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Updated: May 13, 2025

Global Identification of Co-Translational Interaction Networks by Selective Ribosome Profiling

Global Identification of Co-Translational Interaction Networks by Selective Ribosome Profiling

Published on: October 7, 2021

RIBOSS通过结合长短读取的转录组和转录组分析概况来检测新的翻译事件

Chun Shen Lim^1,2, Alexandra K Gibbon^1,2, Anh Thu Tran Nguyen^1,2

¹Department of Biochemistry, School of Biomedical Sciences, University of Otago, 710 Cumberland Street, Dunedin North, Dunedin 9016, New Zealand.

Briefings in bioinformatics

|April 13, 2025

概括

RIBOSS是一个新的计算管道,使用核糖体分析识别新的,可翻译的开放阅读框架 (ORF). 它增强了在细菌和真核生物基因组中的ORF发现,即使有不完整的注释.

科学领域:

基因组学就是基因组学.
生物信息学是一种生物信息学.
分子生物学分子生物学

背景情况:

核糖体分析捕捉了RNA上的核糖体位置,从而推进了转基因组分析.
检测翻译的开放阅读框架 (ORF) 是至关重要的,但基因组注释往往不完整,特别是在细菌转录开始/终结地点.
这限制了在未被翻译的地区发现新的ORF的可能性.

研究的目的:

开发一个计算管道,RIBOSS,用于发现非正规的ORF并评估它们的翻译潜力.
使用RIBOSS.分析原生生物和真核生物数据.
为了证明RIBOSS在有不完整转录组注释的生物中的实用性.

主要方法:

使用Python模块开发RIBOSS计算管道.
对Homo sapiens,Arabidopsis thaliana和Salmonella enterica的核糖体分析数据进行分析.
整合长读和短读测序数据用于转录组组装和ORF检测.

主要成果:

确定在人类,植物和细菌物种中具有高转化潜力的非正规ORF清单.
证明RIBOSS在分析具有有限转录组注释的生物体中的有效性,例如S. enterica.
成功应用RIBOSS以使用组合测序技术检测新型转化事件.

结论:

RIBOSS是第一个用于非正规ORF检测和转化潜力评估的集成计算管道.
管道有效地结合了长读和短读测序技术来调查翻译.
RIBOSS是免费可用的,并增强了新型ORF的系统发现.

关键词:

纳米孔长读直接RNA测序基因注释基因注释蛋白质合成蛋白质合成核糖体造型分析方法分析方法.转录基因组组合组件

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