Journal article
The regulated retrotransposon transcriptome of mammalian cells
GJ Faulkner, Y Kimura, CO Daub, S Wani, C Plessy, KM Irvine, K Schroder, N Cloonan, AL Steptoe, T Lassmann, K Waki, N Hornig, T Arakawa, H Takahashi, J Kawai, ARR Forrest, H Suzuki, Y Hayashizaki, DA Hume, V Orlando Show all
Nature Genetics | NATURE PORTFOLIO | Published : 2009
DOI: 10.1038/ng.368
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 quart..
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Awarded by European Molecular Biology Organization
Funding Acknowledgements
G.J.F. is supported by an Australian Postgraduate Award through the Australian government Department of Education, Training and Youth Affairs (DETYA). A.RR.F. is funded by a CJ Martin Fellowship from the Australian NHMRC (ID 428261). K. S. and K. M. I. are members of the CRC for Chronic Inflammatory Diseases. P. C. and Y.H. are supported by the National Project on Protein Structural and Functional Analysis from MEXT and the National Project on Genome Network Analysis and the RIKEN Genome Exploration Research Project from the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government. D. A. H. acknowledges the funding of the ARC Special Research Centre for Functional and Applied Genomics and the NHMRC. S. M. G. holds a Senior Research Fellowship with the Australian NHMRC. N.C. is supported by a UQ postdoctoral research fellowship. V.O. is supported by Telethon Foundation (TCP00094), Associazione Italiana Ricerca sul Cancro (AIRC) and Fondazione Compagnia di San Paolo, and N. H. is supported by an EMBO long-term fellowship.