Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance

Alexandre Fort, Kosuke Hashimoto, Daisuke Yamada, Md Salimullah, Chaman A. Keya, Alka Saxena, Alessandro Bonetti, Irina Voineagu, Nicolas Bertin, Anton Kratz, Yukihiko Noro, Chee Hong Wong, Michiel De Hoon, Robin Andersson, Albin Sandelin, Harukazu Suzuki, Chia Lin Wei, Haruhiko Koseki, Yuki Hasegawa, Alistair R.R. ForrestPiero Carninci*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

176 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)558-566
Number of pages9
JournalNature Genetics
Volume46
Issue number6
DOIs
StatePublished - Jun 2014

ASJC Scopus subject areas

  • Genetics

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