Identification of somatic memory genes during bovine nuclear reprogramming by transcriptome sequencing

We hypothesized aberrant transcriptional silence was existed in bovine clone reprogramming as well as abnormal transcriptional activation and the result of RNA-seq confirmed this hypothesis. On the one hand, SCNT (somatic cell nuclear transfer) embryos exhibited excessive RNA processing and translation while these two biological processes were deficient in human and mouse; on the other hand, SCNT embryos exhibited the transcriptional defects of reproduction-related genes. These results proved the existences of active- and silent-memory genes which inherited from donor cells in bovine early SCNT embryos. Then, H3K4me3-specific demethylase 5B (KDM5B) mRNAs were injected into cloned embryos to erase active or silent memory respectively. KDM5B overexpression not only reduced the transcription level of active-memory genes but also promoted the expression of silent-memory genes, especially rescued multiple development-related genes. RNA-Seq profiles from pools of IVF eight-cell embryo (3 replicates), SCNT eight-cell embryo with (3 replicates) or without (3 replicates) KDM5B overexpression were generated using Illumina HiSeq 4000.RNA-Seq profiles from pools of bovine fetal fibroblast (BFF) (3 replicates) were generated using BGIseq-500.