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Updated: Jul 2, 2025

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

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Published on: August 3, 2018

纠正4sU诱导的核酸转换RNA-seq数据中的量化偏差

Kevin Berg^1,2, Manivel Lodha², Isabel Delazer³

¹Chair of Computational Immunology, University of Regensburg, Regensburg, Germany.

Nucleic acids research

|February 21, 2024

概括

在RNA标记过程中,高度的4-thiouridine (4sU) 可能会影响表达估计. 这项研究开发了计算工具,以纠正核酸转换RNA测序数据中的这些偏差.

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:

核酸类类似物如4-thiouridine (4sU) 能够对新合成的RNA进行代谢标记.
将4sU转化为C:T不匹配的化学转换允许同时对总和标记的RNA表达进行分析.
潜在的细胞毒性和广泛的4sU标记对RNA-seq表达估计的影响仍未得到充分研究.

研究的目的:

为了研究4 - 氨酸 (4sU) 剂量升级和延长标记时间对核酸转化RNA测序中的表达估计的影响.
为了确定由广泛的4sU标签引起的表达偏差背后的机制.
开发用于纠正这些偏差的计算和统计方法.

主要方法:

核酸转化RNA测序使用不同度和时间的4sU标记在不同的细胞系进行.
分析的重点是确定与RNA半衰期相关的表达估计中的偏差.
开发一种用于拯救无法映射的读取的计算工具以及用于偏差校正的统计方法.

主要成果:

表达率估计在高4sU度或以后的时间点上以RNA半衰期依赖的方式偏差.
偏差是由于图书馆准备过程中读取可映射性降低,多次转换和标记RNA不足.
一个新的计算工具改善了读取映射,一个统计方法有效地消除了剩余的偏差.

结论:

广泛的4-thiouridine标签可以在RNA测序表达估计中引入显著的偏差.
已开发的计算和统计方法,集成到GRAND-SLAM管道和grandR包中,可以准确地纠正这些偏差.
这些进展使得使用核酸转换RNA-seq. 的新合成RNA能够更可靠地量化.

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相关概念视频

RNA-seq

RNA-seq

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...