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Elías-Villalobos A, Duncan C, Mata J, Helmlinger D. Quantitative analysis of protein-RNA interactions in fission yeast. STAR Protoc 2022; 3:101373. [PMID: 35586315 PMCID: PMC9108979 DOI: 10.1016/j.xpro.2022.101373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Characterizing the interactions between RNAs and proteins in vivo is key to better understand how organisms regulate gene expression. Here, we describe a robust and quantitative protocol to measure specific RNA-protein interactions in a native context using RNA immunoprecipitation (RIP). We provide a comprehensive experimental framework to detect cotranslational interactions and detail the quantitative analysis of purified RNAs by PCR and high-throughput sequencing. Although we developed the protocol in fission yeast, it can be readily implemented in other yeast species. For complete details on the use and execution of this protocol, please refer to Toullec et al. (2021). Simple and robust detection of RNA-protein interactions in a native context Ribonucleoprotein complex isolated by immunoprecipitation Quantitative analysis of purified RNA by PCR or high-throughput sequencing Detailed experimental pipeline to demonstrate cotranslational interactions
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Affiliation(s)
- Alberto Elías-Villalobos
- CRBM, University of Montpellier, CNRS, Montpellier, France.,Instituto de Biomedicina de Sevilla (IBiS), Universidad de Sevilla-Hospital Universitario Virgen del Rocío-CSIC, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Caia Duncan
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Juan Mata
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
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Takemura M, Bowden N, Lu YS, Nakato E, O'Connor MB, Nakato H. Drosophila MOV10 regulates the termination of midgut regeneration. Genetics 2021; 218:6156853. [PMID: 33693718 DOI: 10.1093/genetics/iyab031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 02/23/2021] [Indexed: 12/22/2022] Open
Abstract
The molecular mechanisms by which stem cell proliferation is precisely controlled during the course of regeneration are poorly understood. Namely, how a damaged tissue senses when to terminate the regeneration process, inactivates stem cell mitotic activity, and organizes ECM integrity remain fundamental unanswered questions. The Drosophila midgut intestinal stem cell (ISC) offers an excellent model system to study the molecular basis for stem cell inactivation. Here, we show that a novel gene, CG6967 or dMOV10, is induced at the termination stage of midgut regeneration, and shows an inhibitory effect on ISC proliferation. dMOV10 encodes a putative component of the microRNA (miRNA) gene silencing complex (miRISC). Our data, along with previous studies on the mammalian MOV10, suggest that dMOV10 is not a core member of miRISC, but modulates miRISC activity as an additional component. Further analyses identified direct target mRNAs of dMOV10-containing miRISC, including Daughter against Dpp (Dad), a known inhibitor of BMP/TGF-β signaling. We show that RNAi knockdown of Dad significantly impaired ISC division during regeneration. We also identified six miRNAs that are induced at the termination stage and their potential target transcripts. One of these miRNAs, mir-1, is required for proper termination of ISC division at the end of regeneration. We propose that miRNA-mediated gene regulation contributes to the precise control of Drosophila midgut regeneration.
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Affiliation(s)
- Masahiko Takemura
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nanako Bowden
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yi-Si Lu
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Eriko Nakato
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael B O'Connor
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Hiroshi Nakato
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
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3
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He JJ, Li Z, Rong ZX, Gao J, Mu Y, Guan YD, Ren XX, Zi YY, Liu LY, Fan Q, Zhou M, Duan YM, Zhou Q, Deng YZ, Sun LQ. m 6A Reader YTHDC2 Promotes Radiotherapy Resistance of Nasopharyngeal Carcinoma via Activating IGF1R/AKT/S6 Signaling Axis. Front Oncol 2020; 10:1166. [PMID: 32850334 PMCID: PMC7411471 DOI: 10.3389/fonc.2020.01166] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/09/2020] [Indexed: 12/24/2022] Open
Abstract
N6-methyladenosine (m6A) modification has been reported as a critical regulator of gene transcript expression. Although m6A modification plays important roles in tumor development, its role in therapeutic resistance remains unknown. In this study, we aimed to examine the expression level of m6A-modification related proteins and elucidate the effect of m6A-related proteins on radiation response in nasopharyngeal carcinoma (NPC). Among the genes that participated in m6A modification, YTHDC2, a m6A reader, was found to be consistently highly expressed in radioresistant NPC cells. Knocking down of YTHDC2 expression in radioresistant NPC cells improved the therapeutic effect of radiotherapy in vitro and in vivo, whereas overexpression of YTHDC2 in radiosensitive NPC cells exerted an opposite effect. Bioinformatics and mechanistic studies revealed that YTHDC2 could physically bound to insulin-like growth factor 1 receptor (IGF1R) messenger RNA and promoted translation initiation of IGF1R mRNA, which in turn activated the IGF1R-AKT/S6 signaling pathway. Thus, the present study suggests that YTHDC2 promotes radiotherapy resistance of NPC cells by activating the IGF1R/ATK/S6 signaling axis and may serve as a potential therapeutic target in radiosensitization of NPC cells.
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Affiliation(s)
- Jun-Ju He
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, China
| | - Zhi Li
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, China
| | - Zhuo-Xian Rong
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, China
| | - Jie Gao
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, China
| | - Yun Mu
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, China
| | - Yi-Di Guan
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, China
| | - Xin-Xin Ren
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, China
| | - Yu-Yuan Zi
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, China
| | - Li-Yu Liu
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, China
| | - Qi Fan
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, China
| | - Ming Zhou
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, China
| | - Yu-Mei Duan
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, China
| | - Qin Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Yue-Zhen Deng
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, China
| | - Lun-Quan Sun
- Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, China.,Hunan International Science and Technology Collaboration Base of Precision Medicine for Cancer, Changsha, China.,National Clinical Research Center for Gerontology, Changsha, China
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5
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Kachaev ZM, Lebedeva LA, Kozlov EN, Toropygin IY, Schedl P, Shidlovskii YV. Paip2 is localized to active promoters and loaded onto nascent mRNA in Drosophila. Cell Cycle 2018; 17:1708-1720. [PMID: 29995569 DOI: 10.1080/15384101.2018.1496738] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Paip2 (Poly(A)-binding protein - interacting protein 2) is a conserved metazoan-specific protein that has been implicated in regulating the translation and stability of mRNAs. However, we have found that Paip2 is not restricted to the cytoplasm but is also found in the nucleus in Drosophila embryos, salivary glands, testes, and tissue culture cells. Nuclear Paip2 is associated with chromatin, and in chromatin immunoprecipitation experiments it maps to the promoter regions of active genes. However, this chromatin association is indirect, as it is RNA-dependent. Thus, Paip2 is one more item in the growing list of translation factors that are recruited to mRNAs co-transcriptionally.
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Affiliation(s)
- Zaur M Kachaev
- a Laboratory of Gene Expression Regulation in Development , Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia
| | - Lyubov A Lebedeva
- a Laboratory of Gene Expression Regulation in Development , Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia
| | - Eugene N Kozlov
- a Laboratory of Gene Expression Regulation in Development , Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia
| | - Ilya Y Toropygin
- d Center of Common Use "Human Proteome" , V.I. Orekhovich Research Institute of Biomedical Chemistry , Moscow , Russia
| | - Paul Schedl
- a Laboratory of Gene Expression Regulation in Development , Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia.,b Department of Molecular Biology , Princeton University , Princeton , NJ , USA
| | - Yulii V Shidlovskii
- a Laboratory of Gene Expression Regulation in Development , Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia.,c Department of Biology and General Genetics , I.M. Sechenov First Moscow State Medical University , Moscow , Russia
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