TY - JOUR
T1 - The regulated retrotransposon transcriptome of mammalian cells
AU - Faulkner, Geoffrey J
AU - Kimura, Yasumasa
AU - Daub, Carsten O
AU - Wani, Shivangi
AU - Plessy, Charles
AU - Irvine, Katharine M
AU - Schroder, Kate
AU - Cloonan, Nicole
AU - Steptoe, Anita L
AU - Lassmann, Timo
AU - Waki, Kazunori
AU - Hornig, Nadine
AU - Arakawa, Takahiro
AU - Takahashi, Hazuki
AU - Kawai, Jun
AU - Forrest, Alistair R R
AU - Suzuki, Harukazu
AU - Hayashizaki, Yoshihide
AU - Hume, David A
AU - Orlando, Valerio
AU - Grimmond, Sean M
AU - Carninci, Piero
PY - 2009
Y1 - 2009
N2 - 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.
AB - 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.
UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19377475
U2 - 10.1038/ng.368
DO - 10.1038/ng.368
M3 - Article
VL - 41
SP - 563
EP - 571
JO - Nature Genetics
JF - Nature Genetics
SN - 1061-4036
IS - 5
ER -