Alternative Polyadenylation and RNA Splicing Profile during Sheep Zygotic Genome Activation

Zygotic genome activation (ZGA) is essential for early embryo development. Here, we reported that ZGA is initiated at 16-cell stage in sheep, as extensive alterations in gene expression and DNA methylation patterns, along with elevated levels of RNA polymerase II and developmental arrest was found at the 16-cell embryos. To uncover the sophisticated RNA metabolism during ZGA, we conducted weighted gene co-expression network analysis and identified 1957 critical maternal genes. Using dapars, we found 1058 and 933 lengthened alternative polyadenylation (APA) events, and genes exhibiting shorten APA were highly expressed in both sheep and mice ZGA-stage embryos. Using rMATs, we reported 2675 and 1963 genes showed exon skipping during ZGA in sheep and mice. These genes are related to RNA binding, translation, gamete generation, and reproduction. Briefly, 20 mature oocytes were transferred to a 100-μL micro-drop of BO-IVF medium (#71004, IVF Bioscience, Falmouth, UK) with mineral oil covering the surface. Then, capacitated sperm were added to the micro-drops and cultured for 16 h at 38.5℃, 5% CO2, and saturated humidity. The zygotes were transferred to BO-IVC embryo culture medium (#71005, IVF bioscience) for further culture. The 2-, 4-, 8-, and 16-cell stage embryos, as well as the mature oocytes, morula, early blastocysts, and the expanded blastocysts were collected at defined points for RNA sequencing (RNA-seq).