School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, Ireland.
RNA. 2018 Oct;24(10):1297-1304. doi: 10.1261/rna.065235.117. Epub 2018 Jul 26.
The process of translation is characterized by irregularities in the local decoding rates of specific mRNA codons. This includes the occurrences of long pauses that can take place when ribosomes decode certain peptide sequences, encounter strong RNA secondary structures, or decode "hungry" codons. Examples are known where such pausing or stalling is used for regulating protein synthesis. This can be achieved at the level of translation via direct alteration of ribosome progression through mRNA or by altering mRNA stability via NoGo decay. Ribosome pausing has also been implicated in the cotranslational folding of proteins. Ribosome profiling data often are used for inferring the locations of ribosome pauses. However, no dedicated online software is available for this purpose. Here we present PausePred (https://pausepred.ucc.ie/), which can be used to infer ribosome pauses from ribosome profiling (Ribo-seq) data. Peaks of ribosome footprint density are scored based on their magnitude relative to the background density within the surrounding area. The scoring allows the comparison of peaks across the transcriptome or genome. In addition to the score, PausePred reports the coordinates of the pause, the footprint density at the pause site, and the surrounding nucleotide sequence. The pauses can be visualized in the context of Ribo-seq and RNA-seq density plots generated for specific transcripts or genomic regions with the Rfeet tool. PausePred does not require input on the location of protein coding ORFs (although gene annotations can be optionally supplied). As a result, it can be used universally and its output does not depend on ever evolving annotations.
翻译过程的特点是特定 mRNA 密码子的局部解码率不规则。这包括核糖体在解码某些肽序列、遇到强 RNA 二级结构或解码“饥饿”密码子时可能发生的长时间停顿。已知有这种停顿或停滞用于调节蛋白质合成的例子。这可以通过直接改变核糖体通过 mRNA 的进展或通过改变 mRNA 稳定性来实现通过 NoGo 衰变。核糖体暂停也与蛋白质的共翻译折叠有关。核糖体图谱数据通常用于推断核糖体暂停的位置。然而，目前没有专门为此目的而设计的在线软件。在这里，我们提出了 PausePred（https://pausepred.ucc.ie/），它可以用于从核糖体图谱（Ribo-seq）数据中推断核糖体暂停。基于与周围区域内背景密度的相对大小，对核糖体足迹密度的峰进行评分。评分允许在转录组或基因组中比较峰。除了得分之外，PausePred 还报告暂停的坐标、暂停部位的足迹密度以及周围的核苷酸序列。可以使用 Rfeet 工具在特定转录物或基因组区域的 Ribo-seq 和 RNA-seq 密度图中可视化暂停。PausePred 不需要输入蛋白质编码 ORF 的位置（尽管可以选择提供基因注释）。因此，它可以通用使用，并且其输出不依赖于不断发展的注释。
