相关实验视频

Updated: Jul 13, 2025

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

在长时间读取的RNA测序数据中识别和量化小的含有外子子的异型

Zhen Liu^1,2, Chenchen Zhu³, Lars M Steinmetz^3,4

¹Lingang Laboratory, Shanghai, Shanghai 200031, China.

Nucleic acids research

|October 16, 2023

概括

我们开发了MisER,这是一种新方法,可以在长时间读取的RNA测序数据中准确量化小外子. 这种工具有助于分析涉及微外显子的基因调节,特别是在神经组织中.

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:

小型外子,包括微外子 (≤30个核酸),在基因转录组中很常见,对基因功能至关重要.
使用牛津纳米孔技术 (ONT) 的长读RNA测序 (RNA-seq) 提供了完整的转录覆盖,但由于基准精度较低,在准确量化小异构体方面面临挑战.
含有小异构体的错位读取可能导致不准确的转录量化.

研究的目的:

开发和验证一种计算方法,以提高ONT长时间读取的RNA-seq数据中的小外子的量化.
为了评估 misaligned 读数对小 exon 量化的影响.
识别新的神经特异性微子和了解它们的调节作用.

主要方法:

使用合成和人类ONT RNA-seq数据集对小型外子子量化的系统评估.
开发MisER (不对齐的外显子重映射器),一种局部调整方法来纠正含有小外显子的不对齐的读数.
使用合成和模拟数据集验证MisER的敏感性和特异性.
在14个神经和16个非神经人体组织中比较微埃克森百分比拼接 (PSI) 指数.

主要成果:

含有小外子的读数在标准ONTRNA-seq分析中经常错位,从而损害了转录量化.
MisER有效地重新映射了错位的读数,证明了高灵敏度和特异性,用于量化具有小外型子的转录.
与非神经组织相比,MisER发现神经组织中微子子的百分比拼接 (PSI) 指数高于非神经组织中的微子子,突出了神经特异性的微子子调节.
该方法有助于发现功能相关的小外体.

结论:

MisER显著提高了从ONT长时间读取的RNA-seq数据中小外子量化的准确性.
这一进步对于研究涉及小微子的基因调节至关重要,特别是在神经生物学中.
这些发现为研究人员研究转录异形变异及其功能影响,特别是神经发育和功能的研究提供了宝贵的工具.

更多相关视频

Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms

Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms

Published on: February 2, 2024

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

Published on: December 9, 2016

相关概念视频

Ribosome Profiling

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...

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...