The regulated retrotransposon transcriptome of mammalian cells.
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.
Faulkner
Geoffrey J
GJ
Institute for Molecular Bioscience, University of Queensland, Australia.
Kimura
Yasumasa
Y
Daub
Carsten O
CO
Wani
Shivangi
S
Plessy
Charles
C
Irvine
Katharine M
KM
Schroder
Kate
K
Cloonan
Nicole
N
Steptoe
Anita L
AL
Lassmann
Timo
T
Waki
Kazunori
K
Hornig
Nadine
N
Arakawa
Takahiro
T
Takahashi
Hazuki
H
Kawai
Jun
J
Forrest
Alistair R R
AR
Suzuki
Harukazu
H
Hayashizaki
Yoshihide
Y
Hume
David A
DA
Orlando
Valerio
V
Grimmond
Sean M
SM
Carninci
Piero
P
D020413:3' Untranslated Regions / Q000235:genetics / Q000378:metabolism; D000818:Animals; D002478:Cells, Cultured; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D008322:Mammals / Q000235:genetics; D051379:Mice; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger; D022661:RNA, Untranslated / Q000378:metabolism; D018626:Retroelements / Q000235:genetics*
D020413:3' Untranslated Regions; D012333:RNA, Messenger; D022661:RNA, Untranslated; D018626:Retroelements