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Proteomic Profiling of Messenger Ribonucleoproteins in Mouse Tissues Based on Formaldehyde Cross-Linking
Jiankun Wang1, Jialin Liu1, Rongbing Huang1
1College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China.
Abstract:
Messenger ribonucleoprotein particles (mRNPs) are vital for tissue-specific gene expression via mediating posttranscriptional regulations. However, proteomic profiling of proteins in mRNPs, i.e., mRNA-associated proteins (mRAPs), has been challenging at the tissue level. Herein, we report the development of formaldehyde cross-linking-based mRNA-associated protein profiling (FAXRAP), a chemical strategy that enables the identification of mRAPs in both cultured cells and intact mouse organs. Applying FAXRAP, tissue-specific mRAPs were systematically profiled in the mouse liver, kidney, heart, and brain. Furthermore, brain mRAPs in Parkinson's disease (PD) mouse model were investigated, which revealed a global decrease of mRNP assembly in the brain of mice with PD. We envision that FAXRAP will facilitate uncovering the posttranscriptional regulation networks in various biological systems.
Insights
Messenger ribonucleoprotein particles (mRNPs) are crucial for gene expression. A new method, FAXRAP, allows scientists to identify mRNA-associated proteins (mRAPs) in tissues, revealing insights into diseases like Parkinson's.
Area of Science:
- Molecular Biology
- Proteomics
- Gene Expression Regulation
Background:
- Messenger ribonucleoprotein particles (mRNPs) regulate tissue-specific gene expression through posttranscriptional mechanisms.
- Identifying mRNA-associated proteins (mRAPs) within mRNPs at the tissue level presents significant proteomic challenges.
Purpose of the Study:
- To develop a novel chemical strategy for profiling mRAPs in intact tissues.
- To systematically identify tissue-specific mRAPs in various mouse organs.
- To investigate changes in brain mRAPs in a Parkinson's disease model.
Main Methods:
- Development of formaldehyde cross-linking-based mRNA-associated protein profiling (FAXRAP).
- Application of FAXRAP to cultured cells and intact mouse organs (liver, kidney, heart, brain).
- Proteomic analysis of mRAPs in wild-type and Parkinson's disease model mice.
Main Results:
- FAXRAP successfully enabled the identification of mRAPs in diverse mouse organs.
- Systematic profiling revealed tissue-specific mRAP landscapes.
- Investigation in a Parkinson's disease model showed a global decrease in mRNP assembly in the brain.
Conclusions:
- FAXRAP is an effective chemical strategy for identifying tissue-specific mRAPs.
- The study provides novel insights into mRNP alterations in Parkinson's disease.
- FAXRAP is expected to advance the understanding of posttranscriptional regulatory networks.
