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Nature Genetics 41, 563–571 (1 May 2009) | doi:10.1038/ng.368

The regulated retrotransposon transcriptome of mammalian cells

Geoffrey J Faulkner , Yasumasa Kimura , Carsten O Daub , Shivangi Wani , Charles Plessy , Katharine M Irvine , Kate Schroder , Nicole Cloonan , Anita L Steptoe , Timo Lassmann , Kazunori Waki , Nadine Hornig , Takahiro Arakawa , Hazuki Takahashi , Jun Kawai , Alistair R R Forrest , Harukazu Suzuki , Yoshihide Hayashizaki , David A Hume , Valerio Orlando , Sean M Grimmond & Piero Carninci

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|[prime]| 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|[prime]| 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.