An ultra low-input method for global RNA structure probing uncovers Regnase-1-mediated regulation in macrophages
To enable diverse functions and precise regulation, an RNA sequence often folds into complex yet distinct structures in different cellular states. Probing RNA in its native environment is essential to uncovering RNA structures of biological contexts. However, current methods generally require large...
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| Format: | Article |
| Language: | English |
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KeAi Communications Co. Ltd.
2022-01-01
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| Series: | Fundamental Research |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2667325821003113 |
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| author | Meiling Piao Pan Li Xiaomin Zeng Xi-Wen Wang Lan Kang Jinsong Zhang Yifan Wei Shaojun Zhang Lei Tang Jianghui Zhu Chun Kit Kwok Xiaoyu Hu Qiangfeng Cliff Zhang |
| author_facet | Meiling Piao Pan Li Xiaomin Zeng Xi-Wen Wang Lan Kang Jinsong Zhang Yifan Wei Shaojun Zhang Lei Tang Jianghui Zhu Chun Kit Kwok Xiaoyu Hu Qiangfeng Cliff Zhang |
| author_sort | Meiling Piao |
| collection | DOAJ |
| description | To enable diverse functions and precise regulation, an RNA sequence often folds into complex yet distinct structures in different cellular states. Probing RNA in its native environment is essential to uncovering RNA structures of biological contexts. However, current methods generally require large amounts of input RNA and are challenging for physiologically relevant use. Here, we report smartSHAPE, a new RNA structure probing method that requires very low amounts of RNA input due to the largely reduced artefact of probing signals and increased efficiency of library construction. Using smartSHAPE, we showcased the profiling of the RNA structure landscape of mouse intestinal macrophages upon inflammation, and provided evidence that RNA conformational changes regulate immune responses. These results demonstrate that smartSHAPE can greatly expand the scope of RNA structure-based investigations in practical biological systems, and also provide a research paradigm for the study of post-transcriptional regulation. |
| first_indexed | 2024-04-11T04:49:12Z |
| format | Article |
| id | doaj.art-c8472c096ac64398870774cb118fa017 |
| institution | Directory Open Access Journal |
| issn | 2667-3258 |
| language | English |
| last_indexed | 2024-04-11T04:49:12Z |
| publishDate | 2022-01-01 |
| publisher | KeAi Communications Co. Ltd. |
| record_format | Article |
| series | Fundamental Research |
| spelling | doaj.art-c8472c096ac64398870774cb118fa0172022-12-27T04:43:01ZengKeAi Communications Co. Ltd.Fundamental Research2667-32582022-01-0121213An ultra low-input method for global RNA structure probing uncovers Regnase-1-mediated regulation in macrophagesMeiling Piao0Pan Li1Xiaomin Zeng2Xi-Wen Wang3Lan Kang4Jinsong Zhang5Yifan Wei6Shaojun Zhang7Lei Tang8Jianghui Zhu9Chun Kit Kwok10Xiaoyu Hu11Qiangfeng Cliff Zhang12MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, ChinaMOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, ChinaInstitute for Immunology and School of Medicine, Tsinghua University, Beijing, China; Beijing Key Laboratory for Immunological Research on Chronic Diseases, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, ChinaMOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, ChinaInstitute for Immunology and School of Medicine, Tsinghua University, Beijing, China; Beijing Key Laboratory for Immunological Research on Chronic Diseases, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, ChinaMOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, ChinaMOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, ChinaMOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, ChinaMOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, ChinaMOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, ChinaDepartment of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, ChinaInstitute for Immunology and School of Medicine, Tsinghua University, Beijing, China; Beijing Key Laboratory for Immunological Research on Chronic Diseases, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China; Corresponding authors.MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; Corresponding authors.To enable diverse functions and precise regulation, an RNA sequence often folds into complex yet distinct structures in different cellular states. Probing RNA in its native environment is essential to uncovering RNA structures of biological contexts. However, current methods generally require large amounts of input RNA and are challenging for physiologically relevant use. Here, we report smartSHAPE, a new RNA structure probing method that requires very low amounts of RNA input due to the largely reduced artefact of probing signals and increased efficiency of library construction. Using smartSHAPE, we showcased the profiling of the RNA structure landscape of mouse intestinal macrophages upon inflammation, and provided evidence that RNA conformational changes regulate immune responses. These results demonstrate that smartSHAPE can greatly expand the scope of RNA structure-based investigations in practical biological systems, and also provide a research paradigm for the study of post-transcriptional regulation.http://www.sciencedirect.com/science/article/pii/S2667325821003113RNA structure probing methodLow-inputRNA structure elementMacrophageRNA structureRNA structurome |
| spellingShingle | Meiling Piao Pan Li Xiaomin Zeng Xi-Wen Wang Lan Kang Jinsong Zhang Yifan Wei Shaojun Zhang Lei Tang Jianghui Zhu Chun Kit Kwok Xiaoyu Hu Qiangfeng Cliff Zhang An ultra low-input method for global RNA structure probing uncovers Regnase-1-mediated regulation in macrophages Fundamental Research RNA structure probing method Low-input RNA structure element Macrophage RNA structure RNA structurome |
| title | An ultra low-input method for global RNA structure probing uncovers Regnase-1-mediated regulation in macrophages |
| title_full | An ultra low-input method for global RNA structure probing uncovers Regnase-1-mediated regulation in macrophages |
| title_fullStr | An ultra low-input method for global RNA structure probing uncovers Regnase-1-mediated regulation in macrophages |
| title_full_unstemmed | An ultra low-input method for global RNA structure probing uncovers Regnase-1-mediated regulation in macrophages |
| title_short | An ultra low-input method for global RNA structure probing uncovers Regnase-1-mediated regulation in macrophages |
| title_sort | ultra low input method for global rna structure probing uncovers regnase 1 mediated regulation in macrophages |
| topic | RNA structure probing method Low-input RNA structure element Macrophage RNA structure RNA structurome |
| url | http://www.sciencedirect.com/science/article/pii/S2667325821003113 |
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