Dissecting the role of nanog in stem cell pluripotency in silico

Abstract

Nanog is associated with the pluripotency and constitute an important factor in cellular reprogramming. Thus, dissecting the molecular function of Nanog would provide better understanding of the process of reprogramming, cellular replication and differentiation. This study was designed to utilize the Next Generation Sequencing (RNA-Seq) data to identify, discover and profile the RNA transcripts influenced by RNA silencing of Nanog in mouse embryonic stem (ES) cell. Data from mouse induced pluripotent stem (iPS) and mouse embryonic fibroblast (MEF) cells were used as controls. GALAXY, an online open source software platform, was used and Tuxedo Protocol was followed to identify the differentially expressed genes and transcripts. The differentially expressed genes and transcripts were functionally annotated for biological and molecular functions and identify splice junction, exon-intron boundaries, and identification of primary transcripts. Results showed that, in Nanog null cell lines, Sgol2, Mcm7, Psma4 were up-regulated by a factor of 1.36 whereas several pluripotency related genes were down regulated. The up-regulated genes were associated with the regulation of cell cycle and regulation of pre replication complex whereas down-regulated genes were found to be associated with protein synthesis pathways, cellular proliferation and differentiation pathways besides pluripotency. Further, upon Nanog knock-down, genes associated with the process of replication were activated while genes associated with the cellular differentiation were down-regulated by a relative expression in the range of (0.3-0.9). In conclusion, the results of the present study suggests that Nanog may not only be responsible for determining the pluripotency and reprogramming of cells but also for the process of cellular replication .