Epigenomic and transcriptomic analyses reveal early activation of the HPG axis in in vitro-produced male dairy calves

Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans

BACKGROUND

We recently identified ~ 10,000 correlated regions of systemic interindividual epigenetic variation (CoRSIVs) in the human genome. These methylation variants are amenable to population studies, as DNA methylation measurements in blood provide information on epigenetic regulation throughout the body. Moreover, establishment of DNA methylation at human CoRSIVs is labile to periconceptional influences such as nutrition. Here, we analyze publicly available whole-genome bisulfite sequencing data on multiple tissues of each of two Holstein cows to determine whether CoRSIVs exist in cattle.

RESULTS

Focusing on genomic blocks with ≥ 5 CpGs and a systemic interindividual variation index of at least 20, our approach identifies 217 cattle CoRSIVs, a subset of which we independently validate by bisulfite pyrosequencing. Similar to human CoRSIVs, those in cattle are strongly associated with genetic variation. Also as in humans, we show that establishment of DNA methylation at cattle CoRSIVs is particularly sensitive to early embryonic environment, in the context of embryo culture during assisted reproduction.

CONCLUSIONS

Our data indicate that CoRSIVs exist in cattle, as in humans, suggesting these systemic epigenetic variants may be common to mammals in general. To the extent that individual epigenetic variation at cattle CoRSIVs affects phenotypic outcomes, assessment of CoRSIV methylation at birth may become an important tool for optimizing agriculturally important traits. Moreover, adjusting embryo culture conditions during assisted reproduction may provide opportunities to tailor agricultural outcomes by engineering CoRSIV methylation profiles.

Health assessment of Holstein calves born after in vitro fertilization, biopsy-based genotyping at the blastocyst stage and subsequent embryo transfer

Establishing methods for evaluating genomic estimated breeding values of bovine embryos can potentially increase the efficiency of breeding programs by transferring only embryos with a high genomic estimated breeding value. This may be achieved by analyzing DNA from trophectoderm biopsies. However, manipulation of bovine embryos is associated with a risk of impaired conceptus health. More knowledge on the health implications of embryonic handling procedures is required. In this study, we followed pregnancies after transfer of in vitro-produced (IVP) embryos and assessed the health of the offspring during the first 2 weeks of life. Three groups of calves were studied: i) freshly transferred non-biopsied embryos (39 transfers, 17 calves; Group B-/C-); ii) biopsied and freshly transferred IVP embryos (42 transfers, 21 calves; Group B+/C-); iii) biopsied and cryopreserved IVP embryos (17 transfers, 6 calves; Group B+/C+). Blood biochemical and hematologic values were compared between groups and to a control group of 13 calves produced by conventional artificial insemination. The pregnancy rate on day 50 and the calving rate did not differ among the groups, but the average gestation length of the B+/C+ group was significantly shorter and with wider variation than the two other groups. There was a tendency toward a higher average body weight at birth in group B+/C+ (45.1 kg) and the standard deviation in body weight was larger (11.7 kg) compared to the B-/C- (39.5 kg; 3.2 kg) and B+/C- (41.8 kg; 6 kg) groups. Body weight on day 14 was higher in the B+/C+ calves compared to the other groups. There was no difference in the biochemical and hematological values at birth between the groups and these were within the normal range. However, when compared to a group of calves produced by standard artificial insemination, significantly higher concentrations were found for the hepatic-related enzymes ALAT, ASAT, ALP, and GGT in group B-/C-and B+/C-, while only higher ALP concentrations were found in B+/C+ calves. The biochemical findings indicate higher heterogeneity in IVP calves compared to calves produced by artificial insemination. The more manipulated IVP embryos also showed increased heterogeneity in body weight at birth, with a shift toward heavier calves, which calls for closer attendance at parturition to handle dystocia in a timely manner and minimize fetal losses.

Review: Some challenges and unrealized opportunities toward widespread use of the in vitro-produced embryo in cattle production

The embryo produced by in vitro oocyte maturation, fertilization, and embryonic development is an important resource for genetic improvement and has the potential to improve female fertility and to be programmed to produce offspring with superior ability for health and production. The cultured embryo is also an important component of several realized and potential technologies such as gene editing, somatic cell nuclear cloning, stem cell technologies and gamete generation in vitro. Full realization of the opportunities afforded by the in vitro-produced embryo will require overcoming some technical obstacles to cost-effective implementation of an embryo transfer program. Among the research goals for improving the penetration of embryo transfer in the cattle industry are development of methods to increase the supply of oocytes from genetically elite females, enhance the proportion of oocytes that become transferrable embryos, improve the fraction of embryos that establish pregnancy after transfer, reduce pregnancy wastage after pregnancy diagnosis, and identify culture conditions to optimize postnatal phenotype.

Sexing of cattle embryos using RNA-sequencing data or polymerase chain reaction based on a complete sequence of cattle chromosome Y

