo culture (IVC). The endpoints evaluated included nuclear maturation, mitochondrial redistribution, cumulus cell expansion, apoptosis, and steroidogenesis. DES-exposed oocytes were fertilized to record embryo cleavage and blastocyst rates to uncover effects on developmental competence. Similarly, the development of embryos exposed to DES during IVC was monitored to assess the impact on early embryo development. Exposure to 10^–9 M or 10^–7 M DES did not affect the endpoints addressing oocyte maturation or embryo development. However, there were considerable detrimental effects observed in oocytes exposed to 10^–5 M DES. Specifically, compared to vehicle-treated oocytes, there was a statistically significant reduction in nuclear maturation (3% vs 84%), cumulus expansion (2.8-fold vs 3.6-fold) and blastocyst rate (3% vs 32%). Additionally, progesterone and pregnenolone concentrations measured in IVM culture media were increased. The screening method described here shows that bovine oocytes were sensitive to the action of this particular chemical (i.e., DES), albeit at high concentrations. In principle, this method provides a valuable tool to assess the oocyte maturation process and early embryo development that can be used for reproductive toxicity screening and possibly EDC identification. Further studies should include EDCs with different mechanisms of action and additional endpoints to further demonstrate the applicability of the bovine oocyte model for chemical risk assessment purposes and EDC identification.

Interplay Between Stress and Reproduction: Novel Epigenetic Markers in Response to Shearing Patterns in Australian Merino Sheep (Ovis aries)

In this study, we determined the effect(s) of early shearing on Australian Merino ewes (Ovis aries) and their lambs. To test this research question, we used a suite of field and laboratory methods including GPS collars, wool cortisol, and epigenetic change between ewes and lambs identified using Illumina NovaSeq RRBS. Once shorn ewes (n = 24) were kept on their full fleece throughout the entire gestation period, whereas twice (early) shorn ewes (n = 24) had their wool shorn pre-joining. Top-knot wool sample was taken from ewes during pre-joining, day 50 (mid-gestation), and day 90 (late gestation) for laboratory analysis. Ewes were pregnancy scanned at mid-gestation to determine whether they were early or late parturition (this confirmation is provided by the pregnancy scanner based on fetus size). Top-knot wool sample was also taken from the lambs at weaning for hormone and wool quality testing. Ear tissue was taken from ewes at day 50 (mid-gestation) and from lambs at lamb marking for DNA analysis. Results showed that twice or early shorn ewes grazed 10% higher and maintained stronger body condition than once shorn ewes. Wool cortisol levels were also significantly lower in the early shorn ewes between mid- and late gestation. Lambs bred from twice shorn ewes had on average better visual wool quality parameters in terms of micron, spin finesses, and curvature. For the DNA methylation results, when comparing a group of once sheared with twice sheared ewes, we have discovered one locus (Chr20:50404014) that was significantly differentially methylated [False Discovery Rate (FDR) = 0.005]. This locus is upstream of a protein-coding gene (ENSOARG00000002778.1), which shows similarities to the forkhead box C1 (FOXC1) mRNA using BLAST searches. To further our understanding of the potential interaction between pregnancy status and shearing frequency of the ewes, we performed further differential methylation analysis using a combination of shearing treatment and pregnancy scanning status. The comparisons (1) late pregnancy vs. early pregnancy for ewes with one shearing treatment and (2) late pregnancy vs. early pregnancy for sheep with two shearing treatments were carried out to identify associations between loci and pregnancy duration for sheep with either one or two shearing events. We discovered that 36 gene loci were significantly modulated either between different shearing treatments or late vs. early pregnancy status of ewes. This result suggests that maternal pregnancy and nutritional status during gestation influence DNA methylation. We further investigated DNA methylation in lambs and identified 16 annotated gene loci that showed epigenetic modulation as a result of being born from an early or late stage pregnancy. From the genomics data, we pointed out that ewes go through epigenetic modifications during gestation, and there is a degree of intra-individual variation in the reproductive performance of ewes, which could be due to combination of intrinsic (genetic and physiological) and extrinsic (management and climatic) factors. Collectively, this research provides novel dataset combining physiological, molecular epigenetics, and digital tracking indices that advances our understanding of how Merino ewes respond to shearing frequency, and this information could guide further research on Merino sheep breeding and welfare.

Impact of oocyte donor age and breed on in vitro embryo production in cattle, and relationship of dairy and beef embryo recipients on pregnancy and the subsequent performance of offspring: A review

Genomic selection combined with in vitro embryo production (IVEP) with oocytes from heifer calves provides a powerful technology platform to reduce generation interval and significantly increase the rate of genetic gain in cattle. The ability to obtain oocytes with developmental competence from calves has been recognised for more than 60years. There is renewed interest in the potential of this reproductive technology as the beef and dairy industries seek to identify and multiply animals that satisfy consumer demand for efficient utilisation of natural resources, with minimal environmental impact and high product quality. Heifer calves show a good follicular response to FSH stimulation and oocytes can be recovered by ovum pick-up (OPU). However, the efficiency of OPU/IVEP remains lower for calves compared with peripubertal heifers and cows, in both indicus (Zebu, Bos indicus ) and taurus (Bos taurus ) breeds. Indicus cattle generally have more follicles, yield a greater number of oocytes, and have a better IVEP outcome, compared with taurus cattle. The treatment of prepubertal heifers with bovine somatotrophin (bST) and propylene glycol before OPU/IVEP has yet to show a major improvement in embryo production. Holstein (taurus) dairy heifers derived from different reproductive technologies (AI, MOET, OPU/IVEP) showed a similar age at puberty and first-lactation milk production. OPU/IVEP Holstein embryos transferred to beef or dairy cows likewise yielded heifers with the same performance. The gains in productivity that can be achieved with strategic use of OPU/IVEP in heifer calves make this a relevant and highly important reproductive technology in cattle breeding. Ongoing optimisation of the technology is needed for the potential of OPU/IVEP in young donors to be fully realised.

