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Le Franc L, Petton B, Favrel P, Rivière G. m 6A Profile Dynamics Indicates Regulation of Oyster Development by m 6A-RNA Epitranscriptomes. Genomics Proteomics Bioinformatics 2023; 21:742-755. [PMID: 36496129 PMCID: PMC10787124 DOI: 10.1016/j.gpb.2022.12.002] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/23/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
The N6-methylation of RNA adenosines (N6-methyladenosine, m6A) is an important regulator of gene expression with critical implications in vertebrate and insect development. However, the developmental significance of epitranscriptomes in lophotrochozoan organisms remains unknown. Using methylated RNA immunoprecipitation sequencing (MeRIP-seq), we generated transcriptome-wide m6A-RNA methylomes covering the entire development of the oyster from oocytes to juveniles. Oyster RNA classes display specific m6A signatures, with messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) exhibiting distinct profiles and being highly methylated compared to transposable element (TE) transcripts. Epitranscriptomes are dynamic and correspond to the chronological steps of development (cleavage, gastrulation, organogenesis, and metamorphosis), with minimal mRNA and lncRNA methylation at the morula stage followed by a global increase. mRNA m6A levels are correlated with transcript levels, and shifts in methylation profiles correspond to expression kinetics. Differentially methylated transcripts cluster according to embryo-larval stages and bear the corresponding developmental functions (cell division, signal transduction, morphogenesis, and cell differentiation). The m6A level of TE transcripts is also regulated and peaks during the gastrulation. We demonstrate that m6A-RNA methylomes are dynamic and associated with gene expression regulation during oyster development. The putative epitranscriptome implication in the cleavage, maternal-to-zygotic transition, and cell differentiation in a lophotrochozoan model brings new insights into the control and evolution of developmental processes.
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Affiliation(s)
- Lorane Le Franc
- Laboratoire de Biologie des Organismes et des Ecosystèmes Aquatiques (BOREA), Muséum d'Histoire Naturelle, Sorbonne Université, Université de Caen Normandie, Université des Antilles, CNRS UMR 8067, IRD, 14032 Caen, France
| | - Bruno Petton
- Ifremer, Laboratoire des Sciences de l'Environnement Marin, UMR 6539 CNRS/UBO/IRD/Ifremer, Centre Bretagne, 29280 Plouzané, France
| | - Pascal Favrel
- Laboratoire de Biologie des Organismes et des Ecosystèmes Aquatiques (BOREA), Muséum d'Histoire Naturelle, Sorbonne Université, Université de Caen Normandie, Université des Antilles, CNRS UMR 8067, IRD, 14032 Caen, France
| | - Guillaume Rivière
- Laboratoire de Biologie des Organismes et des Ecosystèmes Aquatiques (BOREA), Muséum d'Histoire Naturelle, Sorbonne Université, Université de Caen Normandie, Université des Antilles, CNRS UMR 8067, IRD, 14032 Caen, France.
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Schwartz J, Réalis-Doyelle E, Le Franc L, Favrel P. A Novel Dop2/Invertebrate-Type Dopamine Signaling System Potentially Mediates Stress, Female Reproduction, and Early Development in the Pacific Oyster (Crassostrea gigas). Mar Biotechnol (NY) 2021; 23:683-694. [PMID: 34365528 DOI: 10.1007/s10126-021-10052-5] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
The dopaminergic signaling pathway is involved in many physiological functions in vertebrates, but poorly documented in protostome species except arthropods. We functionally characterized a novel dopamine receptor in the Pacific oyster (Crassostrea gigas), activated by dopamine and tyramine with different efficacy and potency orders. This receptor - Cragi-DOP2R - belongs to the D1-like family of receptors and corresponds to the first representative of the Dop2/invertebrate-type dopamine receptor (Dop2/INDR) group ever identified in Lophotrochozoa. Cragi-DOP2R transcripts were expressed in various adult tissues, with higher expression levels in the visceral ganglia and the gills. Following an experiment under acute osmotic conditions, Cragi-DOP2R transcripts significantly increased in the visceral ganglia and decreased in the gills, suggesting a role of dopamine signaling in the mediation of osmotic stress. Furthermore, a role of the Cragi-DOP2R signaling pathway in female gametogenesis and in early oyster development was strongly suggested by the significantly higher levels of receptor transcripts in mature female gonads and in the early embryonic stages.
