Project 2: Large ncRNAs and Epigenetic Regulation in Pluripotency

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Recent advances in our understanding of stem cell biology offer unprecedented hope for medical advancement. For example, it is now possible to transform fibroblasts from human skin to induced pluripotent stem cells (iPSCs) by induction of four master regulatory proteins. In turn these factors regulate a complex choreography that remodels the differentiated epigenetic landscapes to the pluripotent state. This process paves the way for limitless supply of genetically tailored cell types for transplantation medicine, drug discovery and the study of human disease. Although some progress has been made in understanding the key protein coding factors needed for IPSC reprogramming much less is known about the finely tuned genetic switches that guide this process and maintain the pluripotent state. We have recently demonstrated that large intergenic non-coding RNAs (lincRNAs) may serve as such switches in maintaining key cellular states such as pluripotency. Indeed, we recently discovered a new facet of lincRNA regulation of the human iPSC reprogramming process. Specifically, we identified lincRNA-RoR (Regulator of Reprogramming) that is required for reprogramming human fibroblast to iPSCs. Further consistent with this idea are three additional findings we recently reported: (i) Over 100 lincRNAs are directly regulated by the 'core stem-cell' transcription factors (Oct4, Sox2 and Nanog); (ii) lincRNAs interact with key chromatin modifying complexes that maintain the differentiation states of cells, and many convey their specificity; cell switches, (iii) lincRNAs exhibit distinctive gene- expression profiles similar to those of the few known master pluripotency switches. Collectively, these studies demonstrate a functionally important regulatory cascade initiated by reprogramming factors, which activate lincRNAs that have the potential to interface with and modulate downstream epigenetic machinery to successfully complete the reprogramming process. Here we aim to (1) Comprehensively identify lincRNAs involved in reprogramming (2) their functional roles in reprogramming and epigenetic regulation and (3) Their biochemical mechanisms. RELEVANCE (See instructions): Induced pluripotent stem cells is a potential revolutionary tool for disease modeling, drug screening and regenerative medicine. This proposal aims to fully characterize the roles of large intergenic non-coding RNAs (lincRNAs) and their functional relevance to establishing pluripotency and epigenetic states, which is an essential step towards ensuring that their use in biomedicine is effective and safe