dc.contributor.author | Faulkner, Geoffrey | |
dc.contributor.author | Kimura, Yasumasa | |
dc.contributor.author | Daub, Carsten | |
dc.contributor.author | Wani, Shivangi | |
dc.contributor.author | Plessy, Charles | |
dc.contributor.author | Irvine, Katharine | |
dc.contributor.author | Schroder, Kate | |
dc.contributor.author | Cloonan, Nicole | |
dc.contributor.author | Steptoe, Anita | |
dc.contributor.author | Lassmann, Timo | |
dc.contributor.author | Waki, Kazunori | |
dc.contributor.author | Hornig, Nadine | |
dc.contributor.author | Arakawa, Takahiro | |
dc.contributor.author | Takahash, Hazuki | |
dc.contributor.author | Kawai, Jun | |
dc.contributor.author | Forrest, Alistair | |
dc.contributor.author | Suzuki, Harukazu | |
dc.contributor.author | Hayashizaki, Yoshihide | |
dc.contributor.author | Hume, David | |
dc.contributor.author | Orlando, Valerio | |
dc.contributor.author | Grimmond, Sean | |
dc.contributor.author | Carninci, Piero | |
dc.date.accessioned | 2017-05-03T14:38:39Z | |
dc.date.available | 2017-05-03T14:38:39Z | |
dc.date.issued | 2009 | |
dc.date.modified | 2010-07-08T01:06:50Z | |
dc.identifier.issn | 1061-4036 | |
dc.identifier.doi | 10.1038/ng.368 | |
dc.identifier.uri | http://hdl.handle.net/10072/30227 | |
dc.description.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⠯f 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⠕TR, 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. | |
dc.description.peerreviewed | Yes | |
dc.description.publicationstatus | Yes | |
dc.language | English | |
dc.language.iso | eng | |
dc.publisher | Nature Publishing Group | |
dc.publisher.place | United States | |
dc.relation.ispartofstudentpublication | N | |
dc.relation.ispartofpagefrom | 563 | |
dc.relation.ispartofpageto | 571 | |
dc.relation.ispartofissue | 5 | |
dc.relation.ispartofjournal | Nature Genetics | |
dc.relation.ispartofvolume | 41 | |
dc.rights.retention | Y | |
dc.subject.fieldofresearch | Genetics not elsewhere classified | |
dc.subject.fieldofresearch | Biological Sciences | |
dc.subject.fieldofresearch | Medical and Health Sciences | |
dc.subject.fieldofresearchcode | 060499 | |
dc.subject.fieldofresearchcode | 06 | |
dc.subject.fieldofresearchcode | 11 | |
dc.title | The regulated retrotransposon transcriptome of mammalian cells | |
dc.type | Journal article | |
dc.type.description | C1 - Articles | |
dc.type.code | C - Journal Articles | |
gro.date.issued | 2009 | |
gro.hasfulltext | No Full Text | |
gro.griffith.author | Forrest, Alistair RR. | |