Multi-omics analysis of mouse Padi6-mutant embryos

ABSTRACT Maternal effect genes (MEGs) play a central role in early mammalian development, epigenetic reprogramming, maternal-to-zygotic transition (MZT), and specification of early embryo cell lineages. Among these genes, PADI6, a key component of the subcortical maternal complex (SCMC), is essential for oocyte maturation and the assembly of cytoplasmic lattices (CPLs). In humans, loss-of function mutations in PADI6 have been linked to female reproductive issues, early embryonic arrest, and progeny affected by imprinting disorders (ImpDis), including Beckwith-Wiedemann syndrome (BWS) with multilocus imprinting disturbance (MLID). In this thesis, I characterised oocyte and early embryos from homozygous Padi6 mutant female mice to determine how maternal PADI6 influences epigenetic regulation and preimplantation development. The two-cell embryos displayed impairment of zygotic genome activation (ZGA). We observed the downregulation of major ZGA genes, underlying the developmental arrest at the two-cell stage. Only a small number of embryos were able to develop beyond the two-cell stage, reaching the blastocyst stage. In these blastocysts, the deficiency of PADI6 specifically affected the development of the inner cell mass (ICM), whereas the formation of the trophectoderm (TE) was unaffected. Transcriptomic analysis also revealed changes in genes related to mitochondrial function and energy metabolism, suggesting a metabolic shift that may contribute to lineage imbalance. In extended culture, mutant embryos failed to maintain ICM growth, supporting a role for PADI6 in sustaining pluripotent cell populations during blastocyst maturation. Moreover, we found that loss of maternal PADI6 affected the localisation and the expression of the epigenetic factors DNMT1 and UHRF1 in both oocytes and embryos, resulting in a global DNA methylation defect. Notably, we observed global hypermethylation, involving LINE and LTR elements, but no imprinting defects in two-cell embryos. In blastocysts, however, we found global hypomethylation affecting certain LTR subfamilies and gDMRs, causing the deregulation of several imprinted genes. This study provides mechanistic insights into how PADI6 deficiency contributes to preimplantation developmental failure and imprinting disorders, highlighting the essential role of the maternal effect gene Padi6 in reproductive biology.