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.
Bibliographical noteFunding Information:
A.R.R.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.
G.J.F. is supported by an Australian Postgraduate Award through the Australian government Department of Education, Training and Youth Affairs (DETYA).
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