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Jabs S, Biton A, Bécavin C, Nahori MA, Ghozlane A, Pagliuso A, Spanò G, Guérineau V, Touboul D, Giai Gianetto Q, Chaze T, Matondo M, Dillies MA, Cossart P. Impact of the gut microbiota on the m 6A epitranscriptome of mouse cecum and liver. Nat Commun 2020; 11:1344. [PMID: 32165618 PMCID: PMC7067863 DOI: 10.1038/s41467-020-15126-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 02/17/2020] [Indexed: 12/28/2022] Open
Abstract
The intestinal microbiota modulates host physiology and gene expression via mechanisms that are not fully understood. Here we examine whether host epitranscriptomic marks are affected by the gut microbiota. We use methylated RNA-immunoprecipitation and sequencing (MeRIP-seq) to identify N6-methyladenosine (m6A) modifications in mRNA of mice carrying conventional, modified, or no microbiota. We find that variations in the gut microbiota correlate with m6A modifications in the cecum, and to a lesser extent in the liver, affecting pathways related to metabolism, inflammation and antimicrobial responses. We analyze expression levels of several known writer and eraser enzymes, and find that the methyltransferase Mettl16 is downregulated in absence of a microbiota, and one of its target mRNAs, encoding S-adenosylmethionine synthase Mat2a, is less methylated. We furthermore show that Akkermansia muciniphila and Lactobacillus plantarum affect specific m6A modifications in mono-associated mice. Our results highlight epitranscriptomic modifications as an additional level of interaction between commensal bacteria and their host.
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Affiliation(s)
- Sabrina Jabs
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, U604 Institut National de la Santé et de la Recherche Médicale, USC 2020 Institut National de la Recherche Agronomique, 25 rue du Dr Roux, F-75015, Paris, France.
| | - Anne Biton
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 rue du Dr Roux, F-75015, Paris, France
| | - Christophe Bécavin
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 rue du Dr Roux, F-75015, Paris, France
| | - Marie-Anne Nahori
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, U604 Institut National de la Santé et de la Recherche Médicale, USC 2020 Institut National de la Recherche Agronomique, 25 rue du Dr Roux, F-75015, Paris, France
| | - Amine Ghozlane
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 rue du Dr Roux, F-75015, Paris, France
| | - Alessandro Pagliuso
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, U604 Institut National de la Santé et de la Recherche Médicale, USC 2020 Institut National de la Recherche Agronomique, 25 rue du Dr Roux, F-75015, Paris, France
| | - Giulia Spanò
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, U604 Institut National de la Santé et de la Recherche Médicale, USC 2020 Institut National de la Recherche Agronomique, 25 rue du Dr Roux, F-75015, Paris, France
| | - Vincent Guérineau
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - David Touboul
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Quentin Giai Gianetto
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 rue du Dr Roux, F-75015, Paris, France
- Unité de spectrométrie de masse et Protéomique, CNRS USR 2000, Institut Pasteur, 28 rue du Dr Roux, F-75015, Paris, France
| | - Thibault Chaze
- Unité de spectrométrie de masse et Protéomique, CNRS USR 2000, Institut Pasteur, 28 rue du Dr Roux, F-75015, Paris, France
| | - Mariette Matondo
- Unité de spectrométrie de masse et Protéomique, CNRS USR 2000, Institut Pasteur, 28 rue du Dr Roux, F-75015, Paris, France
| | - Marie-Agnès Dillies
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 rue du Dr Roux, F-75015, Paris, France
| | - Pascale Cossart
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, U604 Institut National de la Santé et de la Recherche Médicale, USC 2020 Institut National de la Recherche Agronomique, 25 rue du Dr Roux, F-75015, Paris, France.
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Zhao W, Cui Y, Liu L, Ma X, Qi X, Wang Y, Liu Z, Ma S, Liu J, Wu J. METTL3 Facilitates Oral Squamous Cell Carcinoma Tumorigenesis by Enhancing c-Myc Stability via YTHDF1-Mediated m 6A Modification. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 20:1-12. [PMID: 32145676 PMCID: PMC7057159 DOI: 10.1016/j.omtn.2020.01.033] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 01/02/2023]
Abstract
N6-Methyladenosine (m6A) is the most common internal modification of eukaryotic messenger RNA (mRNA) that occurred on the N6 nitrogen of adenosine. However, the roles of m6A in oral squamous cell carcinoma (OSCC) are still elusive. Here, we investigate the function and mechanism of methyltransferase-like 3 (METTL3) in OSCC tumorigenesis. Clinically, METTL3 was significantly upregulated in tissue samples and correlated with the poor prognosis of OSCC patients. Functionally, loss and gain studies illustrated that METTL3 promoted the proliferation, invasion, and migration of OSCC cells in vitro, and METTL3 knockdown inhibited tumor growth in vivo. Mechanistically, methylated RNA immunoprecipitation sequencing (MeRIP-seq) illustrated that METTL3 targeted the 3′ UTR (near to stop codon) of the c-Myc transcript to install the m6A modification, thereby enhancing its stability. Furthermore, results revealed that YTH N6-methyladenosine RNA binding protein 1 (YTH domain family, member 1 [YTHDF1]) mediated the m6A-increased stability of c-Myc mRNA catalyzed by METTL3. In conclusion, our findings herein identify that METTL3 accelerates the c-Myc stability via YTHDF1-mediated m6A modification, thereby giving rise to OSCC tumorigenesis.
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Affiliation(s)
- Wei Zhao
- The School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300070, China
| | - Yameng Cui
- Department of Integrative Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Lina Liu
- Department of Prosthodontics, Tianjin Stomatological Hospital, Hospital of Stomatology, NanKai University, Tianjin 300041, China
| | - Xiaozhou Ma
- The School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300070, China
| | - Xiaoqian Qi
- The School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300070, China
| | - Yue Wang
- The School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300070, China
| | - Zihao Liu
- The School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300070, China
| | - Shiqing Ma
- The School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300070, China
| | - Jingwen Liu
- The School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300070, China.
| | - Jie Wu
- The School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300070, China.
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Li J, Yang X, Qi Z, Sang Y, Liu Y, Xu B, Liu W, Xu Z, Deng Y. The role of mRNA m 6A methylation in the nervous system. Cell Biosci 2019; 9:66. [PMID: 31452869 PMCID: PMC6701067 DOI: 10.1186/s13578-019-0330-y] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/14/2019] [Indexed: 11/21/2022] Open
Abstract
Epitranscriptomics, also known as “RNA epigenetics”, is a chemical modification for RNA regulation. Ribonucleic acid (RNA) methylation is considered to be a major discovery following the deoxyribonucleic acid (DNA) and histone methylation. Messenger RNA (mRNA) methylation modification accounts for more than 60% of all RNA modifications and N6-methyladenosine (m6A) is known as one of the most common type of eukaryotic mRNA methylation modifications in current. The m6A modification is a dynamic reversible modification, which can directly or indirectly affect biological processes, such as RNA degradation, translation and splicing, and can play important biological roles in vivo. This article introduces the mRNA m6A methylation modification enzymes and binding proteins, and reviews the research progress and related mechanisms of the role of mRNA m6A methylation in the nervous system from the aspects of neural stem cells, learning and memory, brain development, axon growth and glioblastoma.
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Affiliation(s)
- Jiashuo Li
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Xinxin Yang
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Zhipeng Qi
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Yanqi Sang
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Yanan Liu
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Bin Xu
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Wei Liu
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Zhaofa Xu
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Yu Deng
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
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