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Affiliation(s)
- Julie Schwartz
- UMR BOREA, Normandie Université, UNICAEN, Sorbonne Universités, IRD-207, Esplanade de la Paix, CNRS-806714032, CAEN cedex 5, MNHN, France.
| | - Emilie Réalis-Doyelle
- UMR BOREA, Normandie Université, UNICAEN, Sorbonne Universités, IRD-207, Esplanade de la Paix, CNRS-806714032, CAEN cedex 5, MNHN, France
| | - Lorane Le Franc
- UMR BOREA, Normandie Université, UNICAEN, Sorbonne Universités, IRD-207, Esplanade de la Paix, CNRS-806714032, CAEN cedex 5, MNHN, France
| | - Pascal Favrel
- UMR BOREA, Normandie Université, UNICAEN, Sorbonne Universités, IRD-207, Esplanade de la Paix, CNRS-806714032, CAEN cedex 5, MNHN, France
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Schwartz J, Réalis-Doyelle E, Le Franc L, Favrel P. Correction to: A Novel Dop2/Invertebrate-Type Dopamine Signaling System Potentially Mediates Stress, Female Reproduction, and Early Development in the Pacific Oyster (Crassostrea gigas). Mar Biotechnol (NY) 2021; 23:695. [PMID: 34626272 DOI: 10.1007/s10126-021-10070-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Julie Schwartz
- UMR BOREA, Normandie Université, UNICAEN, Sorbonne Universités, IRD 207, Esplanade de la Paix, CNRS-806714032 CAEN cedex 5, MNHN, France.
| | - Emilie Réalis-Doyelle
- UMR BOREA, Normandie Université, UNICAEN, Sorbonne Universités, IRD 207, Esplanade de la Paix, CNRS-806714032 CAEN cedex 5, MNHN, France
| | - Lorane Le Franc
- UMR BOREA, Normandie Université, UNICAEN, Sorbonne Universités, IRD 207, Esplanade de la Paix, CNRS-806714032 CAEN cedex 5, MNHN, France
| | - Pascal Favrel
- UMR BOREA, Normandie Université, UNICAEN, Sorbonne Universités, IRD 207, Esplanade de la Paix, CNRS-806714032 CAEN cedex 5, MNHN, France
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Le Franc L, Bernay B, Petton B, Since M, Favrel P, Rivière G. A functional m 6 A-RNA methylation pathway in the oyster Crassostrea gigas assumes epitranscriptomic regulation of lophotrochozoan development. FEBS J 2020; 288:1696-1711. [PMID: 32743927 DOI: 10.1111/febs.15500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 02/07/2020] [Revised: 06/13/2020] [Accepted: 07/28/2020] [Indexed: 11/30/2022]
Abstract
N6 -methyladenosine (m6 A) is a prevalent epitranscriptomic mark in eukaryotic RNA, with crucial roles for mammalian and ecdysozoan development. Indeed, m6 A-RNA and the related protein machinery are important for splicing, translation, maternal-to-zygotic transition and cell differentiation. However, to date, the presence of an m6 A-RNA pathway remains unknown in more distant animals, questioning the evolution and significance of the epitranscriptomic regulation. Therefore, we investigated the m6 A-RNA pathway in the oyster Crassostrea gigas, a lophotrochozoan model whose development was demonstrated under strong epigenetic influence. Using mass spectrometry and dot blot assays, we demonstrated that m6 A-RNA is actually present in the oyster and displays variations throughout early oyster development, with the lowest levels at the end of cleavage. In parallel, by in silico analyses, we were able to characterize at the molecular level a complete and conserved putative m6 A machinery. The expression levels of the identified putative m6 A writers, erasers and readers were strongly regulated across oyster development. Finally, RNA pull-down coupled to LC-MS/MS allowed us to prove the actual presence of readers able to bind m6 A-RNA and exhibiting specific developmental patterns. Altogether, our results demonstrate the conservation of a complete m6 A-RNA pathway in the oyster and strongly suggest its implication in early developmental processes including MZT. This first demonstration and characterization of an epitranscriptomic regulation in a lophotrochozoan model, potentially involved in the embryogenesis, bring new insights into our understanding of developmental epigenetic processes and their evolution.
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Affiliation(s)
- Lorane Le Franc
- UNICAEN, CNRS, BOREA, Normandie Univ, Caen, France.,Laboratoire Biologie des organismes et Ecosystèmes aquatiques (BOREA), Muséum d'Histoire naturelle, CNRS, IRD, Sorbonne Université, Université de Caen Normandie, Université des Antilles, Caen, France
| | - Benoit Bernay
- UNICAEN, ICORE, PROTEOGEN Core Facility, Caen, SF, France
| | - Bruno Petton
- Ifremer, Laboratoire des Sciences de l'Environnement Marin, UMR 6539 CNRS/UBO/IRD/Ifremer, Centre Bretagne, Normandie Univ, Plouzané, France
| | - Marc Since
- UNICAEN, Comprehensive Cancer Center F. Baclesse, SF ICORE, PRISMM Core Facility, Normandie Univ, Caen, France
| | - Pascal Favrel
- UNICAEN, CNRS, BOREA, Normandie Univ, Caen, France.,Laboratoire Biologie des organismes et Ecosystèmes aquatiques (BOREA), Muséum d'Histoire naturelle, CNRS, IRD, Sorbonne Université, Université de Caen Normandie, Université des Antilles, Caen, France
| | - Guillaume Rivière
- UNICAEN, CNRS, BOREA, Normandie Univ, Caen, France.,Laboratoire Biologie des organismes et Ecosystèmes aquatiques (BOREA), Muséum d'Histoire naturelle, CNRS, IRD, Sorbonne Université, Université de Caen Normandie, Université des Antilles, Caen, France
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