Expression profiling reveals differential expressed genes between bovine IVF and SCNT embryos

Alternative splicing (AS) is generally observed in different developmental processes in mammals. In mammalian development, totipotency which is defined as the ability of a cell to give rise to all cell types of an entire organism is limited to early-stage preimplantation embryos. Somatic cell nuclear transfer (SCNT) can reprogram terminally differentiated cells into a totipotent state. However, studies addressing the functional role of AS in mammalian preimplantation embryonic development are lacking. Here we show that AS has important physiological functions in mammalian preimplantation embryonic development as a regulator. We discovered abundant AS transitions during both key events in preimplantation embryonic development, fertilization and embryonic genome activation. We also found that the RNA-binding protein hnRNPK govern the oocyte-to-embryo transition by regulating the MII oocyte-specific exon exclusion in mouse. Furthermore, we demonstrated that SCNT embryos had abnormal alternative splicing compared to in vitro fertilized (IVF) embryos in bovine. We used RNA-targeting system CRISPR-Cas13d to target cis elements of ABI2 pre-mRNA to operate alternative splicing, reducing abnormal isoform ratios of SCNT embryos and greatly improve the production of cloned cows. Our results advance the understanding of SCNT-mediated reprogramming and its potential applications for both reproductive and therapeutic cloning. Overall design: RNA-Seq profiles from pools of 6 two-embryos from bovine IVF (3 replicates) and SCNT (3 replicates) and 3 MII-embryos (3 replicates) using Illumina HiSeq 4000.