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长读Ribo-STAMP同时测量转录和翻译的异形分辨率

Pratibha Jagannatha^1,2,3,4, Alexandra T Tankka^1,2,3, Daniel A Lorenz⁵

¹Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA.

Genome research

|June 21, 2024

概括

我们开发了长时间读取的Ribo-STAMP (LR-Ribo-STAMP) 来在异形水平上描述mRNA翻译. 这种方法揭示了在不同氧气条件下,三阴性乳腺癌细胞中的基因表达和翻译如何转变.

科学领域:

分子生物学分子生物学
基因组学就是基因组学.
癌症研究癌症研究

背景情况:

转录和翻译是基本的生物过程,mRNA异型作为关键中间体.
目前的方法在分析mRNA异形水平的翻译方面存在局限性,这阻碍了对基因调节的全面理解.
现有的技术往往无法捕捉不同mRNA变异的翻译控制的全部频谱.

研究的目的:

开发一个集成的计算和实验框架,以在基因和mRNA异型水平上同时对转录和翻译进行分析.
引入一种新型指标,EditsC,用于使用单分子全长转录数据量化RNA编辑.
调查翻译法规及其与上游开放阅读框架 (uORF) 等监管特征的联系.

主要方法:

开发长读Ribo-STAMP (LR-Ribo-STAMP),将长读测序与RNA基编辑相结合.
在基因和mRNA异形水平上同时对转录和翻译进行分析.
应用EditsC指标来量化RNA编辑事件.

主要成果:

在基因层面上,LR-Ribo-STAMP证明了与现有的短读方法的一致性.
该框架成功地分析了mRNA异形翻译,并将uORF等监管元素与翻译联系起来.
在正常氧和缺氧下对三阴性乳腺癌细胞的分析揭示了明显的转录和转化转变,LR-Ribo-STAMP有效地划分了这些变化.
发现了区分异构体水平转化差异的特定调节元素,以GRK6为例,其中缺氧促进了截断的蛋白质异构体.

结论:

LR-Ribo-STAMP提供了一种强大的新方法,用于测量具有高异型敏感性的mRNA翻译.
该框架使得在基因和mRNA异型水平上发现新的调节机制成为可能.
这一进步为复杂的生物过程和癌症等疾病中的基因调节提供了更深入的见解.

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