Whole-genome transcriptome and DNA methylome analyses reveal molecular abnormalities during the oocyte-to-embryo transition in preimplantation embryos derived from prepubertal lamb oocytes

The juvenile in vitro embryo transfer technology holds the potential to accelerate livestock breeding. However, its application is limited due to the weak in vitro development of oocytes and embryos from prepubertal lambs. To dissect the regulatory networks of gene expression of sheep embryos and identify the defects in gene expression in prepubertal lamb embryos during the oocyte-to-embryo transition, full-length RNA sequencing and whole-genome bisulfite sequencing based on trace cells were conducted on in vitro-derived embryos generated from adult sheep and prepubertal lamb oocytes. We found that the maternal transcript degradation occurred selectively in adult sheep embryos in multiple waves and was most completed until the morula stage. Major embryonic genome activation was found to occur at the morula stage. By comparing with the patterns of adult embryos, we observed incomplete maternal transcript degradation and abnormal embryonic genome activation in lamb embryos and analyzed their potential molecular mechanisms. Furthermore, we explored dynamic DNA methylation concerning the paternal and maternal genomes during the preimplantation development of sheep embryos, revealing the negative regulatory role of promoter DNA methylation on embryonic genome activation process. Lamb embryos generally displayed higher DNA methylation levels than adults, potentially repressing the embryonic genome activation gene expression, especially the genes associated with ribosomal and mitochondrial organization. We also found abnormalities in the methylation status of imprinted genes in lamb embryos. Our findings advance the understanding of sheep in vitro embryo development and offer insights for improving the juvenile in vitro embryo transfer technology in livestock.