Single-cell multiomic analysis reveals deviations following oocyte maturation in vitro
In vitro maturation of oocytes is a routine step in assisted reproduction, however, it is associated with lower embryo development rates compared to oocyte maturation in vivo. The objective of the current study was to characterize the genomic profile of oocytes derived from the same cow, but submitted to maturation either in vivo or in vitro. To this end single-cell methylome and transcriptome sequencing of individual oocytes and transcriptome analysis of their corresponding cumulus cells was carried out. The resulting data revealed alterations in both the transcriptome and methylome of the  oocytes matured in vitro, suggesting compromised oocyte maturation. Notable changes included alterations in CpG islands associated with imprinted genes, including decreased methylation levels in MEST (PEG1), NNAT (both implicated in large offspring syndrome), and MIMT1 following in vitro maturation. Additionally, transcriptomic analysis of their cumulus cells highlighted significant alterations in gene expression linked to impaired mitochondrial function and altered responses to hypoxia and cell adhesion. Our findings highlight the extent to which the maturation environment can influence the key epigenetic regulators and mRNA profiles that affect oocyte quality and subsequent developmental outcomes. The data provides a valuable resource for optimising assisted reproduction technologies. Overall design: scRNA-seq and scBS-seq were perfomed on bovine MII oocytes after in vivo or in vitro maturation. scRNA-seq was also performed on MII oocytes after in vivo + in vivo maturation. We sequenced 88 MII oocytes and 2 Negative control.