RNA sequencing of mRNA 5'-ends reveals regulators of bovine embryonic genome activation

The maternal-to-zygotic transition (MZT) in embryo development involves the degradation of maternal transcripts and the initiation of zygotic transcription, known as embryonic genome activation (EGA). EGA is marked by the upregulation of several PRDL homeobox family genes in humans. Many orthologues of these genes have recently been identified in bovine based on a comparative analysis with human EGA. Although studies on bovine EGA exist, a comprehensive analysis integrating 5' end mRNA sequencing with PRDL homeobox gene annotations based on cDNA evidence from bovine early embryo development is still lacking.

This study employs STRT-N RNA sequencing (RNA-seq) to profile the 5' ends of transcripts in single bovine oocytes and preimplantation embryos, identifying transcription factors (TFs) involved in EGA. We observed significant transcript degradation at the 2- and 16-cell stages, with the latter marking the onset of EGA. Our analysis characterized bovine EGA through the transient upregulation of PRDL homeobox family genes, similar to human EGA, and by identifying several marker genes. Furthermore, promoter analysis revealed potential EGA-inducing TFs, including PRDL homeodomain (DUXA, PHOX2A, UNCX, ALX1, LEUTX, and TPRXs) and other TFs (GABPA, EBF1, RELA, and KLFs).

Our findings provide a comprehensive view of the dynamic transcriptome regulation during bovine preimplantation development and highlight key regulatory elements and TFs that may drive EGA.