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Bozděchová L, Rudolfová A, Hanáková K, Fojtová M, Fajkus J. Optimizing ChIRP-MS for Comprehensive Profiling of RNA-Protein Interactions in Arabidopsis thaliana: A Telomerase RNA Case Study. Plants (Basel) 2024; 13:850. [PMID: 38592918 PMCID: PMC10975786 DOI: 10.3390/plants13060850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/05/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024]
Abstract
The current repertoire of methods available for studying RNA-protein interactions in plants is somewhat limited. Employing an RNA-centric approach, particularly with less abundant RNAs, presents various challenges. Many of the existing methods were initially designed for different model systems, with their application in plants receiving limited attention thus far. The Comprehensive Identification of RNA-Binding Proteins by Mass Spectrometry (ChIRP-MS) technique, initially developed for mammalian cells, has been adapted in this study for application in Arabidopsis thaliana. The procedures have been meticulously modified and optimized for telomerase RNA, a notable example of a low-abundance RNA recently identified. Following these optimization steps, ChIRP-MS can serve as an effective screening method for identifying candidate proteins interacting with any target RNA of interest.
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Affiliation(s)
- Lucie Bozděchová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (L.B.); (K.H.); (M.F.)
| | - Anna Rudolfová
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic;
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Kateřina Hanáková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (L.B.); (K.H.); (M.F.)
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (L.B.); (K.H.); (M.F.)
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic;
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (L.B.); (K.H.); (M.F.)
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic;
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Zhou H, Gan X, He S, Wang Y, Zhang S, Chen J, Zhou Y, Hou C, Hua L, Zhang Q, Jia E. Identification of circular RNA BTBD7_hsa_circ_0000563 as a novel biomarker for coronary artery disease and the functional discovery of BTBD7_hsa_circ_0000563 based on peripheral blood mononuclear cells: a case control study. Clin Proteomics 2022; 19:37. [PMID: 36329387 PMCID: PMC9630807 DOI: 10.1186/s12014-022-09374-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND BTBD7_hsa_circ_0000563 is a novel circRNA and contains conserved binding sites with RNA-binding proteins. However, BTBD7_hsa_circ_0000563 has not been fully studied in coronary artery disease (CAD). We aimed to clarify the diagnostic value and the possible functional role of BTBD7_hsa_circ_0000563 in CAD. METHODS A total of 276 human peripheral blood mononuclear cell (PBMC) samples were employed. The circularization of BTBD7_hsa_circ_0000563 was verified via Sanger sequencing. The expression level of BTBD7_hsa_circ_0000563 in CAD samples and control individuals was analysed via qRT-PCR. The diagnostic potential of BTBD7_hsa_circ_0000563 was evaluated using Spearman's analysis, univariate and multivariable logistic regression analysis, and receiver-operator characteristic (ROC) curve analysis. ChIRP-MS was performed to directly explore the proteins bound to BTBD7_hsa_circ_0000563. Bioinformatic analysis was conducted to investigate the possible functions and interactions of proteins bound to BTBD7_hsa_circ_0000563. RESULTS In the present study, BTBD7_hsa_circ_0000563 was verified as a circular RNA in the PBMCs of CAD patients. The expression level of BTBD7_hsa_circ_0000563 in the CAD group was significantly lower than that in the control group. The area under the ROC curve was 0.690. ChIRP-MS found seven proteins that were directly bound to BTBD7_hsa_circ_0000563. Bioinformatic analysis of these seven proteins showed that the mitophagy and DNA repair pathways were enriched. These proteins interacted with each other to a certain extent. CONCLUSION BTBD7_hsa_circ_0000563 may be a novel biomarker for the diagnosis of CAD and may influence the initiation and progression of CAD. These studies may reveal new possibilities for the diagnosis and treatment of CAD.
