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- Title
The regulated retrotransposon transcriptome of mammalian cells.
- Authors
Faulkner, Geoffrey J.; Kimura, Yasumasa; Daub, Carsten O.; Shivangi Wani; Plessy, Charles; Irvine, Katharine M.; Schroder, Kate; Cloonan, Nicole; Steptoe, Anita L.; Lassmann, Timo; Waki, Kazunori; Hornig, Nadine; Arakawa, Takahiro; Takahashi, Hazuki; Kawai, Jun; Forrest, Alistair R. R.; Suzuki, Harukazu; Hayashizaki, Yoshihide; Hume, David A.; Orlando, Valerio
- Abstract
Although repetitive elements pervade mammalian genomes, their overall contribution to transcriptional activity is poorly defined. Here, as part of the FANTOM4 project, we report that 6–30% of cap-selected mouse and human RNA transcripts initiate within repetitive elements. Analysis of approximately 250,000 retrotransposon-derived transcription start sites shows that the associated transcripts are generally tissue specific, coincide with gene-dense regions and form pronounced clusters when aligned to full-length retrotransposon sequences. Retrotransposons located immediately 5′ of protein-coding loci frequently function as alternative promoters and/or express noncoding RNAs. More than a quarter of RefSeqs possess a retrotransposon in their 3′ UTR, with strong evidence for the reduced expression of these transcripts relative to retrotransposon-free transcripts. Finally, a genome-wide screen identifies 23,000 candidate regulatory regions derived from retrotransposons, in addition to more than 2,000 examples of bidirectional transcription. We conclude that retrotransposon transcription has a key influence upon the transcriptional output of the mammalian genome.
- Subjects
GENOMES; GENOMICS; GENETIC transcription; NUCLEOTIDE sequence; GENE expression; GENE mapping; GENETIC research
- Publication
Nature Genetics, 2009, Vol 41, Issue 5, p563
- ISSN
1061-4036
- Publication type
Article
- DOI
10.1038/ng.368