识别和可视化通过Ribo-Seq,转录组合和ggRibo的新型小型开放阅读框架 (sORFs)
Hsin-Yen Larry Wu1, Isaiah D Kaufman1, Polly Yingshan Hsu2
1Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA.
Methods in molecular biology (Clifton, N.J.)
|November 16, 2025
概括
我们开发了一种生物信息学管道,使用Ribo-seq数据找到和可视化小说翻译小开放阅读框架 (sORFs). 这种工具有助于揭示隐藏的sORF及其在基因调节中的功能.
科学领域:
- 基因组学就是基因组学.
- 分子生物学分子生物学
- 生物信息学是一种生物信息学.
背景情况:
- 小开放的读取框架 (sORFs) 对于细胞调节至关重要,但在基因组注释中经常被遗漏.
- sORFs的转化活性与非编码RNA生物发生和信号通路有关.
- 由于它们的小尺寸和缺乏正典特征,准确识别翻译的sORF是具有挑战性的.
研究的目的:
- 提出一种新的生物信息管道,用于从Ribo-seq数据中识别和可视化翻译的sORF.
- 为了能够在Arabidopsis中发现以前未被注释的sORFs.
- 为新型sORFs提供一个功能性特征的框架.
主要方法:
- 整合Ribo-seq/RNA-seq预处理和映射.
- 可选的转录组组件用于检测未注释的转录.
- 使用RiboTaper发现ORF,并使用ggRibo基因查看器进行可视化.
主要成果:
- 为Ribo-seq数据分析建立了一个全面的管道.
- 该管道有助于发现和高分辨率可视化翻译的sORFs.
- 在阿拉比多普西斯 (Arabidopsis) 发现隐藏的sORF的实用性已被证明.
结论:
- 开发的管道为系统的sORF识别和可视化提供了一个强大的方法.
- 这种方法有助于发现和未来对新型sORFs的功能研究.
- 该管道可适应在各种生物体中进行sORF发现.
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