title: Conserved expression of transposon-derived non-coding transcripts in primate stem cells.
abstract: 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).
  
  
  
  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.
  
  
  
  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.
authors.affiliation: Department of Human Genetics, McGill University, Dr Penfield Avenue, Montreal, H3A 1B1, Canada.
authors.forename: LeeAnn
authors.initials: L
authors.lastname: Ramsay
authors.affiliation: Lab of Genetics, Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA.
authors.forename: Maria C
authors.initials: MC
authors.lastname: Marchetto
authors.affiliation: Department of Human Genetics, McGill University, Dr Penfield Avenue, Montreal, H3A 1B1, Canada.|McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, H3A 1A4, Canada.
authors.forename: Maxime
authors.initials: M
authors.lastname: Caron
authors.affiliation: McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, H3A 1A4, Canada.
authors.forename: Shu-Huang
authors.initials: SH
authors.lastname: Chen
authors.affiliation: McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, H3A 1A4, Canada.
authors.forename: Stephan
authors.initials: S
authors.lastname: Busche
authors.affiliation: Department of Human Genetics, McGill University, Dr Penfield Avenue, Montreal, H3A 1B1, Canada.|McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, H3A 1A4, Canada.
authors.forename: Tony
authors.initials: T
authors.lastname: Kwan
authors.affiliation: Department of Human Genetics, McGill University, Dr Penfield Avenue, Montreal, H3A 1B1, Canada.|McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, H3A 1A4, Canada.
authors.forename: Tomi
authors.initials: T
authors.lastname: Pastinen
authors.affiliation: Lab of Genetics, Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA.
authors.forename: Fred H
authors.initials: FH
authors.lastname: Gage
authors.affiliation: Department of Human Genetics, McGill University, Dr Penfield Avenue, Montreal, H3A 1B1, Canada. guil.bourque@mcgill.ca.|McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, H3A 1A4, Canada. guil.bourque@mcgill.ca.
authors.forename: Guillaume
authors.identifier: 0000-0002-3933-9656
authors.initials: G
authors.lastname: Bourque
mesh_terms: D000818:Animals; D017124:Conserved Sequence; D004251:DNA Transposable Elements / Q000235:genetics*; D020869:Gene Expression Profiling; D023281:Genomics; D006801:Humans; D011323:Primates / Q000235:genetics*; D062085:RNA, Long Noncoding / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics*; D013045:Species Specificity; D013234:Stem Cells / Q000378:metabolism*
chemical_list: D004251:DNA Transposable Elements; D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D022661:RNA, Untranslated
keywords: Induced pluripotent stem cells; Long non-coding RNAs; Transposable elements