虫 Perturb-Seq:大规模并行全动物RNAi和RNA-seq.
Hefei Zhang1, Xuhang Li1, Dongyuan Song2
1Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
bioRxiv : the preprint server for biology
|February 20, 2025
概括
虫扰乱测序 (WPS) 能够对活体动物中的基因扰乱进行高分辨率的RNA测序. 这种方法与EmpirDE分析框架相结合,揭示了基因调节网络,在C. elegans中具有新的对式模块化.
科学领域:
- 基因组学就是基因组学.
- 分子生物学分子生物学
- 系统生物学 系统生物学
背景情况:
- 转录组是一个关键的分子表型,将基因型与表型联系起来,通常通过RNA测序 (RNA-seq) 来测量.
- 扰乱每个基因和测量转录基因变化是一个目标,但在完整的生物体中具有挑战性.
- 现有的方法面临实验和计算的障碍,大规模扰动分析.
研究的目的:
- 介绍Worm Perturb-Seq (WPS),一种高分辨率RNA-seq的方法,可以在体内复制多种乱.
- 介绍EmpirDE,一个针对大型WPS数据集设计的分析框架,用于识别差异表达基因 (DEG).
- 应用WPS和EmpirDE来划分一个基因调控网络 (GRN) 对于Caenorhabditis elegans核激素受体 (NHRs).
主要方法:
- WPS结合了大量和单细胞RNA-seq的实验进步,用于活体动物的高通量分析.
- EmpirDE利用基因特异性的实证零分布来识别DEG,消除技术偏差并增强统计的严谨性.
- 该方法应用于103个C. elegans的NHR,以构建一个GRN.
主要成果:
- WPS为数百个重复扰动同时提供高分辨率的RNA-seq配置文件.
- 通过利用经验式零分布,EmpirDE有效地识别了DEG,从而提高了统计能力.
- 对C. elegans中103个NHR的分析揭示了一种具有显著"对式模块化"的GRN,其中NHR对共同调节基因.
结论:
- 在活体中,WPS为大规模的基因扰动研究提供了强大的方法.
- 该EmpirDE框架增强了从大型转录组数据集的DEG分析的统计稳定性.
- 在NHR GRN中发现的对式模块化为C. elegans和潜在的其他模型系统 (包括人类细胞) 中的基因调节提供了新的见解.
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