AUG_hairpin: prediction of a downstream secondary structure influencing the recognition of a translation start site.
AUG_hairpin: prediction of a downstream secondary structure influencing the recognition of a translation start site.
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DOI：
10.1186/1471-2105-8-318
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发表时间：
2007-08-30
影响因子：
3
通讯作者：
Kolchanov NA
中科院分区：
文献类型：
--
作者：
Kochetov AV;Palyanov A;Titov II;Grigorovich D;Sarai A;Kolchanov NA
翻译起始位点对真核mrna的翻译效率起着重要的控制作用。真核核糖体对起始AUG密码子的识别被认为取决于其核苷酸背景。然而，在次优环境下具有起始密码子的真核mrna的比例相对较大。可以预期，mRNA应该具有一些提供有效翻译的特征，包括正确识别翻译起始位点。实验表明，位于起始密码子特定位置的下游发夹可以部分补偿次优的AUG上下文，并且还可以增加非AUG起始密码子的翻译。这种补偿性发夹的预测可能有助于评估真核mRNA的翻译特性。我们评估了CDS起始密码子上下文与mRNA二级结构之间的相互依赖性：发现次优起始密码子上下文与人类和小鼠mRNA CDS第13 - 17位碱基配对概率显著相关。这可能是下游发夹被用来增强一些哺乳动物mrna在体内的翻译。因此，我们开发了一种工具，AUG_hairpin，用于预测位于mRNA编码部分开始的定义区域内的局部茎环结构。所实现的算法是基于现有的已发表的关于位于cds位置的茎环结构影响上游起始密码子识别的实验数据。在次优环境下，起始AUG密码子下游（或潜在的非AUG起始密码子下游）可能出现潜在的二级结构，这可能为研究人员提供了一个可验证的假设，即存在影响mRNA翻译起始率和起始密码子选择的额外调节信号。AUG_hairpin具有方便的web界面和可调整的参数，将使这样的评估变得简单和高效。
The translation start site plays an important role in the control of translation efficiency of eukaryotic mRNAs. The recognition of the start AUG codon by eukaryotic ribosomes is considered to depend on its nucleotide context. However, the fraction of eukaryotic mRNAs with the start codon in a suboptimal context is relatively large. It may be expected that mRNA should possess some features providing efficient translation, including the proper recognition of a translation start site. It has been experimentally shown that a downstream hairpin located in certain positions with respect to start codon can compensate in part for the suboptimal AUG context and also increases translation from non-AUG initiation codons. Prediction of such a compensatory hairpin may be useful in the evaluation of eukaryotic mRNA translation properties. We evaluated interdependency between the start codon context and mRNA secondary structure at the CDS beginning: it was found that a suboptimal start codon context significantly correlated with higher base pairing probabilities at positions 13 – 17 of CDS of human and mouse mRNAs. It is likely that the downstream hairpins are used to enhance translation of some mammalian mRNAs in vivo. Thus, we have developed a tool, AUG_hairpin, to predict local stem-loop structures located within the defined region at the beginning of mRNA coding part. The implemented algorithm is based on the available published experimental data on the CDS-located stem-loop structures influencing the recognition of upstream start codons. An occurrence of a potential secondary structure downstream of start AUG codon in a suboptimal context (or downstream of a potential non-AUG start codon) may provide researchers with a testable assumption on the presence of additional regulatory signal influencing mRNA translation initiation rate and the start codon choice. AUG_hairpin, which has a convenient Web-interface with adjustable parameters, will make such an evaluation easy and efficient.
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遗传密码产生的mRNA二级结构的周期性模式。
影响因子：
14.9
作者：
Shabalina, Svetlana A.;Ogurtsov, Aleksey Y.;Spiridonov, Nikolay A.
通讯作者：
Spiridonov, Nikolay A.
影响因子：
3.8
作者：
Hwang, WL;Su, TS
通讯作者：
Su, TS
DOI：
10.1016/s0006-291x(02)02579-2
发表时间：
2002-11-22
影响因子：
3.1
作者：
Kobayashi, Y;Dokiya, Y;Sugita, M
通讯作者：
Sugita, M
影响因子：
10.5
作者：
Pisarev, AV;Kolupaeva, VG;Pestova, TV
通讯作者：
Pestova, TV
影响因子：
2.9
作者：
MCCASKILL, JS
通讯作者：
MCCASKILL, JS