Identification of whole-cell dsRNA-binding proteins by phase separation
Interactions between double-stranded RNA (dsRNA) and proteins play an important role in cellular homeostasis by regulating the editing, stability, and splicing of intracellular RNA. The identification of dsRNA-binding proteins (dsRBPs) is key; however, it has long been challenging to purify dsRBPs f...
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| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Taylor & Francis Group
2024-12-01
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| Series: | RNA Biology |
| Subjects: | |
| Online Access: | https://www.tandfonline.com/doi/10.1080/15476286.2024.2386498 |
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| _version_ | 1846127934140579840 |
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| author | Zhixiang Yang Junwei Zhou Zhuang Li Jiahui Guo Liurong Fang Xun Xiao Shaobo Xiao |
| author_facet | Zhixiang Yang Junwei Zhou Zhuang Li Jiahui Guo Liurong Fang Xun Xiao Shaobo Xiao |
| author_sort | Zhixiang Yang |
| collection | DOAJ |
| description | Interactions between double-stranded RNA (dsRNA) and proteins play an important role in cellular homeostasis by regulating the editing, stability, and splicing of intracellular RNA. The identification of dsRNA-binding proteins (dsRBPs) is key; however, it has long been challenging to purify dsRBPs from cells. In this study, we developed a novel method, dsRBPC (dsRNA-binding protein capture), to purify cellular dsRBPs based on classic phase separation purification procedures. A global dsRNA-binding proteome of LLC-PK1 cells was obtained, and we identified 1326 dsRBPs, including 1303 putative novel dsRBPs. Functional analyses suggested that these enriched dsRBPs are mainly associated with rRNA processing, RNA splicing, transcriptional regulation, and nucleocytoplasmic transport. We also found that the ARM (armadillo/beta-catenin-like repeats) motif is a previously unknown dsRNA-binding domain, as demonstrated by biochemical experiments. Collectively, this study provides a useful approach for dsRBP identification and the discovery of a global dsRNA-binding proteome to comprehensively map the dsRNA – protein interaction network. |
| format | Article |
| id | doaj-art-03c2f8681f7143a1abae7ee543f8e3b9 |
| institution | Kabale University |
| issn | 1547-6286 1555-8584 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | RNA Biology |
| spelling | doaj-art-03c2f8681f7143a1abae7ee543f8e3b92024-12-11T07:47:43ZengTaylor & Francis GroupRNA Biology1547-62861555-85842024-12-0121182083310.1080/15476286.2024.2386498Identification of whole-cell dsRNA-binding proteins by phase separationZhixiang Yang0Junwei Zhou1Zhuang Li2Jiahui Guo3Liurong Fang4Xun Xiao5Shaobo Xiao6National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, ChinaNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, ChinaNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, ChinaNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, ChinaNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, ChinaNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, ChinaNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, ChinaInteractions between double-stranded RNA (dsRNA) and proteins play an important role in cellular homeostasis by regulating the editing, stability, and splicing of intracellular RNA. The identification of dsRNA-binding proteins (dsRBPs) is key; however, it has long been challenging to purify dsRBPs from cells. In this study, we developed a novel method, dsRBPC (dsRNA-binding protein capture), to purify cellular dsRBPs based on classic phase separation purification procedures. A global dsRNA-binding proteome of LLC-PK1 cells was obtained, and we identified 1326 dsRBPs, including 1303 putative novel dsRBPs. Functional analyses suggested that these enriched dsRBPs are mainly associated with rRNA processing, RNA splicing, transcriptional regulation, and nucleocytoplasmic transport. We also found that the ARM (armadillo/beta-catenin-like repeats) motif is a previously unknown dsRNA-binding domain, as demonstrated by biochemical experiments. Collectively, this study provides a useful approach for dsRBP identification and the discovery of a global dsRNA-binding proteome to comprehensively map the dsRNA – protein interaction network.https://www.tandfonline.com/doi/10.1080/15476286.2024.2386498dsRNA-binding proteinsdsRNA-binding protein capturedsRNA-binding proteomedsRNA-binding domainphase separation |
| spellingShingle | Zhixiang Yang Junwei Zhou Zhuang Li Jiahui Guo Liurong Fang Xun Xiao Shaobo Xiao Identification of whole-cell dsRNA-binding proteins by phase separation RNA Biology dsRNA-binding proteins dsRNA-binding protein capture dsRNA-binding proteome dsRNA-binding domain phase separation |
| title | Identification of whole-cell dsRNA-binding proteins by phase separation |
| title_full | Identification of whole-cell dsRNA-binding proteins by phase separation |
| title_fullStr | Identification of whole-cell dsRNA-binding proteins by phase separation |
| title_full_unstemmed | Identification of whole-cell dsRNA-binding proteins by phase separation |
| title_short | Identification of whole-cell dsRNA-binding proteins by phase separation |
| title_sort | identification of whole cell dsrna binding proteins by phase separation |
| topic | dsRNA-binding proteins dsRNA-binding protein capture dsRNA-binding proteome dsRNA-binding domain phase separation |
| url | https://www.tandfonline.com/doi/10.1080/15476286.2024.2386498 |
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