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

Nat Genet. 2014 Jun;46(6):558-66. doi: 10.1038/ng.2965. Epub 2014 Apr 28.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Nucleus / metabolism
  • Chromatin / chemistry
  • Cytoplasm / metabolism
  • Enhancer Elements, Genetic
  • Gene Expression Profiling
  • Gene Regulatory Networks
  • Humans
  • Lymphocytes / cytology
  • Mice
  • MicroRNAs / metabolism
  • Oligonucleotides, Antisense / genetics
  • Pluripotent Stem Cells / cytology*
  • Retroelements*
  • Terminal Repeat Sequences
  • Transcriptome*


  • Chromatin
  • MicroRNAs
  • Oligonucleotides, Antisense
  • Retroelements