Effect of vitrification on global gene expression dynamics of bovine elongating embryos.

Embryo vitrification involves exposure to high concentrations of cryoprotectants and osmotic stress during cooling and warming in the cryopreservation process. Many of these factors can potentially affect gene expression. In this study, invitro-produced bovine embryos at the blastocyst stage were subjected to vitrification. Four recipients each were used for transferring non-vitrified (n=80) and vitrified (n=80) embryos. A total of 12 non-vitrified and 9 vitrified viable day-14 (D14) embryos were recovered by uterine flushing. RNA-seq analysis of the whole embryo or isolated trophectoderm (TE) from vitrified and fresh recovered D14 embryos revealed a total of 927 and 4376 genes with changed expression in embryos and TE isolates, respectively, as a result of vitrification. In addition, we found 671 and 61 genes commonly up- or downregulated in both vitrified whole embryos and TE. Commonly upregulated pathways by vitrification included epithelial adherens junctions, sirtuin signalling, germ cell-sertoli cell junction, ATM signalling, NER and protein ubiquitination pathways. The commonly downregulated pathways included EIF2 signalling, oxidative phosphorylation, mitochondrial dysfunction, regulation of eIF4 and p70S6K signalling and mTOR signalling pathways. Our analysis identified specific pathways and implicated specific gene expression patterns affecting embryo developmental competence that are important to cryopreservation.

The effects of microtubule stabilizing and recovery agents on vitrified bovine oocytes.

Oocyte vitrification, while beneficial for research and species conservation applications, has limited success due to cryoinjury to the meiotic spindle. This study aimed to improve meiotic spindle recovery in vitrified bovine oocytes by investigating the effects of treatment with either a microtubule stabilizing agent, or a microtubule recovery agent. In the first two experiments, either paclitaxel or epothilone B were used to treat bovine oocytes before vitrification. Both compounds have microtubule stabilizing properties and are known antimitotic compounds used to disrupt microtubule dynamics in rapidly proliferating cancer cells. Paclitaxel treatment at 2.0 µM significantly increased the proportion of oocytes with normal microtubule distribution and chromosome arrangement after warming. Treatment with 1.0 µM had no effect and 0.5 µM had a negative effect on meiotic spindle recovery. Epothilone B treatment at all concentrations significantly increased the proportion of oocytes with meiotic spindle disruption and abnormally dispersed chromosomes. In the second set of experiments, Rho-associated coiled-coil kinase inhibition and glutathione accumulation were investigated as recovery treatments after vitrification. Oocytes were incubated with either Y-27632 or combinations of cysteine and cysteamine for 4 h after warming. Treatment with 5 µM and 10 µM of Y-27632 to inhibit rho-associated coiled-coil kinase activity significantly increased the proportion of vitrified oocytes with normal microtubule distribution and chromosome arrangement. When oocytes were incubated with 20 µM of Y-27632 there was no effect on spindle recovery. Incubation with 100 µM of cysteamine also had no effect on spindle recovery while 0.6 mM of cysteine and both 0.6 mM of cysteine and 100 µM of cysteamine significantly increased oocytes with normal microtubule distribution and chromosome arrangement.

The landscape of accessible chromatin in bovine oocytes and early embryos.

Chromatin reorganization governs the regulation of gene expression during preimplantation development. However, the landscape of chromatin dynamics in this period has not been explored in bovine. In this study, we constructed a genome-wide map of accessible chromatin in bovine oocytes and early embryos using an improved assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) which revealed unique features of the accessible chromatin during bovine early embryo development. We found that chromatin accessibility is low in oocytes and 2-/4-cell embryos, followed by a significant increase in embryos during major embryonic genome activation (EGA), and peaked in elongating day 14 embryos. Genome-wide characteristics of open chromatin showed that ATAC-seq signals in both transcription start sites (TSS) and transcription end sites (TES) were strong. Additionally, the distal ATAC-seq peaks were enriched in repeat elements in a type-specific and stage-specific manner. We further unveiled a series of transcription factor (TF) motifs with distinct variation of enrichment from distal ATAC-seq peaks. By integrated analysis of chromatin accessibility with transcriptomes and DNA methylomes in bovine early embryos, we showed that promoter accessibility was positively correlated with gene expression, especially during major EGA, and was strongly correlated to DNA methylation and CpG density. Finally, we identified the critical chromatin signatures and TFs that differ between in vivo and in vitro derived blastocysts, which provides insights to the potential mechanisms leading to low quality of embryos produced in vitro. Together, this comprehensive analysis revealed critical features of chromatin landscape and epigenetic reprogramming during bovine preimplantation embryo development.