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Albihlal WS, Chan WY, van Werven FJ. Budding yeast as an ideal model for elucidating the role of N 6-methyladenosine in regulating gene expression. Yeast 2024; 41:148-157. [PMID: 38238962 DOI: 10.1002/yea.3925] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 02/24/2024] Open
Abstract
N6-methyladenosine (m6A) is a highly abundant and evolutionarily conserved messenger RNA (mRNA) modification. This modification is installed on RRACH motifs on mRNAs by a hetero-multimeric holoenzyme known as m6A methyltransferase complex (MTC). The m6A mark is then recognised by a group of conserved proteins known as the YTH domain family proteins which guide the mRNA for subsequent downstream processes that determine its fate. In yeast, m6A is installed on thousands of mRNAs during early meiosis by a conserved MTC and the m6A-modified mRNAs are read by the YTH domain-containing protein Mrb1/Pho92. In this review, we aim to delve into the recent advances in our understanding of the regulation and roles of m6A in yeast meiosis. We will discuss the potential functions of m6A in mRNA translation and decay, unravelling their significance in regulating gene expression. We propose that yeast serves as an exceptional model organism for the study of fundamental molecular mechanisms related to the function and regulation of m6A-modified mRNAs. The insights gained from yeast research not only expand our knowledge of mRNA modifications and their molecular roles but also offer valuable insights into the broader landscape of eukaryotic posttranscriptional regulation of gene expression.
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Affiliation(s)
- Waleed S Albihlal
- The Francis Crick Institute, Cell Fate and Gene Regulation Laboratory, London, UK
| | - Wei Yee Chan
- The Francis Crick Institute, Cell Fate and Gene Regulation Laboratory, London, UK
| | - Folkert J van Werven
- The Francis Crick Institute, Cell Fate and Gene Regulation Laboratory, London, UK
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Yan C, Xiong J, Zhou Z, Li Q, Gao C, Zhang M, Yu L, Li J, Hu MM, Zhang CS, Cai C, Zhang H, Zhang J. A cleaved METTL3 potentiates the METTL3-WTAP interaction and breast cancer progression. eLife 2023; 12:RP87283. [PMID: 37589705 PMCID: PMC10435237 DOI: 10.7554/elife.87283] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023] Open
Abstract
N6-methyladenosine (m6A) methylation of RNA by the methyltransferase complex (MTC), with core components including METTL3-METTL14 heterodimers and Wilms' tumor 1-associated protein (WTAP), contributes to breast tumorigenesis, but the underlying regulatory mechanisms remain elusive. Here, we identify a novel cleaved form METTL3a (residues 239-580 of METTL3). We find that METTL3a is required for the METTL3-WTAP interaction, RNA m6A deposition, as well as cancer cell proliferation. Mechanistically, we find that METTL3a is essential for the METTL3-METTL3 interaction, which is a prerequisite step for recruitment of WTAP in MTC. Analysis of m6A sequencing data shows that depletion of METTL3a globally disrupts m6A deposition, and METTL3a mediates mammalian target of rapamycin (mTOR) activation via m6A-mediated suppression of TMEM127 expression. Moreover, we find that METTL3 cleavage is mediated by proteasome in an mTOR-dependent manner, revealing positive regulatory feedback between METTL3a and mTOR signaling. Our findings reveal METTL3a as an important component of MTC, and suggest the METTL3a-mTOR axis as a potential therapeutic target for breast cancer.
