期刊
NATURE GENETICS
卷 41, 期 5, 页码 563-571出版社
NATURE PORTFOLIO
DOI: 10.1038/ng.368
关键词
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资金
- Australian Postgraduate Award through the Australian government Department of Education, Training and Youth Affairs
- CJ Martin Fellowship from the Australian NHMRC [ID 428261]
- MEXT
- Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government
- ARC Special Research Centre for Functional and Applied Genomics
- NHMRC
- Australian NHMRC
- UQ postdoctoral research fellowship
- Telethon Foundation [TCP00094]
- Associazione Italiana Ricerca sul Cancro (AIRC)
- Fondazione Compagnia di San Paolo
- EMBO long-term fellowship
- Medical Research Council [G9900991B] Funding Source: researchfish
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.
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