Dysregulated Gene Expression of Imprinted and X-Linked Genes: A Link to Poor Development of Bovine Haploid Androgenetic Embryos

Mammalian uniparental embryos are efficient models for genome imprinting research and allow studies on the contribution of the paternal and maternal genomes to early embryonic development. In this study, we analyzed different methods for production of bovine haploid androgenetic embryos (hAE) to elucidate the causes behind their poor developmental potential. Results indicate that hAE can be efficiently generated by using intracytoplasmic sperm injection and oocyte enucleation at telophase II. Although androgenetic haploidy does not disturb early development up to around the 8-cell stage, androgenetic development is disturbed after the time of zygote genome activation and hAE that reach the morula stage are less capable to reach the blastocyst stage of development. Karyotypic comparisons to parthenogenetic- and ICSI-derived embryos excluded chromosomal segregation errors as causes of the developmental constraints of hAE. However, analysis of gene expression indicated abnormal levels of transcripts for key long non-coding RNAs involved in X chromosome inactivation and genomic imprinting of the KCNQ1 locus, suggesting an association with X chromosome and some imprinted loci. Moreover, transcript levels of methyltransferase 3B were significantly downregulated, suggesting potential anomalies in hAE establishing de novo methylation. Finally, the methylation status of imprinted control regions for XIST and KCNQ1OT1 genes remained hypomethylated in hAE at the morula and blastocyst stages, confirming their origin from spermatozoa. Thus, our results exclude micromanipulation and chromosomal abnormalities as major factors disturbing the normal development of bovine haploid androgenotes. In addition, although the cause of the arrest remains unclear, we have shown that the inefficient development of haploid androgenetic bovine embryos to develop to the blastocyst stage is associated with abnormal expression of key factors involved in X chromosome activity and genomic imprinting.

Erasing gametes to write blastocysts: metabolism as the new player in epigenetic reprogramming

Understanding preimplantation embryonic development is crucial for the improvement of assisted reproductive technologies and animal production. To achieve this goal, it is important to consider that gametes and embryos are highly susceptible to environmental changes. Beyond the metabolic adaptation, the dynamic status imposed during follicular growth and early embryogenesis may create marks that will guide the molecular regulation during prenatal development, and consequently impact the offspring phenotype. In this context, metaboloepigenetics has gained attention, as it investigates the crosstalk between metabolism and molecular control, i.e., how substrates generated by metabolic pathways may also act as players of epigenetic modifications. In this review, we present the main metabolic and epigenetic events of pre-implantation development, and how these systems connect to open possibilities for targeted manipulation of reproductive technologies and animal production systems.

Catalytic inhibition of H3K9me2 writers disturbs epigenetic marks during bovine nuclear reprogramming

Orchestrated events, including extensive changes in epigenetic marks, allow a somatic nucleus to become totipotent after transfer into an oocyte, a process termed nuclear reprogramming. Recently, several strategies have been applied in order to improve reprogramming efficiency, mainly focused on removing repressive epigenetic marks such as histone methylation from the somatic nucleus. Herein we used the specific and non-toxic chemical probe UNC0638 to inhibit the catalytic activity of the histone methyltransferases EHMT1 and EHMT2. Either the donor cell (before reconstruction) or the early embryo was exposed to the probe to assess its effect on developmental rates and epigenetic marks. First, we showed that the treatment of bovine fibroblasts with UNC0638 did mitigate the levels of H3K9me2. Moreover, H3K9me2 levels were decreased in cloned embryos regardless of treating either donor cells or early embryos with UNC0638. Additional epigenetic marks such as H3K9me3, 5mC, and 5hmC were also affected by the UNC0638 treatment. Therefore, the use of UNC0638 did diminish the levels of H3K9me2 and H3K9me3 in SCNT-derived blastocysts, but this was unable to improve their preimplantation development. These results indicate that the specific reduction of H3K9me2 by inhibiting EHMT1/2 during nuclear reprogramming impacts the levels of H3K9me3, 5mC, and 5hmC in preimplantation bovine embryos.

Cellular Mechanisms and Epigenetic Changes: Role of Nutrition in Livestock

In the context of physiologic responses that determine the growth, development, and health status of livestock, the role of epigenetics and the underlying cellular mechanisms it affects remain to be fully elucidated. Although recent work has provided evidence that maternal dietary energy level, carbohydrate type, or intestinal supply of methyl donors can elicit molecular changes in tissues of the embryo, fetus, or neonate, there are few data linking epigenetics with biochemical and physiologic outcomes. Therefore, efforts linking the epigenome with physiologic and developmental outcomes offer exciting opportunities for discoveries that can impact efficiency of nutrient use and well-being of livestock.