Gene expression transcriptome of porcine induced pluripotent stem cell by RNA-seq and small RNA-seq. Sus scrofa

The wide application of pig disease model has caused a surge of interest in the study of derivation of pig induced pluripotent cells (iPSCs). While major progress has been made in defining the molecular networks that control pluripotentcy in human and mouse, the mechanism underlying the maintainence of pluripotency in pig remain largely unknown. Here we performed genome-wide analysis of gene expression profiling by RNA seq and small RNA seq and DNA methylation profile by MeDIP-seq in pig iPSCs through comparison with somatic cells. We identified mRNA and miroRNA transcripts that were specifically expressed in pig iPSCs. Our analysis identify the genes upregulated in pig iPS compared with somatic cells. These genes may led to the identification of factors which maintain or confer the pluripotent nature of pig iPSCs. We then pursued comprehensive bioinformatics analyses, including functional annotation of the generated data within the context of biological pathways, to uncover novel biological functions associated with maintenance of pluripotency in pig. This result supports that pig iPS have transcript profiles linked to “ribosome”, “chromatin remodeling”, and genes involved in “cell cycle “that may be critical to maintain their pluripotency, plasticity, and stem cell function. These findings demonstrate the key role of RNA splicing in regulating the pluripotency phenotype of pig cells. We also reveal a plethora of novel candidate genes and microRNA for induction of pig iPS. This information will ultimately advance our efforts at generating stable naïve pluripotency in pig cells.