Epigenetic characteristics of cloned and in vitro-fertilized swamp buffalo (Bubalus bubalis) embryos1

Effect of a High Estrogen Level in Early Pregnancy on the Development and Behavior of Marmoset Offspring

The use of assisted reproductive technology (ART) has risen steadily worldwide over the past 3 decades and helps many infertile families. However, ART treatments lead to an abnormal internal environment in the uterus, which may increase the risks of health problems for the offspring. Higher maternal estradiol (E₂) is a notable feature in women who use ART treatments, and this has been suggested as a key factor for the risk of diseases in the offspring. In the current study, we have established a marmoset model with a high E₂ level in early pregnancy to examine its potential risk to the development and behavior of the offspring. In comparison with the normal group, babies of the high E₂ group exhibited lower average survival rates and birth weights. However, those who survived in the high E₂ group demonstrated normal vocal production with rich call repertoires, normal speed during locomotion, and normal behaviors in the home cage. In contrast to the normal group, surviving babies of the high E₂ group spent more time sleeping during development without signs of sleep disorders. In summary, our study revealed that high estrogen in early pregnancy may cause low survival rates and birth weights of the offspring, though the surviving infants did not show obvious behavioral deficiencies during development. The current study is a valuable and highly important non-human primate study for evaluating the safety of ART treatments. However, it is worth noting that some results did not reach the significant level, which may be due to the small sample size caused by animal shortage stemming from the COVID-19 epidemic.

Global DNA methylation profiles of buffalo (Bubalus bubalis) preimplantation embryos produced by handmade cloning and in vitro fertilization

Somatic cell nuclear transfer technique (SCNT) has proved to be an outstanding method of multiplication of elite animals but accompanied with low efficiency and live birth rate of cloned animals. Epigenetic alterations of DNA has been one of the culprits behind this issue. Cloned embryos are found to deviate slightly from regular pattern of demethylation and re-methylation at the time of nuclear reprogramming and embryonic development when compared with embryos produced by in vitro fertilization (IVF). Thus, the present study was aimed at evaluating global DNA methylation profiles of cloned embryos at 2-cell, 8-cell and blastocyst stages and compare it with corresponding stages of embryos produced by IVF by using MeDIP-Sequencing on Illumina-based platform. We found out that cloned embryos exhibited significantly different DNA methylation pattern as compared to IVF embryos with respect to distribution of differentially methylated regions in different components of genome, CpG islands distribution and methylation status, gene ontological profiles and pathways affected throughout the developmental stages. The data generated from MeDIP-Seq was validated at blastocyst stage cloned and IVF embryos by bisulfite-sequencing PCR on five randomly selected gene regions.

Current status of assisted reproductive technologies in buffaloes

Buffaloes are raised by small farm holders primarily as source of draft power owing to its resistance to hot climate, disease, and stress conditions. Over the years, transformation of these animals from draft to dairy was deliberately carried out through genetic improvement program leading to the development of buffalo-based enterprises. Buffalo production is now getting more attention and interest from buffalo raisers due to its socioeconomic impact as well as its contribution to propelling the livestock industry in many developing countries. Reproduction of buffaloes, however, is confronted with huge challenge and concern as being generally less efficient to reproduce compared with cattle due to both intrinsic and extrinsic factors such as poor estrus manifestation, silent heat, marked seasonal infertility, postpartum anestrus, long calving interval, delayed puberty, inherently low number of primordial follicles in their ovaries, high incidence of atresia, and apoptosis. Assisted reproductive technologies (ARTs) are major interventions for the efficient utilization of follicle reserve in buffaloes. The present review focuses on estrus and ovulation synchronization for fixed time artificial insemination, in vitro embryo production, intracytoplasmic sperm injection, cryopreservation of oocytes and embryos, somatic cell nuclear transfer, the factors affecting utilization in various ARTs, and future perspectives in buffaloes.

Programming of Embryonic Development

Assisted reproductive techniques (ART) and parental nutritional status have profound effects on embryonic/fetal and placental development, which are probably mediated via "programming" of gene expression, as reflected by changes in their epigenetic landscape. Such epigenetic changes may underlie programming of growth, development, and function of fetal organs later in pregnancy and the offspring postnatally, and potentially lead to long-term changes in organ structure and function in the offspring as adults. This latter concept has been termed developmental origins of health and disease (DOHaD), or simply developmental programming, which has emerged as a major health issue in animals and humans because it is associated with an increased risk of non-communicable diseases in the offspring, including metabolic, behavioral, and reproductive dysfunction. In this review, we will briefly introduce the concept of developmental programming and its relationship to epigenetics. We will then discuss evidence that ART and periconceptual maternal and paternal nutrition may lead to epigenetic alterations very early in pregnancy, and how each pregnancy experiences developmental programming based on signals received by and from the dam. Lastly, we will discuss current research on strategies designed to overcome or minimize the negative consequences or, conversely, to maximize the positive aspects of developmental programming.

