Bidirectional promoters as important drivers for the emergence of species-specific transcripts.
Bidirectional promoters as important drivers for the emergence of species-specific transcripts.
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DOI：
10.1371/journal.pone.0057323
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Elnitski L
中科院分区：
文献类型：
--
作者：
Gotea V;Petrykowska HM;Elnitski L
基因功能的多样化在很大程度上归因于基因复制过程。新的例子，基因起源于以前的非转录区域最近已被描述，而不考虑一个统一的功能机制，为他们的出现。在这里，我们提出了一个模型机制，可以产生大量的谱系特异性的新的转录在脊椎动物中通过激活双向转录从单向启动子。我们使用人类转录组学和基因组数据在计算机上检查了这个模型，并确定了与1,000多个灵长类动物特异性转录物的出现相一致的证据。这些转录本具有低编码潜力，几乎没有功能注释。它们起始于相反转录的保守蛋白质编码基因上游小于1 kb处，与普遍接受的双向启动子定义一致。我们发现，祖先启动子上游的基因组区域，在我们的数据集中的新的转录本驻留，其特征在于转座因子的优先积累。这增强了位于祖先启动子上游的区域的序列多样性，进一步突出了它们对于转录新奇事物的出现的进化重要性。通过将新开发的阳性选择测试应用于我们的一组新转录本中的转座元件衍生片段，我们在我们的数据集中近3%的新转录本中发现了人类谱系适应性进化的证据。这些发现表明，至少有一些新的转录本可以成为功能相关的，从而突出了启动子的进化重要性，通过其双向转录的能力，新基因的出现。
The diversification of gene functions has been largely attributed to the process of gene duplication. Novel examples of genes originating from previously untranscribed regions have been recently described without regard to a unifying functional mechanism for their emergence. Here we propose a model mechanism that could generate a large number of lineage-specific novel transcripts in vertebrates through the activation of bidirectional transcription from unidirectional promoters. We examined this model in silico using human transcriptomic and genomic data and identified evidence consistent with the emergence of more than 1,000 primate-specific transcripts. These are transcripts with low coding potential and virtually no functional annotation. They initiate at less than 1 kb upstream of an oppositely transcribed conserved protein coding gene, in agreement with the generally accepted definition of bidirectional promoters. We found that the genomic regions upstream of ancestral promoters, where the novel transcripts in our dataset reside, are characterized by preferential accumulation of transposable elements. This enhances the sequence diversity of regions located upstream of ancestral promoters, further highlighting their evolutionary importance for the emergence of transcriptional novelties. By applying a newly developed test for positive selection to transposable element-derived fragments in our set of novel transcripts, we found evidence of adaptive evolution in the human lineage in nearly 3% of the novel transcripts in our dataset. These findings indicate that at least some novel transcripts could become functionally relevant, and thus highlight the evolutionary importance of promoters, through their capacity for bidirectional transcription, for the emergence of novel genes.
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影响因子：
3.3
作者：
Begun, David J.;Lindfors, Heather A.;Jones, Corbin D.
通讯作者：
Jones, Corbin D.
影响因子：
64.8
作者：
INGRAM, VM
通讯作者：
INGRAM, VM
影响因子：
7
作者：
Knowles, David G.;McLysaght, Aoife
通讯作者：
McLysaght, Aoife
DOI：
10.1073/pnas.0509809103
发表时间：
2006-06-27
影响因子：
11.1
作者：
Levine, Mia T.;Jones, Corbin D.;Begun, David J.
通讯作者：
Begun, David J.
影响因子：
64.8
作者：
NEI, M
通讯作者：
NEI, M