The regulated retrotransposon transcriptome of mammalian cells View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2009-05

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. More... »

PAGES

563-571

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/ng.368

    DOI

    http://dx.doi.org/10.1038/ng.368

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1027476610

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/19377475


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