Comparison of Reprogramming Genes in Induced Pluripotent Stem Cells and Nuclear Transfer Cloned Embryos

The most effective reprogramming methods, somatic cell nuclear transfer (SCNT) and induced pluripotent stem cells (iPSCs), are widely used in biological research and regenerative medicine, yet the mechanism that reprograms somatic cells to totipotency remains unclear and thus reprogramming efficiency is still low. Microarray technology has been employed in analyzing the transcriptomes changes during iPS reprogramming. Unfortunately, it is difficult to obtain enough DNA from SCNT reconstructed embryos to take advantage of this technology. In this study, we aimed to identify critical genes from the transcriptional profile for iPS reprogramming and compared expression levels of these genes in SCNT reprogramming. By integrating gene expression information from microarray databases and published studies comparing somatic cells with either miPSCs or mouse embryonic stem cells (ESCs), we obtained two lists of co-upregulated genes. The gene ontology (GO) enriched analysis of these two lists demonstrated that the reprogramming process is associated with numerous biological processes. Specifically, we selected 32 genes related to heterochromatin, embryonic development, and cell cycle from our co-upregulated gene datasets and examined the gene expression level in iPSCs and SCNT embryos by qPCR. The results revealed that some reprogramming related genes in iPSCs were also expressed in SCNT reprogramming. We established the network of gene interactions that occur with genes differentially expressed in iPS and SCNT reprogramming and then performed GO analysis on the genes in the network. The network genes function in chromatin organization, heterochromatin, transcriptional regulation, and cell cycle. Further researches to improve reprogramming efficiency, especially in SCNT, will focus on functional studies of these selected genes.