Characterization of Cell Cycle Phase-Based Micrornas in Pluripotency and Differentiation

Abstract

In addition to signaling pathways, transcription factors and epigenetic regulators, microRNAs (miRNAs) are emerging as important regulators of human pluripotent stem cells (hPSCs). Pluripotent miRNAs that regulate G1-S transition and pluripotency factors to maintain self-renewal have been identified. However, only 4-5 clusters of miRNAs have been identified in human embryonic stem cells (hESCs). We performed cell cycle phase-based (G1, S, and G2/M phases) miRNA array in pluripotent and differentiated hESCs. We demonstrated that embryonic stem cell-cell cycle (ESCC) regulating miRNAs were all highly expressed in three cell cycle phases of undifferentiated hESCs suggesting a non-cell phase regulated mechanism. From cell phase-dependent miRNAs, G2/M-miRNAs was extracted by principle component analysis (PCA) as a significant component in pluripotent hESCs, whereas G1-miRNAs was a significant component in differentiated hESCs. The results indicate that G2/M-miRNAs might function to maintain pluripotency and G1-miRNAs might function to enhance differentiation. By miRNA target site prediction, G2/M-phase miRNA displayed potential target sites on differentiation factors GATA6 and GATA4, G1-phase miRNAs displayed potential target sites on pluripotency gene OCT4, NANOG, and SOX2, which warrant further confirmation and functional study. By statistical and computation analysis of the miRNA array data, we demonstrated that the G2/M-miRNAs could potentially repress differentiation factors to maintain pluripotency, and G1-miRNAs could potentially target pluripotency genes to enhance differentiation.