Expression data from somatic cell nuclear transfer bovine embryo

Since the first cloned animal Dolly Sheep was successfully created by using somatic cell nuclear transfer(SCNT) technique. It has become an irreplaceable tool to understand nuclear reprogramming and totipotency and holds huge potentials for regenerative medicine. However, extremely poor development rate of SCNT embryos indicates it is still questionable. The nature of reprogramming oocyte factors and their mechanism of action remain largely unknown.It is evident that the major barrier that hinders the developing iSCNT embryo mainly appears at the time of embryonic genome activation (EGA), which primarily occurs at the eight-cell stage in mammalian. The interspecies somatic cell nuclear transfer (iSCNT) is desired model for nuclear reprogramming research and a powerful tool for discovering the master genome activation genes. In this study, a valuable transcriptome recourse of iSCNT embryos was established, which derived from more than 2000 clone embryos of four different inter-family donor cells. Based on weighted gene co-expression network (WGCNA) approach, we provide an extensive transcriptome analysis of differentially expressed genes(DEG) for iSCNT embryos. The total gene expression patterns of different iSCNT embryos were discussed. 26 cell-specific modules with were identified, and those module significance and GO enriched categories were analyzed. The regulatory pathways of reprogramming barriers were further enriched. As master genome trigger genes, the transcripts related to TFIID subunit, RNA polymerase and Mediator were incomplete activated in iSCNT embryos. This indicated that pioneer factors, present in the cytoplasm of the oocyte, were failed to bind the sequence target on the heterology nuclear genome. This genomic incompatibility between the nuclear donor cell and the cytoplast may be as a major contributing factor causes the developmental failure of iSCNT cloned embryos. This study demonstrates that the iSCNT embryos undergoes only partial or incomplete reprogramming at eight-cell stage in mammalian. Our results offered convincing evidence that the abnormal expression of key master pathways may be caused the embryo developmental block of cloning embryo. This work will contribute to a better understanding of the molecular interaction between nuclear–cytoplasmic interaction and provides insight into the molecular determinants of nuclear reprogramming, human embryonic stem cell (hESC)-based therapies and rescuing highly endangered species. In this study, the Affymetrix gene chip bovine genome array was used for gene array analysis. The Affymetrix Gene Chip Bovine Genome array contains 24,027 probe sets corresponding to approximately 23,000 transcripts including assemblies from ~19,000 UniGene clusters. The arrays images were first quantified using Gene Chip Operating Software (GCOS, Affymetrix). Samples are divided into two groups, one is embryos, another is the somatic cells. In embryos group, we collected two biological replicates of bovine oocytes, contains 1150 oocytes (BMII, ID-1) and 1000 occytes (BMII, ID-2) respectively; Two biological replicates of bovine-bovine intraspecies cloned embryos (BBNT), replicates contain 309(ID-3) and 552(ID-4) BBNT embryos; 527(ID-5) Przewalski's gazelle –Bovine interspecies nuclear transfer 8- to 16-cell stage embryos (PBNT) , 521(ID-6) Yak-Bovine interspecies nuclear transfer 8- to 16-cell stage embryos ,515(ID-7) Tibetan–bovine interspecies nuclear transfer 8- to 16-cell stage embryos (TBNT). In somatic cell group, we collected two biological replicates Luxi cattle somatic cells (LC, ID- 8,9), Mongolia cattle somatic cells(MC, ID-10,11) , Yak somatic cells(YC, ID-13,14) and Tibetan somatic cells(TC, ID-15,16) respectively. In addition, we also collected Holstein somatic cells (HC, ID-12) and three replicates Przewalski’s gazelle somatic cells(PC, ID-17,18,19)