%0 Journal Article %J Environmental Science & Technology %D 2024 %T Ancestors’ Gift: Parental Early Exposure to the Environmentally Realistic Pesticide Mixture Drives Offspring Phenotype in a Larger Extent Than Direct Exposure in the Pacific Oyster, Crassostrea gigas %A Sol-Dourdin, Thomas %A Guyomard, Killian %A Rabiller, Manuella %A Houssais, Nina %A Cormier, Alexandre %A Le Monier, Pauline %A Sussarellu, Rossana %A Guillaume Rivière %B Environmental Science & Technology %G eng %U https://pubs.acs.org/doi/10.1021/acs.est.3c08201 %! Environ. Sci. Technol. %R 10.1021/acs.est.3c0820110 %0 Journal Article %J General and Comparative Endocrinology %D 2024 %T Structural and functional characterization of an egg-laying hormone signaling system in a lophotrochozoan – The pacific oyster (Crassostrea gigas) %A Favrel, P. %A Dubos, M.P. %A Bernay, B. %A Pasquier, J. %A Schwartz, J. %A Lefranc, B. %A Mouret, L. %A Guillaume Rivière %A Leprince, J. %A Bondon, A. %B General and Comparative Endocrinology %V 346 %P 114417 %8 Jan-01-2024 %G eng %U https://linkinghub.elsevier.com/retrieve/pii/S0016648023002228 %! General and Comparative Endocrinology %R 10.1016/j.ygcen.2023.114417 %0 Journal Article %J Genomics, Proteomics & Bioinformatics %D 2023 %T m6A Profile Dynamics Indicates Regulation of Oyster Development by m6A-RNA Epitranscriptomes %A Le Franc, Lorane %A Petton, Bruno %A Favrel, Pascal %A Guillaume Rivière %B Genomics, Proteomics & Bioinformatics %V 21 %P 742 - 755 %8 Jan-08-2023 %G eng %U https://linkinghub.elsevier.com/retrieve/pii/S1672022922001516 %N 4 %! Genomics, Proteomics & Bioinformatics %R 10.1016/j.gpb.2022.12.002 %0 Journal Article %J Environmental Pollution %D 2023 %T Molecular and phenotypic effects of early exposure to an environmentally relevant pesticide mixture in the Pacific oyster, Crassostrea gigas. %A Sol-Dourdin, Thomas %A Guillaume Rivière %A Cormier, Alexandre %A Di Poi, Carole %A Guyomard, Killian %A Rabiller, Manuella %A Akcha, Farida %A Bah Sadialiou, Thierno %A Le Monier, Pauline %A Sussarellu, Rossana %B Environmental Pollution %V 326 %P 121472 %8 Jan-06-2023 %G eng %U https://linkinghub.elsevier.com/retrieve/pii/S0269749123004748 %! Environmental Pollution %R 10.1016/j.envpol.2023.121472 %0 Journal Article %J Marine Drugs %D 2021 %T Transcriptome Profiling of the Pacific Oyster Crassostrea gigas Visceral Ganglia over a Reproduction Cycle Identifies Novel Regulatory Peptides %A Réalis-Doyelle, Emilie %A Schwartz, Julie %A Cabau, Cédric %A Le Franc, Lorane %A Bernay, Benoît %A Guillaume Rivière %A Klopp, Christophe %A Favrel, Pascal %B Marine Drugs %V 19 %P 452 %8 Jan-08-2021 %G eng %U https://www.mdpi.com/1660-3397/19/8/452 %N 8 %! Marine Drugs %R 10.3390/md19080452 %0 Journal Article %J The FEBS Journal %D 2020 %T A functional m6 A‐RNA methylation pathway in the oyster Crassostrea gigas assumes epitranscriptomic regulation of lophotrochozoan development %A Le Franc, Lorane %A Bernay, Benoît %A Petton, Bruno %A Since, Marc %A Pascal Favrel %A Guillaume Rivière %B The FEBS Journal %8 Jan-09-2020 %G eng %U https://onlinelibrary.wiley.com/doi/abs/10.1111/febs.15500 %! FEBS J %R 10.1111/febs.15500 %0 Journal Article %J Genes %D 2019 %T Histone Methylation Participates in Gene Expression Control during the Early Development of the Pacific Oyster Crassostrea gigas %A Fellous, Alexandre %A Le Franc, Lorane %A Jouaux, Aude %A Goux, Didier %A Pascal Favrel %A Guillaume Rivière %B Genes %V 10 %P 695 %8 Jan-09-2019 %G eng %U https://www.mdpi.com/2073-4425/10/9/695 %N 9 %! Genes %R 10.3390/genes10090695 %0 Journal Article %J Journal of Comparative Endocrinology %D 2019 %T Molecular evolution and functional characterisation of insulin related peptides in molluscs: Contributions of Crassostrea gigas genomic and transcriptomic-wide screening %A Maëva Cherif–Feildel %A Clothilde Berthelin %A Béatrice Adeline %A Guillaume Rivière %A Pascal Favrel %A Kristell Kellner-Cousin %X

