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dc.contributor.authorFaulkner, Geoffrey
dc.contributor.authorKimura, Yasumasa
dc.contributor.authorDaub, Carsten
dc.contributor.authorWani, Shivangi
dc.contributor.authorPlessy, Charles
dc.contributor.authorIrvine, Katharine
dc.contributor.authorSchroder, Kate
dc.contributor.authorCloonan, Nicole
dc.contributor.authorSteptoe, Anita
dc.contributor.authorLassmann, Timo
dc.contributor.authorWaki, Kazunori
dc.contributor.authorHornig, Nadine
dc.contributor.authorArakawa, Takahiro
dc.contributor.authorTakahash, Hazuki
dc.contributor.authorKawai, Jun
dc.contributor.authorForrest, Alistair
dc.contributor.authorSuzuki, Harukazu
dc.contributor.authorHayashizaki, Yoshihide
dc.contributor.authorHume, David
dc.contributor.authorOrlando, Valerio
dc.contributor.authorGrimmond, Sean
dc.contributor.authorCarninci, Piero
dc.date.accessioned2017-05-03T14:38:39Z
dc.date.available2017-05-03T14:38:39Z
dc.date.issued2009
dc.date.modified2010-07-08T01:06:50Z
dc.identifier.issn1061-4036
dc.identifier.doi10.1038/ng.368
dc.identifier.urihttp://hdl.handle.net/10072/30227
dc.description.abstractAlthough 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.peerreviewedYes
dc.description.publicationstatusYes
dc.languageEnglish
dc.language.isoeng
dc.publisherNature Publishing Group
dc.publisher.placeUnited States
dc.relation.ispartofstudentpublicationN
dc.relation.ispartofpagefrom563
dc.relation.ispartofpageto571
dc.relation.ispartofissue5
dc.relation.ispartofjournalNature Genetics
dc.relation.ispartofvolume41
dc.rights.retentionY
dc.subject.fieldofresearchGenetics not elsewhere classified
dc.subject.fieldofresearchBiological Sciences
dc.subject.fieldofresearchMedical and Health Sciences
dc.subject.fieldofresearchcode060499
dc.subject.fieldofresearchcode06
dc.subject.fieldofresearchcode11
dc.titleThe regulated retrotransposon transcriptome of mammalian cells
dc.typeJournal article
dc.type.descriptionC1 - Articles
dc.type.codeC - Journal Articles
gro.date.issued2009
gro.hasfulltextNo Full Text
gro.griffith.authorForrest, Alistair RR.


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