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Affiliation(s)
- Chaojun Yan
- Department of Thyroid and Breast Surgery, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan UniversityWuhanChina
| | - Jingjing Xiong
- Department of Thyroid and Breast Surgery, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan UniversityWuhanChina
| | - Zirui Zhou
- Department of Thyroid and Breast Surgery, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan UniversityWuhanChina
| | - Qifang Li
- Department of Thyroid and Breast Surgery, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan UniversityWuhanChina
| | - Chuan Gao
- Department of Thyroid and Breast Surgery, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan UniversityWuhanChina
| | - Mengyao Zhang
- Department of Thyroid and Breast Surgery, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan UniversityWuhanChina
| | - Liya Yu
- Department of Thyroid and Breast Surgery, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan UniversityWuhanChina
| | - Jinpeng Li
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan UniversityWuhanChina
| | - Ming-Ming Hu
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan UniversityWuhanChina
| | - Chen-Song Zhang
- State Key Laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network School of Life Sciences, Xiamen UniversityFujianChina
| | - Cheguo Cai
- Department of Thyroid and Breast Surgery, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan UniversityWuhanChina
| | - Haojian Zhang
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan UniversityWuhanChina
| | - Jing Zhang
- Department of Thyroid and Breast Surgery, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan UniversityWuhanChina
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Ensinck I, Maman A, Albihlal WS, Lassandro M, Salzano G, Sideri T, Howell SA, Calvani E, Patel H, Bushkin G, Ralser M, Snijders AP, Skehel M, Casañal A, Schwartz S, van Werven FJ. The yeast RNA methylation complex consists of conserved yet reconfigured components with m6A-dependent and independent roles. eLife 2023; 12:RP87860. [PMID: 37490041 PMCID: PMC10393049 DOI: 10.7554/elife.87860] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023] Open
Abstract
N6-methyladenosine (m6A), the most abundant mRNA modification, is deposited in mammals/insects/plants by m6A methyltransferase complexes (MTC) comprising a catalytic subunit and at least five additional proteins. The yeast MTC is critical for meiosis and was known to comprise three proteins, of which two were conserved. We uncover three novel MTC components (Kar4/Ygl036w-Vir1/Dyn2). All MTC subunits, except for Dyn2, are essential for m6A deposition and have corresponding mammalian MTC orthologues. Unlike the mammalian bipartite MTC, the yeast MTC is unipartite, yet multifunctional. The mRNA interacting module, comprising Ime4, Mum2, Vir1, and Kar4, exerts the MTC's m6A-independent function, while Slz1 enables the MTC catalytic function in m6A deposition. Both functions are critical for meiotic progression. Kar4 also has a mechanistically separate role from the MTC during mating. The yeast MTC constituents play distinguishable m6A-dependent, MTC-dependent, and MTC-independent functions, highlighting their complexity and paving the path towards dissecting multi-layered MTC functions in mammals.
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Affiliation(s)
| | - Alexander Maman
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
| | | | | | | | | | | | | | | | - Guy Bushkin
- Whitehead Institute for Biomedical ResearchCambridgeUnited States
| | - Markus Ralser
- The Francis Crick InstituteLondonUnited Kingdom
- Charité Universitätsmedizin Berlin, Department of BiochemistryBerlinGermany
| | | | - Mark Skehel
- The Francis Crick InstituteLondonUnited Kingdom
| | | | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
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Raj N, Wang M, Seoane JA, Zhao RL, Kaiser AM, Moonie NA, Demeter J, Boutelle AM, Kerr CH, Mulligan AS, Moffatt C, Zeng SX, Lu H, Barna M, Curtis C, Chang HY, Jackson PK, Attardi LD. The Mettl3 epitranscriptomic writer amplifies p53 stress responses. Mol Cell 2022; 82:2370-2384.e10. [PMID: 35512709 DOI: 10.1016/j.molcel.2022.04.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 01/05/2022] [Accepted: 04/06/2022] [Indexed: 01/04/2023]
Abstract
The p53 transcription factor drives anti-proliferative gene expression programs in response to diverse stressors, including DNA damage and oncogenic signaling. Here, we seek to uncover new mechanisms through which p53 regulates gene expression using tandem affinity purification/mass spectrometry to identify p53-interacting proteins. This approach identified METTL3, an m6A RNA-methyltransferase complex (MTC) constituent, as a p53 interactor. We find that METTL3 promotes p53 protein stabilization and target gene expression in response to DNA damage and oncogenic signals, by both catalytic activity-dependent and independent mechanisms. METTL3 also enhances p53 tumor suppressor activity in in vivo mouse cancer models and human cancer cells. Notably, METTL3 only promotes tumor suppression in the context of intact p53. Analysis of human cancer genome data further supports the notion that the MTC reinforces p53 function in human cancer. Together, these studies reveal a fundamental role for METTL3 in amplifying p53 signaling in response to cellular stress.
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Knuckles P, Lence T, Haussmann IU, Jacob D, Kreim N, Carl SH, Masiello I, Hares T, Villaseñor R, Hess D, Andrade-Navarro MA, Biggiogera M, Helm M, Soller M, Bühler M, Roignant JY. Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m 6A machinery component Wtap/Fl(2)d. Genes Dev 2018. [PMID: 29535189 PMCID: PMC5900714 DOI: 10.1101/gad.309146.117] [Citation(s) in RCA: 371] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
In this study, Knuckles et al. identified Flacc/Zc3h13 as a novel interactor of m6A methyltransferase complex components in Drosophila and mice. They show that Flacc promotes the recruitment of the methyltransferase to mRNA by bridging Fl(2)d to the mRNA-binding factor Nito, providing novel insights into the conservation and regulation of the m6A machinery. N6-methyladenosine (m6A) is the most abundant mRNA modification in eukaryotes, playing crucial roles in multiple biological processes. m6A is catalyzed by the activity of methyltransferase-like 3 (Mettl3), which depends on additional proteins whose precise functions remain poorly understood. Here we identified Zc3h13 (zinc finger CCCH domain-containing protein 13)/Flacc [Fl(2)d-associated complex component] as a novel interactor of m6A methyltransferase complex components in Drosophila and mice. Like other components of this complex, Flacc controls m6A levels and is involved in sex determination in Drosophila. We demonstrate that Flacc promotes m6A deposition by bridging Fl(2)d to the mRNA-binding factor Nito. Altogether, our work advances the molecular understanding of conservation and regulation of the m6A machinery.
