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Nonsense-mediated mRNA Decay

Nonsense-mediated mRNA Decay

The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...

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相关实验视频

Updated: Jun 18, 2025

Differentiation of a Human Neural Stem Cell Line on Three Dimensional Cultures, Analysis of MicroRNA and Putative Target Genes

Differentiation of a Human Neural Stem Cell Line on Three Dimensional Cultures, Analysis of MicroRNA and Putative Target Genes

Published on: April 12, 2015

NMDtxDB:对人类NMD目标转录的数据驱动识别和注释.

Thiago Britto-Borges^1,2, Niels H Gehring^3,4, Volker Boehm^3,4

¹Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III and Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg University Hospital, 69120 Heidelberg, Germany.

RNA (New York, N.Y.)

|August 2, 2024

概括

这项研究引入了一种数据驱动的方法,用于识别无意义介导RNA衰变 (NMD) 目标转录. NMDtxDB数据库提供了一个全面的资源,用于研究NMD敏感RNA及其调节.

关键词:

替代性拼接是一种替代性的拼接.计算工作流的计算工作流.在mRNA衰变过程中.无意义介导的RNA衰变过早停止 codon 的时间.

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Detection of miRNA Targets in High-throughput Using the 3'LIFE Assay

Detection of miRNA Targets in High-throughput Using the 3'LIFE Assay

Published on: May 25, 2015

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

相关实验视频

Last Updated: Jun 18, 2025

Differentiation of a Human Neural Stem Cell Line on Three Dimensional Cultures, Analysis of MicroRNA and Putative Target Genes

Differentiation of a Human Neural Stem Cell Line on Three Dimensional Cultures, Analysis of MicroRNA and Putative Target Genes

Published on: April 12, 2015

Detection of miRNA Targets in High-throughput Using the 3'LIFE Assay

Detection of miRNA Targets in High-throughput Using the 3'LIFE Assay

Published on: May 25, 2015

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

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:

无意义介导的RNA衰变 (NMD) 途径对于mRNA质量控制至关重要.
目前的NMD基质RNA注释依赖于一般规则而不是经验数据.

研究的目的:

开发一个数据驱动的工作流程来识别NMD目标转录.
创建一个全面的数据库 (NMDtxDB) 的NMD敏感的转录.

主要方法:

利用纳米孔和Illumina测序来进行转录组装.
集成了来自Ensembl,Gencode和OpenProt的编码序列信息,以增强注释.
在四个细胞系中执行了SMG5,SMG6和SMG7基因的淘汰/淘汰.

主要成果:

组装了302,889个成绩单,其中24%不在Ensembl注释中.
确定了48,213个含有过早停止编码子的转录.
发现6433个转录在NMD缺乏细胞和NMD活性细胞中显著上调.

结论:

NMDtxDB数据库提供了对NMD敏感转录的深入查看.
该研究为NMD研究提供了一个开源的分析工作流和Web应用程序.
这项工作提高了对NMD目标的理解和注释.