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: The regulated retrotransposon transcriptome of mammalian cells. In: Nat. Genet., 41 (5), pp. 563–571, 2009.

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.

BibTeX (Download)

@article{Faulkner2009-vh,
title = {The regulated retrotransposon transcriptome of mammalian cells},
author = {Geoffrey J Faulkner and Yasumasa Kimura and Carsten O Daub and Shivangi Wani and Charles Plessy and Katharine M Irvine and Kate Schroder and Nicole Cloonan and Anita L Steptoe and Timo Lassmann and Kazunori Waki and Nadine Hornig and Takahiro Arakawa and Hazuki Takahashi and Jun Kawai and Alistair R R Forrest and Harukazu Suzuki and Yoshihide Hayashizaki and David A Hume and Valerio Orlando and Sean M Grimmond and Piero Carninci},
url = {http://dx.doi.org/10.1038/ng.368},
year  = {2009},
date = {2009-05-01},
journal = {Nat. Genet.},
volume = {41},
number = {5},
pages = {563--571},
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.},
keywords = {Faulknerlab, Major_Publication},
pubstate = {published},
tppubtype = {article}
}