MeDIP-sequencing for profiling global DNA methylation in buffalo embryos produced by in vitro fertilization

Assisted reproductive technique like in vitro fertilization has contributed immensely in producing genetically improved livestock. Production of embryos under in vitro conditions can affect global DNA methylation pattern during the course of embryonic development. The present study is aimed at the generation and comparison of global DNA methylome of embryos at 2-cell, 8-cell and blastocyst stage of buffalo embryos produced by in vitro fertilization using MeDIP-Sequencing. It is observed that there is a profound difference in the global DNA methylation profile of IVF embryos at different developmental stages. These differences are manifested throughout the course of embryonic development. Pathways like Wnt signaling pathway, gonadotropin-releasing hormone receptor pathway and integrin signaling were found to be majorly affected by hypermethylation of DNA in IVF embryos throughout the development.

Developmental Programming of Fetal Growth and Development

Maternal stressors that affect fetal development result in "developmental programming," which is associated with increased risk of various chronic pathologic conditions in the offspring, including metabolic syndrome; growth abnormalities; and reproductive, immune, behavioral, or cognitive dysfunction that can persist throughout their lifetime and even across subsequent generations. Developmental programming thus can lead to poor health, reduced longevity, and reduced productivity. Current research aims to develop management and therapeutic strategies to optimize fetal growth and development and thereby overcome the negative consequences of developmental programming, leading to improved health, longevity, and productivity of offspring.

Comparison of in vitro developmental competence of cloned caprine embryos using donor karyoplasts from adult bone marrow mesenchymal stem cells vs ear fibroblast cells

The aim of this study was to produce cloned caprine embryos using either caprine bone marrow-derived mesenchymal stem cells (MSCs) or ear fibroblast cells (EFCs) as donor karyoplasts. Caprine MSCs were isolated from male Boer goats of an average age of 1.5 years. To determine the pluripotency of MSCs, the cells were induced to differentiate into osteocytes, chondrocytes and adipocytes. Subsequently, MSCs were characterized through cell surface antigen profiles using specific markers, prior to their use as donor karyoplasts for nuclear transfer. No significant difference (p > 0.05) in fusion rates was observed between MSCs (87.7%) and EFCs (91.3%) used as donor karyoplasts. The cleavage rate of cloned embryos derived with MSCs (87.0%) was similar (p > 0.05) to those cloned using EFCs (84.4%). However, the in vitro development of MSCs-derived cloned embryos (25.3%) to the blastocyst stage was significantly higher (p < 0.05) than those derived with EFCs (20.6%). In conclusion, MSCs could be reprogrammed by caprine oocytes, and production of cloned caprine embryos with MSCs improved their in vitro developmental competence, but not in their fusion and cleavage rate as compared to cloning using somatic cells such as EFCs.

Imprinted genes and satellite loci are differentially methylated in bovine somatic cell nuclear transfer clones

In mammals, genome-wide epigenetic reprogramming systems exist in primordial germ cells and zygotes. These reprogramming systems play crucial roles in regulating genome functions during critical stages of embryonic development, and they confer the stability of gene expression during mammalian development. The frequent unexpected loss of progeny from somatic cell nuclear transfer (SCNT) is an ongoing problem. In this study, we used six cloned bovines (named NT-1 to NT-6), which were created by ear fibroblast nuclear transfer and displayed short life spans with multiple organ defects, as an experimental model. We focus here on three imprinted genes (IGF2, H19, and XIST) and four satellite loci (Satellite I, Satellite II, Art2, and VNTR) to investigate their methylation changes. The results revealed that aberrant methylation frequently occurred in the analyzed imprinted genes, but not in the satellite loci, of the cloned bovines. After the bovine fibroblast cells were treated with the 5-aza-2(')-deoxycytidine (5-Aza-dc) demethylation agent, the methylation percentages of the XIST and H19 putative differentially methylated region (DMR) were significantly decreased (XIST, p<0.01; H19, p<0.05) followed by an increase in their mRNA expression levels (p<0.01). Furthermore, we found that five short-lived cloned bovines (NT-1 to NT-5) exhibited more severe aberrant methylation changes in the three imprinted genes examined than the little longer-lived clone (NT-6) compared with wild-type (WT) cows. Our data suggest that the reprogramming of the methylation-controlled regions between the imprinted genes and satellite loci are differences and may be involved with additional mechanisms that need further elucidation.

