Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells.
Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells.
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DOI：
10.1371/journal.pcbi.1002755
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发表时间：
2012
影响因子：
4.3
通讯作者：
Tuller T
中科院分区：
文献类型：
--
作者：
Dana A;Tuller T
核糖体分析是一种很有前途的翻译研究方法。这种方法能够以单个核苷酸的分辨率监测沿着基因的核糖体密度沿着。在这项研究中，我们专注于小鼠胚胎干细胞的核糖体密度分布。我们的分析首次表明，即使在哺乳动物中，如M。在肌肉中，编码序列的决定因素如：1）密码子对tRNA库的适应; 2）编码序列的局部mRNA折叠; 3）密码子序列中编码的氨基酸的局部电荷显著且直接地影响延伸速度。此外，我们的分析表明，一般而言，核糖体的翻译速度在编码序列的开始处较慢，并且倾向于在下游增加。最后，将这些数据与预期的翻译生物物理行为进行比较表明，它存在一些未知的偏差。具体而言，在实验数据上测量的核糖体通量沿编码序列沿着增加;然而，根据缺乏内部起始位点的核糖体运动的任何生物物理模型，预期通量保持恒定或减少。因此，开发实验和/或统计方法来理解，检测和处理这种偏见是非常重要的。基因翻译是核糖体将mRNA分子翻译成蛋白质的过程，这是所有生物体的中心过程。因此，理解基因翻译的生物物理学及其效率在编码序列的不同特征中编码的方式对每个生物医学学科都有影响。最近，一种新的大规模的实验方法命名为“核糖体轮廓”，已被开发用于监测核糖体密度在单个核苷酸的分辨率。在这项研究中，我们分析了小鼠胚胎干细胞的核糖体谱数据。这些数据使我们能够直接表明翻译速度受到密码子对tRNA库的适应、编码序列的局部mRNA折叠以及编码序列中编码的氨基酸的局部电荷的影响。此外，我们的分析表明，核糖体的速度往往是在编码序列的开始较慢。最后，我们报告可能的偏见，在“核糖体分析”的程序，应考虑在未来的研究利用这种方法。
Ribosomal profiling is a promising approach with increasing popularity for studying translation. This approach enables monitoring the ribosomal density along genes at a resolution of single nucleotides. In this study, we focused on ribosomal density profiles of mouse embryonic stem cells. Our analysis suggests, for the first time, that even in mammals such as M. musculus the elongation speed is significantly and directly affected by determinants of the coding sequence such as: 1) the adaptation of codons to the tRNA pool; 2) the local mRNA folding of the coding sequence; 3) the local charge of amino acids encoded in the codon sequence. In addition, our analyses suggest that in general, the translation velocity of ribosomes is slower at the beginning of the coding sequence and tends to increase downstream. Finally, a comparison of these data to the expected biophysical behavior of translation suggests that it suffers from some unknown biases. Specifically, the ribosomal flux measured on the experimental data increases along the coding sequence; however, according to any biophysical model of ribosomal movement lacking internal initiation sites, the flux is expected to remain constant or decrease. Thus, developing experimental and/or statistical methods for understanding, detecting and dealing with such biases is of high importance. Gene translation is the process by which ribosomes translate mRNA molecules to proteins, a central process in all living organisms. Thus, understanding the biophysics of gene translation and the way its efficiency is encoded in the different features of the coding sequence has ramifications to every biomedical discipline. Recently, a new large-scale experimental approach named ‘ribosomal profiling’, has been developed for monitoring the ribosomal density at a resolution of single nucleotides. In this study, we analyzed ribosomal profiling data of mouse embryonic stem cells. These data enabled us to directly show that translation velocity is affected by the adaptation of codons to the tRNA pool, local mRNA folding of coding sequence, and local charge of the amino acids encoded in the coding sequence. In addition, our analyses suggest that ribosomal speed tends to be slower at the beginning of the coding sequence. Finally, we report possible biases in the ‘ribosomal profiling’ procedure that should be considered in future studies utilizing this method.
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影响因子：
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作者：
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影响因子：
5.6
作者：
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DOI：
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发表时间：
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影响因子：
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DOI：
10.1073/pnas.1016719108
发表时间：
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影响因子：
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通讯作者：
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DOI：
10.1126/science.1215110
发表时间：
2012-02-03
期刊：
Science (New York, N.Y.)
影响因子：
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通讯作者：
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