The regulated retrotransposon transcriptome of mammalian cells
The regulated retrotransposon transcriptome of mammalian cells
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DOI：
10.1038/ng.368
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发表时间：
2009-05-01
期刊：
影响因子：
30.8
通讯作者：
Carninci, Piero
中科院分区：
文献类型：
--
作者：
Faulkner, Geoffrey J.;Kimura, Yasumasa;Carninci, Piero
尽管重复元件在哺乳动物基因组中普遍存在，但它们对转录活性的总体贡献尚不明确。在这里，作为FANTOM4项目的一部分，我们报告了6-30%的cap选择的小鼠和人类RNA转录物在重复元件中启动。对大约25万个反转录转座子衍生的转录起始位点的分析表明，相关转录物通常具有组织特异性，与基因密集区域重合，当与全长反转录转座子序列对齐时形成明显的簇。位于蛋白质编码位点5'的反转录转座子经常作为替代启动子和/或表达非编码rna。超过四分之一的RefSeqs在其3' UTR中具有反转录转座子，有力的证据表明，相对于无反转录转座子的转录本，这些转录本的表达减少。最后，全基因组筛选确定了23000个来自反转录转座子的候选调控区域，以及2000多个双向转录的例子。我们得出结论，反转录转座子转录对哺乳动物基因组的转录输出有关键影响。
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.