InPACT:一种计算方法,用于从RNA测序数据中准确地表征内部多化
Xiaochuan Liu1, Hao Chen2, Zekun Li1
1The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
Nature communications
|March 23, 2024
概括
一种新的计算方法InPACT准确地识别了从RNA-seq数据中的内基多化 (IPA) 转录. 该工具揭示了人类细胞中的新型IPA事件,并提供了对细胞过程和疾病的见解.
科学领域:
- 分子生物学分子生物学
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
背景情况:
- 替代多基化 (APA) 是一个关键的转录后调节机制.
- 内部多基化 (IPA) 是一种APA形式,可以产生非编码或截断的转录,影响基因表达和疾病.
- 准确地描述IPA对于理解其生物作用至关重要.
研究的目的:
- 从标准RNA-seq数据开发和验证一种计算方法,以精确地表征内部多基化 (IPA).
- 识别新的IPA事件并评估它们的生物相关性和翻译潜力.
主要方法:
- 开发InPACT,这是IPA识别和量化的一种新型计算工具.
- 应用InPACT来分析来自人类细胞的常规RNA-seq数据.
- 验证使用核糖体分析数据来评估转录翻译.
- 在单细胞激活和从人类胎儿骨髓单细胞RNA-seq数据中分析IPA.
主要成果:
- 在人类细胞中,InPACT成功地识别了许多以前未被注释的IPA转录.
- 发现这些新型IPA转录的很大一部分是翻译的.
- 与现有方法相比,InPACT在IPA识别和量化方面表现优越.
- 分析显示,在单细胞激活过程中出现了临时协调的IPA事件,以及胎儿骨髓中的特定环境IPA异型表达.
结论:
- InPACT 是一种强大而准确的计算工具,用于从RNA-seq数据中表征内基多化.
- 该方法有助于发现新的,生物相关的IPA事件.
- InPACT提供了关于IPA在细胞过程,发育和疾病背景中的作用的宝贵见解.
相关概念视频
02:15Experimental RNAi
6.1K
RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
6.1K
03:21RNA-seq
9.9K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
9.9K
02:01pre-mRNA Processing
52.9K
In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a “cap” to the 5’ end of the growing transcript. In this process, a 5’ phosphate is replaced by modified guanosine that has a methyl group attached to it (7-Methyl...
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a “cap” to the 5’ end of the growing transcript. In this process, a 5’ phosphate is replaced by modified guanosine that has a methyl group attached to it (7-Methyl...
52.9K