通过测序来绘制RNA-蛋白关联的全基因组映射
Zhijie Qi1, Shuanghong Xue1, Junchen Chen2
1Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA.
Nature biotechnology
|September 9, 2025
概括
我们开发了PRIM-seq,这是一种新的测序方法,用于识别RNA结合蛋白及其相关RNAs. 这种方法绘制了成千上万的RNA-蛋白相互作用图,揭示了对基因调节的新见解.
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:
- RNA-蛋白相互作用对于基因表达和细胞功能至关重要.
- 由于RNA和蛋白质的结构多样性,很难对这些相互作用进行全面的映射.
- 现有的方法通常需要基因或蛋白质特定的试剂,限制了广泛的应用.
研究的目的:
- 引入一种新的方法,PRIM-seq (通过测序绘制蛋白-RNA相互作用图),用于同时识别RNA结合蛋白及其相关RNAs.
- 在不需要特定试剂的情况下构建一个全面的人类RNA-蛋白关联网络 (HuRPA).
- 为了使RNA结合蛋白及其标的系统发现和优先级.
主要方法:
- PRIM-seq利用近距离结合,从RNA和蛋白质链接的DNA条形码中生成独特的化学DNA序列.
- 这些模拟序列通过高通量测序来解码.
- 该方法应用于两个人类细胞系,以建立HuRPA网络.
主要成果:
- 人类RNA-蛋白关联网络 (HuRPA) 被构建,详细介绍了大约7000个RNA和11000个蛋白之间的超过35万个关联.
- 确定了2610种与至少10种不同的RNA相互作用的蛋白质.
- 实验验证了与瘤发生相关的lincRNA LINC00339和染色质调节剂 (SMC1A,SMC3,RAD21) 和代谢酶PHGDH的RNA关联能力.
结论:
- PRIM-seq是一种有效的方法,用于重新识别RNA结合蛋白及其RNA标.
- 开发的HuRPA网络为了解人类的RNA-蛋白相互作用提供了宝贵的资源.
- PRIM-seq促进了对RNA结合蛋白和点的系统发现和优先排序,而无需事先的知识或特定的试剂.
相关概念视频
03:21RNA-seq
11.8K
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...
11.8K
02:24Ribosome Profiling
4.1K
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...
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...
4.1K
02:26Protein Networks
4.5K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.5K
01:33Proteomics
9.4K
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
9.4K