The ability to cryopreserve gametes and embryos has been a valuable tool for reproductive management in all mammalian species, especially livestock. Embryo vitrification involves exposure to high concentrations of cryoprotectants and osmotic stress during cooling and warming. These factors have to affect gene expression. The elongating embryo is a stage of embryo development that can be recovered noninvasively in the cow on day (D) 14 and represents a critical stage of development when many embryos die. In this study, we aimed to evaluate the effect of vitrification on the transcriptome dynamics of D14 embryos by RNA sequencing (RNA-seq). Invitro blastocyst-stage embryos were vitrified by exposure to dimethyl sulfoxide and ethylene glycol solution, followed by placing on Cryo Loks and plunging in liquid nitrogen. After warming, embryos were loaded into straws and transferred into eight synchronized recipients, four cows received nonvitrified embryos and four cows received vitrified embryos (20 embryos per cow). Embryo flushing yielded 12 nonvitrified and 9 vitrified viable D14 embryos. Whole embryos (six nonvitrified and two vitrified embryos) or isolated trophectoderm (TE; four nonvitrified and seven vitrified) were processed for RNA-seq. The Smart-sEqn 2 protocol was followed to prepare RNA-seq libraries. Sequencing reads were prefiltered and aligned to the bovine genome, and gene expression values were calculated as fragments per kilobase of transcript per million mapped reads. Genes were deemed differentially expressed between treatments if they showed a false discovery rate P-value<0.05 and fold-change >2. Ingenuity pathway analysis was used to reveal gene ontology and pathways. Expression of 927 genes was changed in D14 embryos as a result of vitrification, with 782 and 145 genes upregulated and downregulated, respectively. In TE, vitrification resulted in 4096 and 280 upregulated or downregulated genes, respectively. Several pathways were upregulated by vitrification in both whole embryos and TE, including epithelial adherens junctions, sirtuin signalling, germ cell-Sertoli cell junction, ATM signalling, nucleotide excision repair, and protein ubiquitination pathways. Downregulated pathways included EIF2 signalling, oxidative phosphorylation, mitochondrial dysfunction, regulation of eIF4 and p70S6K signalling, mammalian target of rapamycin signalling, sirtuin singling, and nucleotide excision repair pathways. In addition, we found 671 and 61 genes upregulated and downregulated in both vitrified whole embryos and TE. Mitochondrial dysfunction and oxidative phosphorylation signalling were upregulated, whereas epithelial adherens junction and sirtuin signalling were downregulated, suggesting mitochondrial function and energy production were impaired in TE after vitrification. Our analysis identified specific pathways and implicated specific genes affected by cryopreservation and potentially affecting embryo developmental competence.
C. elegans TFIIH subunit GTF-2H5/TTDA is a non-essential transcription factor indispensable for DNA repair
