1 Computational and RNA Biology, Department of Biology, Faculty of Science, Københavns Universitet2 Bio-Informatics Group, BRIC Research Groups, BRIC, Københavns Universitet3 RIKEN Center for Life Science Technologies4 unknown5 Computational and RNA Biology, Department of Biology, Faculty of Science, Københavns Universitet
The importance of microRNAs and long noncoding RNAs in the regulation of pluripotency has been documented; however, the noncoding components of stem cell gene networks remain largely unknown. Here we investigate the role of noncoding RNAs in the pluripotent state, with particular emphasis on nuclear and retrotransposon-derived transcripts. We have performed deep profiling of the nuclear and cytoplasmic transcriptomes of human and mouse stem cells, identifying a class of previously undetected stem cell-specific transcripts. We show that long terminal repeat (LTR)-derived transcripts contribute extensively to the complexity of the stem cell nuclear transcriptome. Some LTR-derived transcripts are associated with enhancer regions and are likely to be involved in the maintenance of pluripotency.
Nature Genetics, 2014, Vol 46, Issue 6, p. 558-566