IRescue:在单个细胞水平上对可转换元素表达的不确定性意识量化
Benedetto Polimeni1,2, Federica Marasca1, Valeria Ranzani1
1INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy.
Nucleic acids research
|September 13, 2024
概括
可转移元素 (TE) 是移动DNA序列. 一个新的工具,IRescue,量化了单细胞中TE亚家族的表达,揭示了它们在细胞多样性和疾病中的作用.
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:
- 可转移元素 (TE) 是移动DNA序列,影响真核生物基因组进化.
- TEs显示组织特异性转录,但它们在细胞多样性中的作用很难用单细胞RNA测序 (scRNA-seq) 来研究.
- 挑战包括TE无处不在和遗传相似性,使表达分析复杂化.
研究的目的:
- 介绍IRescue,一种用于量化可转换元素子家族表达在单细胞水平的新型软件.
- 克服scRNA-seq在分析不同组织和条件的TE表达方面的局限性.
- 将TE表达模式与细胞异质性和疾病状态联系起来.
主要方法:
- 开发了一种单细胞RNA测序分析工具IRescue.
- 实现了一个独特的 UMI 免复制算法来纠正序列错误.
- 使用预期最大化程序来实现准确的多映射读数重新分配.
主要成果:
- 使用模拟和真实scRNA-seq数据证明了IRescue的精度.
- 在SARS-CoV-2感染期间分析了人类结直肠癌,大脑,皮肤衰老和PBMC的数据.
- 将TE表达特征与特定的生物环境和疾病状况联系起来.
结论:
- 在单个单元格中,IRescue准确量化了可转换元素表达.
- TE表达模式提供了关于细胞异质性的见解.
- TE特征与特定的生物背景和疾病进展相关,突出显示了它们的功能相关性.
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