Environmental and epigenetic effects upon preimplantation embryo metabolism and development

In vitro fertilization has provided a unique window into the metabolic processes that drive embryonic growth and development from a fertilized ovum to a competent blastocyst. Post-fertilization development is dependent upon a dramatic reshuffling of the parental genomes during meiosis, as well as epigenetic changes that provide a new and autonomous set of instructions to guide cellular differentiation both in the embryo and beyond. Although early literature focused simply on the substrates and culture conditions required for progress through embryonic development, more recent insights lead us to suggest that the surrounding environment can alter the epigenome, which can, in turn, impact upon embryonic metabolism and developmental competence.

Multiplex polymerase chain reaction used for bovine embryo sex determination

Widely used bovine sexing primers were compared in terms of suitability in determining the sex of bovine embryos. Under optimized multiplex PCR conditions, the ConBV/ConEY couple primers did not show accurate results when combined together in multiplex PCR, but worked well when the couple primers were used separately. The S4BF/S4BR primers showed accurate results; however, some unexpected bands were detected. When the BY/BSP couple primers were used to determine one-cell, two-cell, four-cell and eight-cell stage embryos of known sexed SCNT-derived embryos, the results showed 100% accuracy. The BY/BSP couple primers were also able to identify the sex of one-cell and two-cell IVF-derived embryos.

Constant transmission of mitochondrial DNA in intergeneric cloned embryos reconstructed from swamp buffalo fibroblasts and bovine ooplasm

Although interspecies/intergeneric somatic cell nuclear transfer (iSCNT) has been proposed as a tool to produce offspring of endangered species, conflict between donor nucleus and recipient cytoplasm in iSCNT embryos has been identified as an impediment to implementation for agricultural production. To investigate the nuclear-mitochondrial interactions on the developmental potential of iSCNT embryos, we analyzed the mtDNA copy numbers in iSCNT embryos reconstructed with water buffalo (swamp type) fibroblasts and bovine enucleated oocytes (buffalo iSCNT). As controls, SCNT embryos were derived from bovine fibroblasts (bovine SCNT). Buffalo iSCNT and bovine SCNT embryos showed similar rates of cleavage and development to the 8-cell stage (P>0.05). However, buffalo iSCNT embryos did not develop beyond the 16-cell stage. Both bovine and buffalo mtDNA content in buffalo iSCNT embryos was stable throughout the nuclear transfer process, and arrested at the 8- to 16-cell stage (P>0.05). In bovine SCNT embryos that developed to the blastocyst stage, mtDNA copy number was increased (P<0.05). In conclusion, both the donor cell and recipient cytoplast mtDNAs of buffalo iSCNT embryos were identified and maintained through the iSCNT process until the 8-16-cell stage. In addition, the copy number of mtDNA per embryo was a useful monitor to investigate nuclear-mitochondrial interactions.

Multiple histone site epigenetic modifications in nuclear transfer and in vitro fertilized bovine embryos

During mammalian embryonic development, DNA methylation and histone modifications are important in gene expression regulation and epigenetic reprogramming. In cloned embryos, high levels of DNA methylation and abnormal demethylation were widely observed during the preimplantation period. Little is known whether there is a difference in histone modifications between in vitro fertilization (IVF) and cloned embryos during preimplantation development. In the present study, the distributions and intensity patterns of acetylations in H3 lysine 9, 18 and H4 lysine 8, 5 and tri-methyl lysine 4 and dimethyl-lysine 9 in histone H3 were compared in cloned and IVF bovine preimplantation embryos by using indirect immunofluorescence and scanning confocal microscopy. The results showed that the acetylation and methylation levels of H3K9ac, H3K18ac, H4K5ac, H4K8ac, H3K4me3 and H3K9me2 were abnormally high in the cloned embryos from the pronuclear to the 8-cell stage. H4K8ac and H4K5ac in the cloned embryos were particularly abnormal when compared with the IVF controls. At the blastocyst stage differences dissipated between cloned and IVF embryos and the distribution and intensity patterns of all histone modifications showed no obvious difference. These results suggest that somatic cells in recipient oocytes produced aberrant histone modifications at multiple sites before the donor cell genome is activated. After zygotic genome activation, distributions and intensity patterns of histone modifications were comparable with both cloned and IVF embryos.

