Putatively noncoding transcripts show extensive association with ribosomes.
Putatively noncoding transcripts show extensive association with ribosomes.
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DOI：
10.1093/gbe/evr099
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发表时间：
2011
影响因子：
3.3
通讯作者：
Masel J
中科院分区：
文献类型：
--
作者：
Wilson BA;Masel J
最近有令人惊讶的报道称，整个基因可以从非编码序列从头进化而来。如果非编码序列在氨基酸身份方面是随机的，这将是非同寻常的。然而，如果非编码序列先前以低速率翻译，并且通过选择清除了最强烈有害的隐多肽，那么从头开始的基因起源将更有可能。在这里，我们分析了与核糖体相关的酿酒酵母非编码转录物的数据。我们找到了很多这样的抄本。尽管它们的平均核糖体密度低于蛋白质编码基因，但很大比例的非编码转录物的核糖体密度与编码基因相当。大多数核糖体在饥饿反应中表现出增加的核糖体关联，正如先前报道的其他非编码序列，如非翻译区和内含子。在富介质中，核糖体关联与起始密码子相关，但除此之外通常不一致和连续，这表明翻译仅在低速率下发生。其中一个转录本包含一个28个密码子的开放阅读框，我们将其命名为RDT1，它显示了翻译的证据，可能是一个新的蛋白质编码基因，从非编码序列中重新产生。但是大部分核糖体关联不能归因于未注释的蛋白质编码基因。我们的主要发现广泛的核糖体关联表明，选择性清除的必要先决条件得到满足，使从头开始的基因进化更加合理。我们的分析也证明了核糖体分析数据用于基因注释的原理。
There have been recent surprising reports that whole genes can evolve de novo from noncoding sequences. This would be extraordinary if the noncoding sequences were random with respect to amino acid identity. However, if the noncoding sequences were previously translated at low rates, with the most strongly deleterious cryptic polypeptides purged by selection, then de novo gene origination would be more plausible. Here we analyze Saccharomyces cerevisiae data on noncoding transcripts found in association with ribosomes. We find many such transcripts. Although their average ribosomal densities are lower than those of protein-coding genes, a significant proportion of noncoding transcripts nevertheless have ribosomal densities comparable to those of coding genes. Most show increased ribosomal association in response to starvation, as has been previously reported for other noncoding sequences such as untranslated regions and introns. In rich media, ribosomal association is correlated with start codons but is not usually consistent and contiguous beyond that, suggesting that translation occurs only at low rates. One transcript contains a 28-codon open reading frame, which we name RDT1, which shows evidence of translation, and may be a new protein-coding gene that originated de novo from noncoding sequence. But the bulk of the ribosomal association cannot be attributed to unannotated protein-coding genes. Our primary finding of extensive ribosome association shows that a necessary precondition for selective purging is met, making de novo gene evolution more plausible. Our analysis is also proof of principle of the utility of ribosomal profiling data for the purpose of gene annotation.
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DOI：
10.1038/nrg2487
发表时间：
2009-01
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
通讯作者：
--
影响因子：
4.3
作者：
Li CY;Zhang Y;Wang Z;Zhang Y;Cao C;Zhang PW;Lu SJ;Li XM;Yu Q;Zheng X;Du Q;Uhl GR;Liu QR;Wei L
通讯作者：
Wei L
影响因子：
44.1
作者：
Li, Dan;Dong, Yang;Wang, Wen
通讯作者：
Wang, Wen
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：
7
作者：
Knowles, David G.;McLysaght, Aoife
通讯作者：
McLysaght, Aoife