Photocatalytic labelling-enabled subcellular-resolved RNA profiling and synchronous multi-omics investigation
Yunpeng Bi1, Lishan Yu2, Qidong Deng2
1Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
Nature Chemistry
|September 16, 2025
Summary
We developed CAT-seq, a new method for high-resolution mitochondrial RNA profiling in living cells without genetic modification. This technique allows for detailed cellular RNA analysis and multi-omics studies.
Area of Science:
- Cell Biology
- Molecular Biology
- Biochemistry
Background:
- Understanding cellular functions requires analyzing subcellular transcriptome variations.
- Current mitochondrial RNA profiling methods have limitations like low resolution and genetic manipulation dependence.
Purpose of the Study:
- To develop a non-genetic, high-resolution method for in situ mitochondrial RNA profiling in living cells.
- To enable simultaneous RNA and protein multi-omics profiling.
Main Methods:
- Developed CAT-seq, a bioorthogonal photocatalytic labeling and sequencing strategy.
- Utilized a quinone methide probe for efficient RNA labeling.
- Applied the method to HeLa cells and RAW 264.7 macrophages.
Main Results:
- CAT-seq achieved high-resolution, in situ mitochondrial RNA profiling without genetic manipulation.
- Successfully tracked RNA dynamics in HeLa cells.
- Revealed a mitochondrial translational remodeling pathway in macrophages.
- Established an orthogonal labeling system for synchronous RNA and protein multi-omics.
Conclusions:
- CAT-seq provides a general, non-genetic approach for subcellular-resolved RNA and multi-omics investigations.
- The method is compatible with challenging samples like intact primary living cells.
- Facilitates deeper understanding of cellular functions in health and disease.
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