In vitro processes alter the embryonic disc epigenome and transcriptome in the pre-implantation elongated bovine embryo

The objective was to quantify the effect of the in vitro procedures on the epigenome and transcriptome of the embryonic disc (ED) and extra-embryonic membranes (EEM) of day 15 in vitro produced (IVP) conceptuses compared to in vivo (IVV) counterparts. IVP embryos (n = 7) were cultured serum-free until transfer at day 7. IVV embryos (n = 9) were conceived by artificial insemination. Animals were flushed at day 15 of gestation, and sections of ED and EEM were subjected to DNA and mRNA extraction for whole genome bisulfite or RNA sequencing. Raw fastq files were aligned to the ARS-UCD1.3 bovine genome. Processed data were integrated through a multi-omics approach based on machine learning to determine the key ontological terms characterizing each embryonic tissue lineage according to their methylome and transcriptome, followed by overrepresentation analyses (adjusted p-value<0.05) of differentially methylated genes (DMG), differentially expressed genes (DEG) or genes both differentially methylated and differentially expressed in the ED or EEM of IVP compared to IVV conceptuses. Results demonstrated that identified critical ontological terms for the ED (such as somitogenesis, mesoderm formation, gastrulation) and the BMP and Wnt signaling pathways were enriched among hypermethylated DMG, down-regulated DEG, and genes hypermethylated in the promoter and inhibited in expression, in the ED of IVP embryos. Genes hypermethylated in the promoter and inhibited in expression in the EEM of IVP conceptuses were involved in epigenetic regulation. In conclusion, the in vitro process alters the development of main linage tissues in the pre-implantation embryo, even after interaction with the maternal environment.