Although mammalian genomes contain less than 25,000 protein-coding genes, the non-coding RNA (ncRNA) transcription constitutes their most unexplored and prevalent part. Despite such abundance only in the past few years we have started to appreciate their functions in cells.  Embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) are increasingly being used for drug screening as well as for cell-based models of numerous pathologies and regenerative medicine. For such models, understanding the mechanisms that maintain stemness and promote differentiation is critical.

We recently used four complementary high-throughput sequencing technologies to characterize the non-coding transcriptome of mouse pluripotent stem cells. We have identified over 6000 stem cell-specific non-annotated transcripts predominantly expressed in the nucleus. Here we present our latest findings regarding the characterization of these ncRNAs and their intimate association with the chromatin.