a Balavatnick School of Computer Science , Tel Aviv University , Tel Aviv , Israel.
b Department of Biomedical Engineering , Tel Aviv University , Tel Aviv , Israel.
RNA Biol. 2018 Jan 2;15(1):81-94. doi: 10.1080/15476286.2017.1384118. Epub 2017 Nov 22.
The two major steps of gene expression are transcription and translation. While hundreds of studies regarding the effect of sequence features on the translation elongation process have been published, very few connect sequence features to the transcription elongation rate. We suggest, for the first time, that short transcript sub-sequences have a typical effect on RNA polymerase (RNAP) speed: we show that nucleotide 5-mers tend to have typical RNAP speed (or transcription rate), which is consistent along different parts of genes and among different groups of genes with high correlation. We also demonstrate that relative RNAP speed correlates with mRNA levels of endogenous and heterologous genes. Furthermore, we show that the estimated transcription and translation elongation rates correlate in endogenous genes. Finally, we demonstrate that our results are consistent for different high resolution experimental measurements of RNAP densities. These results suggest for the first time that transcription elongation is partly encoded in the transcript, affected by the codon-usage, and optimized by evolution with a significant effect on gene expression and organismal fitness.
基因表达的两个主要步骤是转录和翻译。虽然已经发表了数百项关于序列特征对翻译延伸过程影响的研究，但很少有研究将序列特征与转录延伸率联系起来。我们首次提出，短转录子亚序列对 RNA 聚合酶（RNAP）速度有典型的影响：我们表明，核苷酸 5 mers 往往具有典型的 RNAP 速度（或转录率），这在不同基因的不同部分以及具有高相关性的不同基因群之间是一致的。我们还证明，相对 RNAP 速度与内源性和异源基因的 mRNA 水平相关。此外，我们表明，内源性基因中估计的转录和翻译延伸率相关。最后，我们证明我们的结果与不同的 RNAP 密度高分辨率实验测量一致。这些结果首次表明，转录延伸在一定程度上是由转录本编码的，受密码子使用的影响，并通过进化进行优化，对基因表达和生物体适应性有显著影响。
