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Li Y, Yi Y, Gao X, Wang X, Zhao D, Wang R, Zhang LS, Gao B, Zhang Y, Zhang L, Cao Q, Chen K. 2'-O-methylation at internal sites on mRNA promotes mRNA stability. Mol Cell 2024; 84:2320-2336.e6. [PMID: 38906115 PMCID: PMC11196006 DOI: 10.1016/j.molcel.2024.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/13/2024] [Accepted: 04/17/2024] [Indexed: 06/23/2024]
Abstract
2'-O-methylation (Nm) is a prominent RNA modification well known in noncoding RNAs and more recently also found at many mRNA internal sites. However, their function and base-resolution stoichiometry remain underexplored. Here, we investigate the transcriptome-wide effect of internal site Nm on mRNA stability. Combining nanopore sequencing with our developed machine learning method, NanoNm, we identify thousands of Nm sites on mRNAs with a single-base resolution. We observe a positive effect of FBL-mediated Nm modification on mRNA stability and expression level. Elevated FBL expression in cancer cells is associated with increased expression levels for 2'-O-methylated mRNAs of cancer pathways, implying the role of FBL in post-transcriptional regulation. Lastly, we find that FBL-mediated 2'-O-methylation connects to widespread 3' UTR shortening, a mechanism that globally increases RNA stability. Collectively, we demonstrate that FBL-mediated Nm modifications at mRNA internal sites regulate gene expression by enhancing mRNA stability.
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Affiliation(s)
- Yanqiang Li
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Yang Yi
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Xinlei Gao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Xin Wang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Dongyu Zhao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Rui Wang
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Li-Sheng Zhang
- Department of Chemistry, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China; Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, Chicago, IL, USA
| | - Boyang Gao
- Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, Chicago, IL, USA
| | - Yadong Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Lili Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Qi Cao
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - Kaifu Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Boston, MA, USA; Prostate Cancer Program, Dana-Farber/Harvard Cancer Center, Boston, MA, USA.
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2
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Sklias A, Cruciani S, Marchand V, Spagnuolo M, Lavergne G, Bourguignon V, Brambilla A, Dreos R, Marygold S, Novoa E, Motorin Y, Roignant JY. Comprehensive map of ribosomal 2'-O-methylation and C/D box snoRNAs in Drosophila melanogaster. Nucleic Acids Res 2024; 52:2848-2864. [PMID: 38416577 PMCID: PMC11014333 DOI: 10.1093/nar/gkae139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 02/09/2024] [Accepted: 02/26/2024] [Indexed: 03/01/2024] Open
Abstract
During their maturation, ribosomal RNAs (rRNAs) are decorated by hundreds of chemical modifications that participate in proper folding of rRNA secondary structures and therefore in ribosomal function. Along with pseudouridine, methylation of the 2'-hydroxyl ribose moiety (Nm) is the most abundant modification of rRNAs. The majority of Nm modifications in eukaryotes are placed by Fibrillarin, a conserved methyltransferase belonging to a ribonucleoprotein complex guided by C/D box small nucleolar RNAs (C/D box snoRNAs). These modifications impact interactions between rRNAs, tRNAs and mRNAs, and some are known to fine tune translation rates and efficiency. In this study, we built the first comprehensive map of Nm sites in Drosophila melanogaster rRNAs using two complementary approaches (RiboMethSeq and Nanopore direct RNA sequencing) and identified their corresponding C/D box snoRNAs by whole-transcriptome sequencing. We de novo identified 61 Nm sites, from which 55 are supported by both sequencing methods, we validated the expression of 106 C/D box snoRNAs and we predicted new or alternative rRNA Nm targets for 31 of them. Comparison of methylation level upon different stresses show only slight but specific variations, indicating that this modification is relatively stable in D. melanogaster. This study paves the way to investigate the impact of snoRNA-mediated 2'-O-methylation on translation and proteostasis in a whole organism.
