通过组装RNA-seq和小RNA-seq数据,对长非编码RNA进行深度注释
Jiaming Zhang1, Weibo Hou2, Qi Zhao3
1Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China; Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
The Journal of biological chemistry
|August 5, 2023
概括
这项研究引入了一个新的计算管道,RNA-seq和小RNA-seq联合策略 (RSCS),用于改进长非编码RNA (lncRNA) 特性. 该RSCS方法增强了转录组注释,并识别了新的lncRNAs,包括与内源性逆转录病毒相关的和对胚胎发生至关重要的那些.
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:
- 长非编码RNA (lncRNAs) 在生物过程中起着至关重要的作用.
- 由于表达水平较低,对lncRNAs的系统性表征具有挑战性.
研究的目的:
- 开发和验证一个计算管道,用于全面的转录注释.
- 识别新型lncRNA并了解它们的功能,特别是与内源性逆转录病毒相关的功能.
主要方法:
- 开发一种新的计算管道:RNA-seq和小RNA-seq联合策略 (RSCS).
- 在多种不同的细胞环境中应用RSCS用于转录注释.
- 通过分析结构,基质组成,序列复杂性和监管模式来验证已识别的转录.
主要成果:
- 使用RSCS识别了成千上万个具有高可信度的潜在新型转录.
- 验证转录完整性,包括全长状态.
- 发现了许多内源性逆转录病毒相关的 lncRNAs.
- 鉴定了一种对Yap1表达和早期胚胎发生至关重要的新型内源逆转录病毒-lncRNA.
结论:
- 该RSCS管道产生一个更完整和精确的转录组注释.
- 这一发现显著扩大了已知的哺乳动物转录基因组注释.
- 这项研究强调了 lncRNAs,包括新型逆转录病毒相关的,在胚胎生成等基本生物过程中的重要性.
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