Molecular characterization of bovine embryonic stem cells derived from IVF, cloned, and parthenogenetic embryos

Purpose: Embryonic stem cells (ESC) indefinitely maintain the pluripotent state of the blastocyst epiblast. Stem cells are invaluable for studying development and lineage commitment, and in livestock they constitute a useful tool for genomic improvement and in vitro breeding programs. Although these cells have been recently derived from bovine blastocysts, a detailed characterization of their molecular state is still lacking. Methods: Here, we compared the transcriptomic and epigenomic profiles of bovine ESC (bESC) obtained from in vitro fertilized (IVF), somatic cell nuclear transfer (SCNT), and parthenogenetic (PAR) embryos. Results: Bovine ESC were efficiently derived from SCNT and IVF embryos and expressed pluripotency markers while retaining genome stability. Transcriptome analysis revealed that only 46 genes were differentially expressed between IVF- and SCNT-derived bESC, which did not reflect significant deviation in cellular function. Additionally, by interrogating the histone marks H3K4me3, H3K9me3 and H3K27me3 with CUT&Tag, we found that the epigenomes of bESC subtypes were virtually indistinguishable. Minor epigenetic differences were randomly distributed throughout the genome and were not associated with differentially expressed or developmentally important genes. Finally, categorization of genomic regions according to their combined histone mark signal demonstrated that bESC subtypes shared the same epigenomic signatures, especially at promoters. Conclusions: Overall, we conclude that bESC derived from SCNT and IVF embryos are transcriptomically and epigenetically analogous. Overall design: Gene expression profiles were determined by 3'-Tag-RNA-seq for three independent male bESC lines derived from IVF blastocysts, three independent male bESC lines derived from SCNT blastocysts, one bESC line derived from PAR blastocysts, male fibroblasts used as nuclear donors for SCNT, and two other fibroblast cell lines (one male, one female). CUT&Tag was used to profile H3K4me3, H3K9me3, and H3K27me3 in the same three independent male bESC lines derived from IVF blastocysts, the same three independent male bESC lines derived from SCNT blastocysts, and the male fibroblasts used as nuclear donors for SCNT. Additionally, IgG was profiled by CUT&Tag in one bESC-IVF replicate, one bESC-SCNT replicate, and fibroblast nuclear donor cells.