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Affiliation(s)
- Philip Knuckles
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, Basel 4002, Switzerland
| | - Tina Lence
- Institute of Molecular Biology, 55128 Mainz, Germany
| | - Irmgard U Haussmann
- School of Life Science, Faculty of Health and Life Sciences, Coventry University, Coventry CV1 5FB, United Kingdom.,School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Dominik Jacob
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Nastasja Kreim
- Bioinformatics Core Facility, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Sarah H Carl
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel 4058, Switzerland
| | - Irene Masiello
- Institute of Molecular Biology, 55128 Mainz, Germany.,Laboratory of Cell Biology and Neurobiology, Department of Animal Biology, University of Pavia, Pavia 27100, Italy
| | - Tina Hares
- Institute of Molecular Biology, 55128 Mainz, Germany
| | - Rodrigo Villaseñor
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, Basel 4002, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Miguel A Andrade-Navarro
- Institute of Molecular Biology, 55128 Mainz, Germany.,Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Marco Biggiogera
- Laboratory of Cell Biology and Neurobiology, Department of Animal Biology, University of Pavia, Pavia 27100, Italy
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Matthias Soller
- School of Life Science, Faculty of Health and Life Sciences, Coventry University, Coventry CV1 5FB, United Kingdom
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, Basel 4002, Switzerland
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6
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Knuckles P, Lence T, Haussmann IU, Jacob D, Kreim N, Carl SH, Masiello I, Hares T, Villaseñor R, Hess D, Andrade-Navarro MA, Biggiogera M, Helm M, Soller M, Bühler M, Roignant JY. Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m 6A machinery component Wtap/Fl(2)d. Genes Dev 2018. [PMID: 29535189 DOI: 10.1101/gad.309146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
N6-methyladenosine (m6A) is the most abundant mRNA modification in eukaryotes, playing crucial roles in multiple biological processes. m6A is catalyzed by the activity of methyltransferase-like 3 (Mettl3), which depends on additional proteins whose precise functions remain poorly understood. Here we identified Zc3h13 (zinc finger CCCH domain-containing protein 13)/Flacc [Fl(2)d-associated complex component] as a novel interactor of m6A methyltransferase complex components in Drosophila and mice. Like other components of this complex, Flacc controls m6A levels and is involved in sex determination in Drosophila We demonstrate that Flacc promotes m6A deposition by bridging Fl(2)d to the mRNA-binding factor Nito. Altogether, our work advances the molecular understanding of conservation and regulation of the m6A machinery.
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Affiliation(s)
- Philip Knuckles
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- University of Basel, Basel 4002, Switzerland
| | - Tina Lence
- Institute of Molecular Biology, 55128 Mainz, Germany
| | - Irmgard U Haussmann
- School of Life Science, Faculty of Health and Life Sciences, Coventry University, Coventry CV1 5FB, United Kingdom
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Dominik Jacob
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Nastasja Kreim
- Bioinformatics Core Facility, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Sarah H Carl
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel 4058, Switzerland
| | - Irene Masiello
- Institute of Molecular Biology, 55128 Mainz, Germany
- Laboratory of Cell Biology and Neurobiology, Department of Animal Biology, University of Pavia, Pavia 27100, Italy
| | - Tina Hares
- Institute of Molecular Biology, 55128 Mainz, Germany
| | - Rodrigo Villaseñor
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- University of Basel, Basel 4002, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Miguel A Andrade-Navarro
- Institute of Molecular Biology, 55128 Mainz, Germany
- Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Marco Biggiogera
- Laboratory of Cell Biology and Neurobiology, Department of Animal Biology, University of Pavia, Pavia 27100, Italy
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Matthias Soller
- School of Life Science, Faculty of Health and Life Sciences, Coventry University, Coventry CV1 5FB, United Kingdom
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- University of Basel, Basel 4002, Switzerland
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