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Affiliation(s)
- Hanxiao Zhou
- grid.412676.00000 0004 1799 0784Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, 210029 Nanjing, Jiangsu Province China
| | - Xiongkang Gan
- grid.412676.00000 0004 1799 0784Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, 210029 Nanjing, Jiangsu Province China
| | - Shu He
- grid.412676.00000 0004 1799 0784Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, 210029 Nanjing, Jiangsu Province China
| | - Yanjun Wang
- grid.412676.00000 0004 1799 0784Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, 210029 Nanjing, Jiangsu Province China
| | - Sheng Zhang
- grid.412676.00000 0004 1799 0784Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, 210029 Nanjing, Jiangsu Province China
| | - Jiaxin Chen
- grid.412676.00000 0004 1799 0784Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, 210029 Nanjing, Jiangsu Province China
| | - Yaqing Zhou
- grid.412676.00000 0004 1799 0784Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, 210029 Nanjing, Jiangsu Province China
| | - Can Hou
- grid.412676.00000 0004 1799 0784Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, 210029 Nanjing, Jiangsu Province China
| | - Lei Hua
- grid.412676.00000 0004 1799 0784Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, 210029 Nanjing, Jiangsu Province China
| | - Qian Zhang
- grid.412676.00000 0004 1799 0784Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, 210029 Nanjing, Jiangsu Province China
| | - Enzhi Jia
- grid.412676.00000 0004 1799 0784Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, 210029 Nanjing, Jiangsu Province China
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Flynn RA, Belk JA, Qi Y, Yasumoto Y, Wei J, Alfajaro MM, Shi Q, Mumbach MR, Limaye A, DeWeirdt PC, Schmitz CO, Parker KR, Woo E, Chang HY, Horvath TL, Carette JE, Bertozzi CR, Wilen CB, Satpathy AT. Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions. Cell 2021; 184:2394-2411.e16. [PMID: 33743211 PMCID: PMC7951565 DOI: 10.1016/j.cell.2021.03.012] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/03/2021] [Accepted: 03/04/2021] [Indexed: 12/22/2022]
Abstract
SARS-CoV-2 is the cause of a pandemic with growing global mortality. Using comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS), we identified 309 host proteins that bind the SARS-CoV-2 RNA during active infection. Integration of this data with ChIRP-MS data from three other RNA viruses defined viral specificity of RNA-host protein interactions. Targeted CRISPR screens revealed that the majority of functional RNA-binding proteins protect the host from virus-induced cell death, and comparative CRISPR screens across seven RNA viruses revealed shared and SARS-specific antiviral factors. Finally, by combining the RNA-centric approach and functional CRISPR screens, we demonstrated a physical and functional connection between SARS-CoV-2 and mitochondria, highlighting this organelle as a general platform for antiviral activity. Altogether, these data provide a comprehensive catalog of functional SARS-CoV-2 RNA-host protein interactions, which may inform studies to understand the host-virus interface and nominate host pathways that could be targeted for therapeutic benefit.
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Affiliation(s)
- Ryan A Flynn
- Stanford ChEM-H and Department of Chemistry, Stanford University, Stanford, CA, USA.
| | - Julia A Belk
- Department of Computer Science, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University, Stanford, CA, USA
| | - Yanyan Qi
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Yuki Yasumoto
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, Yale University, New Haven, CT, USA
| | - Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Aditi Limaye
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Peter C DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cameron O Schmitz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Kevin R Parker
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Elizabeth Woo
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Tamas L Horvath
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, Yale University, New Haven, CT, USA
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Carolyn R Bertozzi
- Stanford ChEM-H and Department of Chemistry, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
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Yao X, Lan Z, Lai Q, Li A, Liu S, Wang X. LncRNA SNHG6 plays an oncogenic role in colorectal cancer and can be used as a prognostic biomarker for solid tumors. J Cell Physiol 2020; 235:7620-7634. [PMID: 32239696 DOI: 10.1002/jcp.29672] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 03/06/2020] [Indexed: 12/15/2022]
Abstract
Small nucleolar RNA host gene 6 (SNHG6) has been recognized as an oncogene in numerous cancers and overexpression of SNHG6 was found to promote colorectal cancer (CRC). Hence, we performed a meta-analysis to examine the clinical importance of the long noncoding RNA (lncRNA) SNHG6. Moreover, comprehensive identification of RNA-binding proteins-mass spectrometry (ChIRP-MS) was conducted to explore the carcinogenic mechanism of lncRNA SNHG6 in CRC. Fourteen studies conducted on 1,139 patients were included in this meta-analysis. We also constructed the protein-protein interactive (PPI) network in string based on the ChIRP-MS results and cytoscape was used to identify core modules in the PPI network, which were then analyzed using the bioinformatics websites, cancer single-cell state atlas (CancerSEA) and G:profilter. The clinical outcomes of the meta-analysis indicated that higher expression of SNHG6 was related with a poorer survival outcome (overall survival: hazard ratio (HR) = 1.92; 95% confidence interval [Cl]: 1.48, 2.49; p < .0001; disease-free survival: HR = 1.84; 95% Cl: 1.02, 3.34; p = .044), higher tumor stage (odds ratio [OR] = 3.35; 95% Cl: 2.57, 4.37; p < .0001), distant metastasis (OR = 1.83; 95% Cl: 1.11, 2.99; p = .017) and lymph node metastasis (OR = 1.33; 95% Cl: 0.93, 1.89; p = .119). The ChIRP-MS results showed that core Module 1 of the PPI was significant in ribosomes and core Module 2 was mainly related to spliceosomes and messenger RNA processing. In conclusion, a higher expression of SNHG6 was found to be associated with a poorer survival outcome, high tumor stage, and distant metastasis in various solid tumors. SNHG6 was also found to be able to affect the processes of transcription and translation to promote CRC.
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Affiliation(s)
- Xiang Yao
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhixian Lan
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qiuhua Lai
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Aimin Li
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Side Liu
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xinke Wang
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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