Reproductive biotechniques in buffaloes (Bubalus bubalis): status, prospects and challenges

The swamp buffalo holds tremendous potential in the livestock sector in Asian and Mediterranean countries. Current needs are the faster multiplication of superior genotypes and the conservation of endangered buffalo breeds. Recent advances in assisted reproductive technologies, including in vitro embryo production methodologies, offer enormous opportunities to not only improve productivity, but also to use buffaloes to produce novel products for applications to human health and nutrition. The use of molecular genomics will undoubtedly advance these technologies for their large-scale application and resolve the key problems currently associated with advanced reproductive techniques, such as animal cloning, stem cell technology and transgenesis. Preliminary success in the application of modern reproductive technologies warrants further research at the cellular and molecular levels before their commercial exploitation in buffalo breeding programmes.

Epigenetic regulation of foetal development in nuclear transfer animal models

Somatic cell nuclear transfer (SCNT, 'cloning') holds great potential for agricultural applications, generation of medical model animals, transgenic farm animals or by 'therapeutic cloning' for generating human embryonic stem cells for the treatment of human diseases. However, the low survival rate of SCNT-derived pregnancies represents a serious limitation of the current technology. In order to overcome this hurdle, a deeper understanding of the epigenetic reprogramming of the somatic cell nuclei and its effect on the pregnancy is needed. Here we review the literature on nuclear reprogramming by SCNT, including studies of gene expression, DNA methylation, chromatin remodelling, genomic imprinting and X chromosome inactivation. Reprogramming of genes expressed in the inner cell mass, from which the body of the foetus is formed, seems to be highly efficient. Defects in the extra-embryonic tissues are probably the major cause of the low success rate of reproductive cloning. Methods to partially overcome such problems exist, yet more future research is needed to find practical and efficient methods to remedy this problem. Improvement of the survival of foetuses is a central issue for the future of agricultural SCNT not only for its economic viability, but also because in lack of improvements in animal welfare current regulations can block the use of the method in the EU and several other countries.

DNA methylation changes in cell line from beta-lactoglobulin gene targeted fetus

The gene targeting combined somatic cell nuclear transfer is very useful in agriculture and medicine. Epigenetic modification of DNA by methylation is significant in regulating gene expression during mammalian development. During gene targeting, epigenetic status of donor cell nuclei may be changed in a series of processes, including homologous recombination, cell selection and cloning. We examined DNA methylation of six genes (beta-actin, VEGF, oct4, TERT, H19 and Igf2) and a repetitive sequence art2 in blg(+/-) cell line from beta-lactoglobulin (BLG) gene targeted fetus and the cells used for BLG gene targeting serve as control. The results demonstrated that the widespread changes of DNA methylation were found in blg(+/-) cell line. But the degree of variation was different. DNA methylation of VEGF in blg(+/-) was noticeably decreased. These observations suggest that DNA methylation variations may impact gene expression and finally induce abnormalities and lethality in later developmental stages.

Increased pre-implantation development of cloned bovine embryos treated with 5-aza-2'-deoxycytidine and trichostatin A

Limited success of somatic cell nuclear transfer is attributed to incomplete reprogramming of transferred nuclei. The objective was to determine if 5-aza-2'-deoxycytidine (5-aza-dC) and trichostatin A (TSA) promoted reprogramming and improved development. Relative to untreated controls, treatment of donor cells, cloned embryos, and continuous treatment of both donor cells and cloned embryos with a combination of 0.01microM 5-aza-dC and 0.05microM TSA significantly increased the blastocyst rate (11.9% vs 31.7%, 12.4% vs 25.6%, and 13.3% vs 38.4%, respectively) and total cell number (73.2 vs 91.1, 75.2 vs 93.7, and 74.6 vs 96.7). Moreover, blastocyst rate and inner cell mass (ICM) cell number of embryos continuously exposed to both reagents were significantly higher than that of a TSA-treated group (38.4% vs 23.9% and 27.4 vs 18.2). The DNA methylation level of 2-cell embryos was decreased significantly, whereas the histone acetylation level increased dramatically after donor cell treatment and continuous treatment with both reagents. However, these epigenetic features of cloned blastocysts were not significantly different than the untreated control group. Following embryo treatment, DNA methylation and histone acetylation levels of cloned blastocysts were unchanged, except for the group given 0.5microM TSA (acetylation level was significantly increased, but development potential was reduced). In conclusion, development of cloned bovine embryos was enhanced by 5-aza-dC and TSA; furthermore, the combination was more effective than either one alone.