When necessary, RNA-sequencing data or polymerase chain reaction (PCR) assays can be used to determine the presence of the chromosome Y (ChrY) in samples. This information allows for biological variation due to sexual dimorphism to be studied. A prime example is when researchers conduct RNA-sequencing of single embryos, or conceptuses, prior to the development of gonads. A recent publication of a complete sequence of the ChrY has removed limitations for the development of these procedures in cattle, otherwise imposed by the absence of a ChrY in the reference genome. Using the sequence of the cattle ChrY and transcriptome data, we conducted a systematic search for genes in the ChrY that are exclusively expressed in male tissues. The genes ENSBIXG00000029763, ENSBIXG00000029774, ENSBIXG00000029788, and ENSBIXG00000029892 were consistently expressed across male tissues and lowly expressed or absent in female samples. We observed that the cumulative values of counts per million were 2688-fold greater in males than the equivalent values in female samples. Thus, we deemed these genes suitable for the sexing of samples using RNA-sequencing data. We successfully used this set of genes to infer the sex of 22 cattle blastocysts (8 females and 14 males). Additionally, the completed sequence of the cattle ChrY has segments in the male-specific region that are not repeated. We designed a pair of oligonucleotides that targets one of these non-repeated regions in the male-specific sequence of the ChrY. Using this pair of oligonucleotides, in a multiplexed PCR assay with oligonucleotides that anneal to an autosome chromosome, we accurately identified the sex of cattle blastocysts. We developed efficient procedures for the sexing of samples in cattle using either transcriptome data or their DNA. The procedures using RNA-sequencing will greatly benefit researchers who work with samples limited in cell numbers which are only sufficient to produce transcriptome data. The oligonucleotides used for the accurate sexing of samples using PCR are transferable to other cattle tissue samples.

Fitness of calves born from in vitro-produced fresh and cryopreserved embryos

In cattle, vitrified/warmed (V/W) and frozen/thawed (F/T), in vitro-produced (IVP) embryos, differ in their physiology and survival from fresh embryos. In this study, we analyzed the effects of embryo cryopreservation techniques on the offspring. IVP embryos cultured with albumin and with or without 0.1% serum until Day 6, and thereafter in single culture without protein, were transferred to recipients on Day 7 as F/T, V/W, or fresh, resulting in N = 24, 14, and 13 calves, respectively. Calves were clinically examined at birth, and blood was analyzed before and after colostrum intake (Day 0), and subsequently on Day 15 and Day 30. On Day 0, calves from V/W and F/T embryos showed increased creatinine and capillary refill time (CRT) and reduced heartbeats. Calves from F/T embryos showed lower PCO₂, hemoglobin, and packed cell volume than calves from V/W embryos while V/W embryos led to calves with increased Na⁺ levels. Colostrum effects did not differ between calves from fresh and cryopreserved embryos, indicating similar adaptive ability among calves. However, PCO₂ did not decrease in calves from V/W embryos after colostrum intake. Serum in culture led to calves with affected (P < 0.05) temperature, CRT, HCO 3 - , base excess (BE), TCO₂, creatinine, urea, and anion gap. On Day 15, the effects of embryo cryopreservation disappeared among calves. In contrast, Day 30 values were influenced by diarrhea appearance, mainly in calves from V/W embryos (i.e., lower values of TCO₂, HCO 3 - , and BE; and increased glucose, anion gap, and lactate), although with no more clinical compromise than calves from fresh and F/T embryos. Diarrhea affected PCO₂ and Na⁺ in all groups. Embryo cryopreservation, and/or culture, yield metabolically different calves, including effects on protein and acid-base metabolism.

Developmental Programming of Fertility in Cattle-Is It a Cause for Concern?

Cattle fertility remains sub-optimal despite recent improvements in genetic selection. The extent to which an individual heifer fulfils her genetic potential can be influenced by fetal programming during pregnancy. This paper reviews the evidence that a dam's age, milk yield, health, nutrition and environment during pregnancy may programme permanent structural and physiological modifications in the fetus. These can alter the morphology and body composition of the calf, postnatal growth rates, organ structure, metabolic function, endocrine function and immunity. Potentially important organs which can be affected include the ovaries, liver, pancreas, lungs, spleen and thymus. Insulin/glucose homeostasis, the somatotropic axis and the hypothalamo-pituitary-adrenal axis can all be permanently reprogrammed by the pre-natal environment. These changes may act directly at the level of the ovary to influence fertility, but most actions are indirect. For example, calf health, the timing of puberty, the age and body structure at first calving, and the ability to balance milk production with metabolic health and fertility after calving can all have an impact on reproductive potential. Definitive experiments to quantify the extent to which any of these effects do alter fertility are particularly challenging in cattle, as individual animals and their management are both very variable and lifetime fertility takes many years to assess. Nevertheless, the evidence is compelling that the fertility of some animals is compromised by events happening before they are born. Calf phenotype at birth and their conception data as a nulliparous heifer should therefore both be assessed to avoid such animals being used as herd replacements.

In vitro and in vivo-produced male dairy calves show molecular differences in the hepatic and muscular energy regulation

In cattle, the in vitro production (IVP) of embryos is becoming more relevant than embryos produced in vivo, i.e. after multiple ovulation and embryo transfer (MOET). However, the effects of IVP on the developmental programming of specific organs in the postnatal calves are yet unknown. Previously, we reported an epigenomic and transcriptomic profile of the hypothalamus–pituitary–testicular axis compatible with its earlier activation in IVP calves compared to MOET animals. Here, we studied the hepatic and muscular epigenome and transcriptome of those same male dairy calves (n = 4 per group). Tissue samples from liver and semitendinosus muscle were obtained at 3 months of age, and the extracted gDNA and RNA were sequenced through whole-genome bisulfite sequencing and RNA-sequencing, respectively. Next, bioinformatic analyses determined differentially methylated cytosines or differentially expressed genes [false discovery rate (FDR) < 0.05] for each Omic dataset; and nonparametrically combined genes (NPCG) for both integrated omics (P < 0.05). KEGG pathways enrichment analysis showed that NPCG upregulated in the liver and the muscle of the IVP calves were involved in oxidative phosphorylation and the tricarboxylic acid cycle. In contrast, ribosome and translation were upregulated in the liver but downregulated in the muscle of the IVP calves compared to the MOET calves (FDR < 0.05). A model considering the effect of the methylation levels and the group on the expression of all the genes involved in these pathways confirmed these findings. In conclusion, the multiomics data integration approach indicated an altered hepatic and muscular energy regulation in phenotypically normal IVP calves compared to MOET calves.