Deep transcriptome profiling reveals that retrotransposons regulate pluripotency

Characterization of mammalian transcriptomes has shown that cells use a complex repertoire of RNAs, where non-coding transcripts (ncRNAs) account for a substantial portion. Novel ncRNA classes are continuously discovered: these have in general a lower expression than mRNA and are often located in specific cellular compartments or used at specific cell states. The importance of microRNAs and long-ncRNAs in the regulation of pluripotency has been documented, however the non-coding components of stem cell gene network remain largely unknown. Here, we aim to investigate the role of ncRNA for pluripotent state, with particular emphases on nuclear and retrotransposon-derived transcripts. We sequenced a comprehensive nuclear and cytoplasmic non-coding transcriptome of human and mouse stem cells that we explored to identify non-annotated stem-specific transcripts. We show that LTR derived transcripts counts for an important part of the high nuclear transcriptome complexity of stem cells, are involved in the maintenance of pluripotency and are associated with enhancer regions. This study describes a previously uncharacterized role of retrotransposon-derived transcripts in mammalian stem cells in addition to a comprehensive transcriptomics resource.