Aberrant epigenetic changes and gene expression in cloned cattle dying around birth

Background

Aberrant reprogramming of donor somatic cell nuclei may result in many severe problems in animal cloning. To assess the extent of abnormal epigenetic modifications and gene expression in clones, we simultaneously examined DNA methylation, histone H4 acetylation and expression of six genes (β-actin, VEGF, oct4, TERT, H19 and Igf2) and a repetitive sequence (art2) in five organs (heart, liver, spleen, lung and kidney) from two cloned cattle groups that had died at different stages. In the ED group (early death, n = 3), the cloned cattle died in the perinatal period. The cattle in the LD group (late death, n = 3) died after the perinatal period. Normally reproduced cattle served as a control group (n = 3).

Results

Aberrant DNA methylation, histone H4 acetylation and gene expression were observed in both cloned groups. The ED group showed relatively fewer severe DNA methylation abnormalities (p < 0.05) but more abnormal histone H4 acetylations (p < 0.05) and more abnormal expression (p < 0.05) of the selected genes compared to the LD group. However, our data also suggest no widespread gene expression abnormalities in the organs of the dead clones.

Conclusion

Deaths of clones may be ascribed to abnormal expression of a very limited number of genes.

Trichostatin A and nuclear reprogramming of cloned rabbit embryos

To investigate the influence of histone deacetylases on nuclear reprogramming after nuclear transfer, we treated the cloned embryos with a histone deacetylase inhibitor, Trichostatin A (TSA). In the present study, global changes in acetylation of histone H3-lysine 14, histone H4-lysine 12, and histone H4-lysine 5 were studied in rabbit in vivo fertilized embryos, somatic cell nuclear transfer (SCNT) embryos, and TSA-treated SCNT embryos. From the pronuclear to the morula stage, the deacetylation-reacetylation changes in acetylation of histone H3-lysine 14 and histone H4-lysine 12 occurred in both fertilized embryos and TSA-treated cloned embryos; however, the distribution pattern in untreated cloned embryos failed to display such changes. More interesting, the signal of acetylation of histone H4-lysine 12 in cloned embryos was detected in both the inner cell mass and the trophectoderm, whereas TSA-treated cloned embryos showed the same staining pattern as fertilized embryos and the staining was limited to the inner cell mass. The histone acetylation pattern of TSA-treated SCNT embryos appeared to be more similar to that of normal embryos, indicating that TSA could improve nuclear reprogramming after nuclear transfer.

Reproduction in the Water Buffalo

In this paper, an account of various aspects related to buffalo reproduction are given. Fundamental concepts of the reproductive physiology as well as manipulation of the reproductive function will be presented. This will include an overview of the most recent developments of the oestrous cycle and the ovulation control, new strategies of reproductive management for the improvement of genetic gain and the application of newly developed reproductive technologies, such as in vitro embryo production, embryo and sperm sexing and cloning.

Board-invited review: Applications of genomic information in livestock

The availability of whole genome sequences for individual species will change the landscape for livestock genomic research. Animal scientists will have access to whole-genome sequence-based technologies such as high-throughput SNP genotyping assays, gene expression profiling, methylation profiling, RNA interference, and genome resequencing that will revolutionize the scale upon which research will be conducted. These technologies will also alter the ways we think about addressing industry and scientific problems. In this review, we discuss the scientific bases for these emerging technologies and present recent highlights of their application in human, model species, and livestock as well as their potential for future applications in livestock. Additionally, we discuss strategies for their use in the genetic improvement and management of livestock. In particular, we present a strategy for the simultaneous identification of causal mutations underlying phenotypic traits in livestock and discuss issues that will arise in the application of whole genome selection for the prediction of genetic merit in livestock. We also point out that the statistical analysis that underlies the whole genome selection methodology is a sophisticated enhancement of single marker association mapping analysis to allow the entire genome to be simultaneously analyzed.

Nuclear reprogramming of cloned embryos and its implications for therapeutic cloning

Therapeutic cloning, whereby somatic cell nuclear transfer (SCNT) is used to generate patient-specific embryonic stem cells (ESCs) from blastocysts cloned by nuclear transfer (ntESCs), holds great promise for the treatment of many human diseases. ntESCs have been derived in mice and cattle, but thus far there are no credible reports of human ntESCs. Here we review the recent literature on nuclear reprogramming by SCNT, including studies of gene expression, DNA methylation, chromatin remodeling, genomic imprinting and X chromosome inactivation. Reprogramming of genes expressed in the inner cell mass, from which ntESCs are derived, seems to be highly efficient. Defects in the extraembryonic lineage are probably the major cause of the low success rate of reproductive cloning but are not expected to affect the derivation of ntESCs. We remain optimistic that human therapeutic cloning is achievable and that the derivation of patient-specific ntESC lines will have great potential for regenerative medicine.