Deciphering transcriptional and post-transcriptional regulation of genes modulating stem cell pluripotency and differentiation networks

Abstract

Human embryonic stem cells (hESCs) are undifferentiated cells that hold great promises for therapeutics by producing adult cells to replace lost or damaged cells. The properties of hESCs (i.e., pluripotency and differentiation) add layers of complexity to the transcriptional and post-transcriptional circuit of these cells. In this study, we deciphered important transcriptional and post-transcriptional regulations and regulators including TFs, microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), contributing to hESC maintenance and differentiation. Our study of hESCs lineage specification into fibroblasts (Fibs) identified some key genes playing roles in different stages of differentiation of hESCs into Fibs through embryoid bodies (Ebs). Further, we unraveled miRNA co-regulations in hESCs stemness and differentiation. Our analysis of miRNA synergistic network revealed that hsa-miR-873-5p might be playing a crucial role in maintaining hESCs stemness via hindering epithelial to mesenchyme transition. Apart from this, we conjectured that co-operative suppression of core cohesion sub-units (SMC1A and SMC3) by a set of five miRNAs (hsa-let-7i-5p, hsa-let-7g-5p, hsa-miR-29b-2-5p, hsa-miR-30a-3p, and hsa-miR-98-5p) as an important differentiation-inducing event which is predicted to help in delaying the G1-S phase transition thereby promoting hESCs differentiation into Fibs. In addition, we predicted an active lncRNA-TF-gene regulatory network in hESCs and extracted the G1-S cell cycle phase transition specific lncRNA-TF-gene sub-network that included two crucial lncRNAs, MALAT1 and DANCR. Our analysis revealed that MALAT1 and DANCR might be playing key roles in G1-S phase transition that aid in stemness maintenance of hESCs by acting as RNA decoy via interacting with crucial stemness maintaining TFs such as E2F1 and MYC. In this thesis, we identified new regulators, regulatory interactions, and mechanisms controlling hESCs stemness and differentiation whose knowledgebase might aid in better understanding and achieving precise dedifferentiation of adult cells into induced pluripotent stem cells (iPSCs).