Capturing the interactome of newly transcribed RNA
Xichen Bao1,2, Xiangpeng Guo1,2, Menghui Yin3
1Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, and Guangzhou Medical University, Guangzhou, China.
Nature Methods
|February 13, 2018
Summary
We developed a new method, capture of the newly transcribed RNA interactome using click chemistry (RICK), to identify proteins bound to newly transcribed RNAs. RICK reveals novel RNA-binding proteins and their functions in cells.
Area of Science:
- Molecular Biology
- Biochemistry
- Genomics
Background:
- Understanding the RNA-bound proteome is crucial for cellular function.
- Existing methods often neglect nascent and nonpolyadenylated RNAs.
- Characterizing these neglected RNA populations is essential for a complete cellular picture.
Purpose of the Study:
- To develop a novel method for capturing and identifying proteins bound to newly transcribed RNAs.
- To systematically analyze the interactome of nascent and nonpolyadenylated RNAs.
- To expand the known RNA-bound proteome in mouse embryonic stem cells.
Main Methods:
- Utilized 5-ethynyluridine labeling to tag newly transcribed RNAs.
- Employed click chemistry for the capture of RNA-protein complexes.
- Named the approach capture of the newly transcribed RNA interactome using click chemistry (RICK).
Main Results:
- RICK successfully captured proteins bound to nascent and nonpolyadenylated RNAs.
- Identified novel RNA-binding proteins, including mitotic regulators with affinity for nonpolyadenylated RNAs.
- Revealed connections between metabolic enzymes/factors and nascent RNAs.
- Expanded the catalog of RNA-bound proteins in mouse embryonic stem cells.
Conclusions:
- RICK is an effective method for interrogating the total RNA-bound proteome.
- The approach facilitates the study of RNA-protein interactions in diverse cellular contexts.
- This work provides new insights into the regulation of gene expression by RNA-binding proteins.
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