Ribosome profiling of HEK293T cells overexpressing codon optimized coagulation factor IX.
Ribosome profiling of HEK293T cells overexpressing codon optimized coagulation factor IX.
复制标题
DOI：
10.12688/f1000research.22400.2
复制
发表时间：
2020
期刊：
影响因子：
--
通讯作者：
Kimchi-Sarfaty C
中科院分区：
文献类型：
--
作者：
Alexaki A;Kames J;Hettiarachchi GK;Athey JC;Katneni UK;Hunt RC;Hamasaki-Katagiri N;Holcomb DD;DiCuccio M;Bar H;Komar AA;Kimchi-Sarfaty C
核糖体图谱为评估密码子水平的翻译动力学提供了机会。在这里，我们描述了来自两个HEK293T细胞系的核糖体图谱数据。核糖体图谱数据由RiBO-SEQ(核糖体保护片段的mRNA测序数据)和RNA-SEQ数据(总RNA测序)组成。这两个HEK293T细胞株各自表达一种版本的F9基因，这两种基因都被翻译成氨基酸序列相同的蛋白质。然而，这些F9基因在密码子的使用和预测的mRNA结构上有很大的不同。我们还提供了用于分析数据的管道。进一步分析该数据集具有巨大的潜力，因为它可以用于：一)揭示转录组的组成和调控；二)与其他核糖体图谱数据库进行比较；三)测量蛋白质组中蛋白质合成的速率并确定伸长率的差异；四)发现多肽的先前未知的翻译；五)探索密码子的使用或密码子环境在翻译动力学中的影响；六)研究共翻译折叠。重要的是，与其他可用的核糖体图谱数据相比，该数据集的一个独特特征是F9基因存在于两个非常不同的编码序列中。
Ribosome profiling provides the opportunity to evaluate translation kinetics at codon level resolution. Here, we describe ribosome profiling data, generated from two HEK293T cell lines. The ribosome profiling data are composed of Ribo-seq (mRNA sequencing data from ribosome protected fragments) and RNA-seq data (total RNA sequencing). The two HEK293T cell lines each express a version of the F9 gene, both of which are translated into identical proteins in terms of their amino acid sequences. However, these F9 genes vary drastically in their codon usage and predicted mRNA structure. We also provide the pipeline that we used to analyze the data. Further analyzing this dataset holds great potential as it can be used i) to unveil insights into the composition and regulation of the transcriptome, ii) for comparison with other ribosome profiling datasets, iii) to measure the rate of protein synthesis across the proteome and identify differences in elongation rates, iv) to discover previously unidentified translation of peptides, v) to explore the effects of codon usage or codon context in translational kinetics and vi) to investigate cotranslational folding. Importantly, a unique feature of this dataset, compared to other available ribosome profiling data, is the presence of the F9 gene in two very distinct coding sequences.