翻译签名分数:数据驱动的方法来评估积极翻译的证据
Devika Menon1,2, Owen Rackham1,3, Sonia Chothani4,5
1Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, Singapore.
Methods in molecular biology (Clifton, N.J.)
|November 16, 2025
概括
从小型开放式读取框架 (smORF) 中识别微蛋白是具有挑战性的. 翻译签名方法使用聚合的核糖体分析数据来稳定地识别真正翻译的smORF,帮助基因组注释.
科学领域:
- 基因组学就是基因组学.
- 蛋白质组学是指蛋白质组学.
- 分子生物学分子生物学
背景情况:
- 小开放式读取框架 (smORF) 编码具有潜在生理作用的微蛋白,但很难识别,并且经常被排除在基因组注释之外.
- 核糖体分析 (Ribo-seq) 已经揭示了成千上万的新型ORF,但由于数据的变化,将真正的smORF与噪声区分开来是具有挑战性的.
研究的目的:
- 描述一种强大的方法,即翻译签名方法,用于识别和优先考虑翻译的smORF.
- 为分析大规模的核糖体分析数据提供一个框架,以发现新型微蛋白.
主要方法:
- 利用聚合的核糖体分析 (Ribo-seq) 数据,以增强对个人ORF中翻译的可视化.
- 开发了翻译签名分数,将P站点纳入框架,统一性和掉落指标.
- 使用注释的蛋白质编码ORF作为参考,以建立主动翻译的预期得分范围.
主要成果:
- 翻译签名方法可以更清晰地可视化和量化smORF中的翻译证据.
- 优先考虑的新型ORF显示翻译签名得分,表明正在进行翻译.
- 建立了一个网络资源,用于访问使用此工作流识别的默认smORFs集.
结论:
- 翻译签名方法为识别由smORFs编码的微蛋白提供了一个强大的框架.
- 这种方法通过可靠地检测新的翻译区域来提高基因组注释的准确性.
- 高质量的Ribo-seq数据的可用性增加将进一步加强这种微蛋白发现方法.
相关概念视频
02:07Improving Translational Accuracy
14.0K
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
14.0K
02:07Improving Translational Accuracy
3.5K
3.5K
02:28Leaky Scanning
5.6K
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R...
5.6K
02:24Ribosome Profiling
4.0K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
4.0K
02:33Initiation of Translation
38.2K
Initiating translation is complex because it involves multiple molecules. Initiator tRNA, ribosomal subunits, and eukaryotic initiation factors (eIFs) are all required to assemble on the initiation codon of mRNA. This process consists of several steps that are mediated by different eIFs.
First, the initiator tRNA must be selected from the pool of elongator tRNAs by eukaryotic initiation factor 2 (eIF2). The initiator tRNA (Met-tRNAi) has conserved sequence elements including modified bases at...
First, the initiator tRNA must be selected from the pool of elongator tRNAs by eukaryotic initiation factor 2 (eIF2). The initiator tRNA (Met-tRNAi) has conserved sequence elements including modified bases at...
38.2K
02:33Initiation of Translation
7.8K
7.8K