Title |
The regulated retrotransposon transcriptome of mammalian cells
|
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Published in |
Nature Genetics, April 2009
|
DOI | 10.1038/ng.368 |
Pubmed ID | |
Authors |
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 |
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. |
X Demographics
Geographical breakdown
Country | Count | As % |
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Australia | 2 | 67% |
Sweden | 1 | 33% |
Demographic breakdown
Type | Count | As % |
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Scientists | 2 | 67% |
Members of the public | 1 | 33% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 11 | 1% |
United Kingdom | 8 | 1% |
Japan | 7 | <1% |
Brazil | 7 | <1% |
Germany | 6 | <1% |
Spain | 4 | <1% |
Russia | 3 | <1% |
Canada | 3 | <1% |
Italy | 2 | <1% |
Other | 13 | 2% |
Unknown | 711 | 92% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 192 | 25% |
Researcher | 184 | 24% |
Student > Master | 76 | 10% |
Student > Bachelor | 60 | 8% |
Professor > Associate Professor | 44 | 6% |
Other | 114 | 15% |
Unknown | 105 | 14% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 385 | 50% |
Biochemistry, Genetics and Molecular Biology | 189 | 24% |
Medicine and Dentistry | 29 | 4% |
Neuroscience | 16 | 2% |
Immunology and Microbiology | 13 | 2% |
Other | 27 | 3% |
Unknown | 116 | 15% |