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Affiliation(s)
- Athena Sklias
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Sonia Cruciani
- Center For Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, Epitranscriptomics and RNA sequencing (EpiRNA-Seq) Core Facility (UAR2008/US40 IBSLor) and UMR7365 IMoPA, Nancy, France
| | - Mariangela Spagnuolo
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Guillaume Lavergne
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Valérie Bourguignon
- Université de Lorraine, CNRS, INSERM, Epitranscriptomics and RNA sequencing (EpiRNA-Seq) Core Facility (UAR2008/US40 IBSLor) and UMR7365 IMoPA, Nancy, France
| | - Alessandro Brambilla
- Proteomics and Modomics Experimental Core (PROMEC), Norwegian University of Science and Technology and the Central Norway Regional Health Authority, Trondheim, Norway
| | - René Dreos
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Steven J Marygold
- FlyBase, Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, United Kingdom
| | - Eva Maria Novoa
- Center For Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
- University Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain
| | - Yuri Motorin
- Université de Lorraine, CNRS, INSERM, Epitranscriptomics and RNA sequencing (EpiRNA-Seq) Core Facility (UAR2008/US40 IBSLor) and UMR7365 IMoPA, Nancy, France
| | - Jean-Yves Roignant
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, Germany
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3
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Paraqindes H, Mourksi NEH, Ballesta S, Hedjam J, Bourdelais F, Fenouil T, Picart T, Catez F, Combe T, Ferrari A, Kielbassa J, Thomas E, Tonon L, Viari A, Attignon V, Carrere M, Perrossier J, Giraud S, Vanbelle C, Gabut M, Bergeron D, Scott MS, Castro Vega L, Magne N, Huillard E, Sanson M, Meyronet D, Diaz JJ, Ducray F, Marcel V, Durand S. Isocitrate dehydrogenase wt and IDHmut adult-type diffuse gliomas display distinct alterations in ribosome biogenesis and 2'O-methylation of ribosomal RNA. Neuro Oncol 2023; 25:2191-2206. [PMID: 37531290 PMCID: PMC10708943 DOI: 10.1093/neuonc/noad140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND High-grade adult-type diffuse gliomas (HGGs) constitute a heterogeneous group of aggressive tumors that are mostly incurable. Recent advances highlighting the contribution of ribosomes to cancer development have offered new clinical perspectives. Here, we uncovered that isocitrate dehydrogenase (IDH)wt and IDHmut HGGs display distinct alterations of ribosome biology, in terms of rRNA epitranscriptomics and ribosome biogenesis, which could constitute novel hallmarks that can be exploited for the management of these pathologies. METHODS We analyzed (1) the ribosomal RNA 2'O-ribose methylation (rRNA 2'Ome) using RiboMethSeq and in-house developed bioinformatics tools (https://github.com/RibosomeCRCL/ribomethseq-nfandrRMSAnalyzer) on 3 independent cohorts compiling 71 HGGs (IDHwt n = 30, IDHmut n = 41) and 9 non-neoplastic samples, (2) the expression of ribosome biogenesis factors using medium throughput RT-qPCR as a readout of ribosome biogenesis, and (3) the sensitivity of 5 HGG cell lines to RNA Pol I inhibitors (CX5461, BMH-21). RESULTS Unsupervised analysis demonstrated that HGGs could be distinguished based on their rRNA 2'Ome epitranscriptomic profile, with IDHwt glioblastomas displaying the most significant alterations of rRNA 2'Ome at specific sites. In contrast, IDHmut HGGs are largely characterized by an overexpression of ribosome biogenesis factors compared to non-neoplastic tissues or IDHwt glioblastomas. Finally, IDHmut HGG-derived spheroids display higher cytotoxicity to CX5461 than IDHwt glioblastoma, while all HGG spheroids display a similar cytotoxicity to BMH-21. CONCLUSIONS In HGGs, IDH mutational status is associated with specific alterations of the ribosome biology and with distinct sensitivities to RNA Pol I inhibitors.
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Affiliation(s)
- Hermes Paraqindes
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Nour-El-Houda Mourksi
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Samantha Ballesta
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Plateforme 3D-ONCO, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon (CRCL), Lyon, France
| | - Jordan Hedjam
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Fleur Bourdelais
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Tanguy Fenouil
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Hospices Civils de Lyon, Laboratoire de biologie médicale et d’anatomie pathologique, Lyon, France
| | - Thiébaud Picart
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Hospices Civils de Lyon, Laboratoire de biologie médicale et d’anatomie pathologique, Lyon, France
| | - Frédéric Catez
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Théo Combe
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Anthony Ferrari
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Janice Kielbassa
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Emilie Thomas
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Laurie Tonon
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Alain Viari
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, CEDEX 08, Lyon, France
- INRIA Grenoble Rhône-Alpes, Montbonnot-Saint-Martin, France
| | - Valéry Attignon
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Cancer Genomics Platform, Centre de Recherche en Cancérologie de Lyon, CEDEX 08, Lyon, France
| | - Marjorie Carrere
- Cancer Genomics Platform, Centre de Recherche en Cancérologie de Lyon, CEDEX 08, Lyon, France
| | - Jessie Perrossier
- Cancer Genomics Platform, Centre de Recherche en Cancérologie de Lyon, CEDEX 08, Lyon, France
| | - Stéphane Giraud
- Plateforme 3D-ONCO, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon (CRCL), Lyon, France
| | - Christophe Vanbelle
- Plateforme d’Imagerie Cellulaire, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon (CRCL), Lyon, France
| | - Mathieu Gabut
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Danny Bergeron
- Département de biochimie et génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Michelle S Scott
- Département de biochimie et génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Luis Castro Vega
- Sorbonne Université, Inserm, CNRS, UMRS1127, Institut du Cerveau, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière – Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Nathalie Magne
- Sorbonne Université, Inserm, CNRS, UMRS1127, Institut du Cerveau, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière – Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Emmanuelle Huillard
- Sorbonne Université, Inserm, CNRS, UMRS1127, Institut du Cerveau, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière – Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Marc Sanson
- Sorbonne Université, Inserm, CNRS, UMRS1127, Institut du Cerveau, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière – Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - David Meyronet
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Hospices Civils de Lyon, Laboratoire de biologie médicale et d’anatomie pathologique, Lyon, France
| | - Jean-Jacques Diaz
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - François Ducray
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
- Hospices Civils de Lyon, Service de neuro-oncologie, Hôpital Pierre Wertheimer, Lyon, France
| | - Virginie Marcel
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
| | - Sébastien Durand
- LabEx Dev2CAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon, Centre Léon Bérard, CEDEX 08, Lyon, France
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