Conserved expression of transposon-derived non-coding transcripts in primate stem cells

BMC Genomics. 2017 Feb 28;18(1):214. doi: 10.1186/s12864-017-3568-y.


Background: A significant portion of expressed non-coding RNAs in human cells is derived from transposable elements (TEs). Moreover, it has been shown that various long non-coding RNAs (lncRNAs), which come from the human endogenous retrovirus subfamily H (HERVH), are not only expressed but required for pluripotency in human embryonic stem cells (hESCs).

Results: To identify additional TE-derived functional non-coding transcripts, we generated RNA-seq data from induced pluripotent stem cells (iPSCs) of four primate species (human, chimpanzee, gorilla, and rhesus) and searched for transcripts whose expression was conserved. We observed that about 30% of TE instances expressed in human iPSCs had orthologous TE instances that were also expressed in chimpanzee and gorilla. Notably, our analysis revealed a number of repeat families with highly conserved expression profiles including HERVH but also MER53, which is known to be the source of a placental-specific family of microRNAs (miRNAs). We also identified a number of repeat families from all classes of TEs, including MLT1-type and Tigger families, that contributed a significant amount of sequence to primate lncRNAs whose expression was conserved.

Conclusions: Together, these results describe TE families and TE-derived lncRNAs whose conserved expression patterns can be used to identify what are likely functional TE-derived non-coding transcripts in primate iPSCs.

Keywords: Induced pluripotent stem cells; Long non-coding RNAs; Transposable elements.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Conserved Sequence*
  • DNA Transposable Elements / genetics*
  • Gene Expression Profiling*
  • Genomics
  • Humans
  • Primates / genetics*
  • RNA, Long Noncoding / genetics
  • RNA, Messenger / genetics
  • RNA, Untranslated / genetics*
  • Species Specificity
  • Stem Cells / metabolism*


  • DNA Transposable Elements
  • RNA, Long Noncoding
  • RNA, Messenger
  • RNA, Untranslated