Epigenetic mechanisms play pivotal roles in cell fate determination during development. Long non-coding RNAs (ncRNAs) are in involved in epigenetic gene expression by recruiting epigenetic regulators to target genes. We are dissecting the role of ncRNAs in the stemcellness and differentiation of human embryonic stem cells (hESC). We have used biochemical and molecular approaches to identify ncRNAs, which associate with epigenetic regulators in hESC and are involved in the regulation of the expression of homeotic (HOX) genes. HOX genes encode for key regulators of cell differentiation in Arthropods and Chordates. We have identified 32 ncRNAs, which are transcribed during hESC differentiation. The detailed dissection of the role of two of the identified ncRNAs in HOX gene expression has resulted in novel insights into the role of ncRNAs in hESC differentiation. The ncRNA Mistral plays an important role in ectoderm development, one of the three germ layers that give rise to all cells, tissues and organs. Inactivation of Mistral ncRNA during hESC development prevents ectoderm development, indicating that Mistral is a key regulator of ectoderm development. The second ncRNA Scirocco is involved in epigenetic activation of HOX genes, controlling mesoderm development.
The obtained results support a model in which ncRNAs regulate important steps during hESC differentiation. Our results lay a foundation for the application of ncRNAs in hESC differentiation and the development of diagnostic and therapeutic assays to detect and manipulate the differentiation of hESC. The obtained results open novel areas in the filed of stem cell research by providing tools and assays that actively control the differentiation of hESC. These assays represent valuable additions to the efforts aimed at the active control hESC differentiation in order to obtain desired cell types.