Article abstract
Nature Genetics 41, 563 - 571 (2009)
Published online: 19 April 2009 | doi:10.1038/ng.368
The regulated retrotransposon transcriptome of mammalian cells
Geoffrey J Faulkner1, Yasumasa Kimura2, Carsten O Daub2, Shivangi Wani1, Charles Plessy2, Katharine M Irvine3, Kate Schroder3, Nicole Cloonan1, Anita L Steptoe1, Timo Lassmann2, Kazunori Waki2, Nadine Hornig4,5, Takahiro Arakawa2, Hazuki Takahashi2, Jun Kawai2, Alistair R R Forrest2,6, Harukazu Suzuki2, Yoshihide Hayashizaki2, David A Hume7, Valerio Orlando4,5, Sean M Grimmond1 & Piero Carninci2
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.
- Expression Genomics Laboratory, Institute for Molecular Bioscience, University of Queensland, Queensland, Australia.
- Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan.
- Cooperative Research Centre for Chronic Inflammatory Diseases and Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
- Dulbecco Telethon Institute, IRCCS Fondazione Santa Lucia at EBRI, Rome, Italy.
- Dulbecco Telethon Institute, IGB CNR, Naples, Italy.
- The Eskitis Institute for Cell and Molecular Therapies, Griffith University, Australia.
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Scotland, UK.
Correspondence to: Valerio Orlando4,5 e-mail: vorlando@dti.telethon.it
Correspondence to: Sean M Grimmond1 e-mail: s.grimmond@imb.uq.edu.au
Correspondence to: Piero Carninci2 e-mail: carninci@riken.jp
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