Exploiting functional regions in the viral RNA genome as druggable entities
RNA-targeting compounds or small interfering RNAs (siRNAs) offer a potent means to control viral infections. An essential prerequisite for their design depends on identifying conserved and functional viral RNA structures in cells. Techniques that probe RNA structures in situ have recently been devel...
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2025-07-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/103923 |
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| author | Dehua Luo Yingge Zheng Zhiyuan Huang Zi Wen Lijun Guo Yingxiang Deng Qingling Li Yuqing Bai Shozeb Haider Dengguo Wei |
| author_facet | Dehua Luo Yingge Zheng Zhiyuan Huang Zi Wen Lijun Guo Yingxiang Deng Qingling Li Yuqing Bai Shozeb Haider Dengguo Wei |
| author_sort | Dehua Luo |
| collection | DOAJ |
| description | RNA-targeting compounds or small interfering RNAs (siRNAs) offer a potent means to control viral infections. An essential prerequisite for their design depends on identifying conserved and functional viral RNA structures in cells. Techniques that probe RNA structures in situ have recently been developed including SHAPE-MaP, which has been helpful in the analysis of secondary structures of RNA. In this study, we report on the application of SHAPE-MaP to the porcine epidemic diarrhea virus RNA genome to categorize different functional regions, including potential quadruplex-forming sequence and target sites of siRNA. Our results show that these structures can be exploited to inhibit viral proliferation and that SHAPE-MaP is an effective method to identify secondary structures in RNA genomes. |
| format | Article |
| id | doaj-art-dcc9ab488cdd442eb9f651b4e3dbe73d |
| institution | Kabale University |
| issn | 2050-084X |
| language | English |
| publishDate | 2025-07-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj-art-dcc9ab488cdd442eb9f651b4e3dbe73d2025-08-20T03:29:40ZengeLife Sciences Publications LtdeLife2050-084X2025-07-011310.7554/eLife.103923Exploiting functional regions in the viral RNA genome as druggable entitiesDehua Luo0https://orcid.org/0009-0002-7827-7686Yingge Zheng1Zhiyuan Huang2Zi Wen3Lijun Guo4Yingxiang Deng5Qingling Li6Yuqing Bai7Shozeb Haider8https://orcid.org/0000-0003-2650-2925Dengguo Wei9https://orcid.org/0000-0001-9923-789XNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and National Safety Laboratory of Veterinary Drug (HZAU), MOA Key Laboratory for Detection of Veterinary Drug Residues, MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, ChinaNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and National Safety Laboratory of Veterinary Drug (HZAU), MOA Key Laboratory for Detection of Veterinary Drug Residues, MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, ChinaNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, China; College of Informatics, Huazhong Agricultural University, Wuhan, ChinaNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, China; College of Informatics, Huazhong Agricultural University, Wuhan, ChinaNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and National Safety Laboratory of Veterinary Drug (HZAU), MOA Key Laboratory for Detection of Veterinary Drug Residues, MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, ChinaNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and National Safety Laboratory of Veterinary Drug (HZAU), MOA Key Laboratory for Detection of Veterinary Drug Residues, MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, ChinaNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and National Safety Laboratory of Veterinary Drug (HZAU), MOA Key Laboratory for Detection of Veterinary Drug Residues, MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, ChinaNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, ChinaUniversity of Tabuk (PFSCBR), Tabuk, Saudi Arabia; UCL School of Pharmacy, University College London, London, United Kingdom; UCL Centre for Advanced Research Computing, University College London, London, United KingdomNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and National Safety Laboratory of Veterinary Drug (HZAU), MOA Key Laboratory for Detection of Veterinary Drug Residues, MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Wuhan, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, ChinaRNA-targeting compounds or small interfering RNAs (siRNAs) offer a potent means to control viral infections. An essential prerequisite for their design depends on identifying conserved and functional viral RNA structures in cells. Techniques that probe RNA structures in situ have recently been developed including SHAPE-MaP, which has been helpful in the analysis of secondary structures of RNA. In this study, we report on the application of SHAPE-MaP to the porcine epidemic diarrhea virus RNA genome to categorize different functional regions, including potential quadruplex-forming sequence and target sites of siRNA. Our results show that these structures can be exploited to inhibit viral proliferation and that SHAPE-MaP is an effective method to identify secondary structures in RNA genomes.https://elifesciences.org/articles/103923SHAPE-MaPRNAsiRNA |
| spellingShingle | Dehua Luo Yingge Zheng Zhiyuan Huang Zi Wen Lijun Guo Yingxiang Deng Qingling Li Yuqing Bai Shozeb Haider Dengguo Wei Exploiting functional regions in the viral RNA genome as druggable entities eLife SHAPE-MaP RNA siRNA |
| title | Exploiting functional regions in the viral RNA genome as druggable entities |
| title_full | Exploiting functional regions in the viral RNA genome as druggable entities |
| title_fullStr | Exploiting functional regions in the viral RNA genome as druggable entities |
| title_full_unstemmed | Exploiting functional regions in the viral RNA genome as druggable entities |
| title_short | Exploiting functional regions in the viral RNA genome as druggable entities |
| title_sort | exploiting functional regions in the viral rna genome as druggable entities |
| topic | SHAPE-MaP RNA siRNA |
| url | https://elifesciences.org/articles/103923 |
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