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.
Institute for Molecular Bioscience, University of Queensland, Australia.
Geoffrey J
GJ
Faulkner
Yasumasa
Y
Kimura
Carsten O
CO
Daub
Shivangi
S
Wani
Charles
C
Plessy
Katharine M
KM
Irvine
Kate
K
Schroder
Nicole
N
Cloonan
Anita L
AL
Steptoe
Timo
T
Lassmann
Kazunori
K
Waki
Nadine
N
Hornig
Takahiro
T
Arakawa
Hazuki
H
Takahashi
Jun
J
Kawai
Alistair R R
AR
Forrest
Harukazu
H
Suzuki
Yoshihide
Y
Hayashizaki
David A
DA
Hume
Valerio
V
Orlando
Sean M
SM
Grimmond
Piero
P
Carninci
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