Abstract

Ribosome profiling (riboseq) has opened the possibilities for the genome-wide studies of translation in all living organisms. This method is based on deep sequencing of mRNA fragments protected by the ribosomes from hydrolysis by ribonucleases, the so-called ribosomal footprints (RFPs). Ribosomal profiling together with RNA sequencing allows not only to identify with a reasonable accuracy translated reading frames in the transcriptome, but also to track changes in gene expression in response to various stimuli. Notably, ribosomal profiling in its classical version has certain limitations. The size of the selected mRNA fragments is 25-35 nts, while RFPs of other sizes are usually omitted from analysis. Also, ribosomal profiling “averages” the data from all ribosomes and does not allow to study specific ribosomal complexes associated with particular translation factors. However, recently developed modifications of ribosomal profiling provide answers to a number of questions. Thus, it has become possible to analyze not only elongating, but also scanning and reinitiating ribosomes, to study events associated with the collision of ribosomes during mRNA translation, to discover new ways of cotranslational assembly of multisubunit protein complexes during translation, and to selectively isolate ribosomal complexes associated with certain protein factors. New data obtained using these modified approaches provide a better understanding of the mechanisms of translation regulation and the functional roles of translational apparatus components.

中文翻译：

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为翻译规则提供新数据的核糖体分析的修改

摘要

核糖体分析 (riboseq) 为在所有生物体中进行全基因组翻译研究开辟了可能性。该方法基于对受核糖体保护免受核糖核酸酶水解的 mRNA 片段的深度测序，即所谓的核糖体足迹 (RFP)。核糖体分析与 RNA 测序不仅可以以合理的准确度识别转录组中翻译的阅读框，还可以跟踪响应各种刺激的基因表达变化。值得注意的是，经典版本的核糖体分析有一定的局限性。所选 mRNA 片段的大小为 25-35 nts，而其他大小的 RFP 通常会从分析中省略。还，核糖体分析“平均”来自所有核糖体的数据，并且不允许研究与特定翻译因子相关的特定核糖体复合物。然而，最近开发的核糖体分析修改为许多问题提供了答案。因此，不仅可以分析延伸核糖体，还可以分析扫描和重新启动核糖体，研究与 mRNA 翻译过程中核糖体碰撞相关的事件，发现翻译过程中多亚基蛋白质复合物共翻译组装的新方法，以及选择性分离与某些蛋白质因子相关的核糖体复合物。使用这些修改后的方法获得的新数据可以更好地理解翻译调节机制和翻译装置组件的功能作用。