Insulin Related Peptides (IRPs) belong to the insulin superfamily and possess a typical structure with two chains,
B and A, linked by disulphide bonds. As the sequence conservation is usually low between members, IRPs are
classified according to the number and position of their disulphide bonds. In molluscan species, the first IRPs
identified, named Molluscan Insulin-related Peptides (MIPs), exhibit four disulphide bonds. The genomic and
transcriptomic data screening in the Pacific oyster Crassostrea gigas (Mollusc, Bivalvia) allowed us to identify six
IRP sequences belonging to three structural groups. Cg-MIP1 to 4 have the typical structure of MIPs with four
disulphide bonds. Cg-ILP has three disulphide bonds like vertebrate Insulin-Like Peptides (ILPs). The last one,
Cg-MILP7 has a significant homology with Drosophila ILP7 (DILP7) associated with two additional cysteines
allowing the formation of a fourth disulphide bond. The phylogenetic analysis points out that ILPs may be the
most ancestral form. Moreover, it appears that ILP7 orthologs are probably anterior to lophotrochozoa and
ecdysozoa segregation. In order to investigate the diversity of physiological functions of the oyster IRPs, we
combine in silico expression data, qPCR measurements and in situ hybridization. The Cg-ilp transcript, mainly
detected in the digestive gland and in the gonadal area, is potentially involved in the control of digestion and
gametogenesis. The expression of Cg-mip4 is mainly associated with the larval development. The Cg-mip
transcript shared by the Cg-MIP1, 2 and 3, is mainly expressed in visceral ganglia but its expression was also
observed in the gonads of mature males. This pattern suggested the key roles of IRPs in the control of sexual
reproduction in molluscan species.

%B Journal of Comparative Endocrinology %V 271 %P 15-29 %G eng %9 research %0 Journal Article %J Aquat Toxicol %D 2018 %T Copper induces expression and methylation changes of early development genes in Crassostrea gigas embryos %A Sussarellu, Rossana %A Lebreton Morgane %A Rouxel Julien %A Akcha Farida %A Guillaume Rivière %K Oyster Embryotoxicity Copper Gene expression DNA methylation %B Aquat Toxicol %V 196 %P 70-78 %G eng %U https://www.sciencedirect.com/science/article/pii/S0166445X18300018?via%3Dihub %R doi: 10.1016/j.aquatox.2018.01.001 %0 Journal Article %J PLoS Genetics %D 2017 %T Dynamics of DNA methylomes underlie oyster development %A Guillaume Rivière %A Yan He %A Samuele Tecchio %A Elizabeth Crowell %A Michaël Gras %A Pascal Sourdaine %A Guo, Ximing %A Pascal Favrel %B PLoS Genetics %V 13 %P e1006807 %8 06/2017 %G eng %U https:// doi.org/10.13 71/journal.p gen.1006807 %N 6 %9 Research Paper %0 Journal Article %J BMC Bioinformatics %D 2015 %T GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas. %A Guillaume Rivière %A Klopp, Christophe %A Ibouniyamine, Nabihoudine %A Huvet, Arnaud %A Boudry, Pierre %A Pascal Favrel %K Animals %K Base Sequence %K Computational Biology %K Crassostrea %K Databases, Genetic %K Gene Library %K Gene Ontology %K Genome %K High-Throughput Nucleotide Sequencing %K Molecular Sequence Data %K Sequence Analysis, RNA %K Software %K Transcriptome %X

BACKGROUND: The Pacific oyster, Crassostrea gigas, is one of the most important aquaculture shellfish resources worldwide. Important efforts have been undertaken towards a better knowledge of its genome and transcriptome, which makes now C. gigas becoming a model organism among lophotrochozoans, the under-described sister clade of ecdysozoans within protostomes. These massive sequencing efforts offer the opportunity to assemble gene expression data and make such resource accessible and exploitable for the scientific community. Therefore, we undertook this assembly into an up-to-date publicly available transcriptome database: the GigaTON (Gigas TranscriptOme pipeliNe) database.

DESCRIPTION: We assembled 2204 million sequences obtained from 114 publicly available RNA-seq libraries that were realized using all embryo-larval development stages, adult organs, different environmental stressors including heavy metals, temperature, salinity and exposure to air, which were mostly performed as part of the Crassostrea gigas genome project. This data was analyzed in silico and resulted into 56621 newly assembled contigs that were deposited into a publicly available database, the GigaTON database. This database also provides powerful and user-friendly request tools to browse and retrieve information about annotation, expression level, UTRs, splice and polymorphism, and gene ontology associated to all the contigs into each, and between all libraries.

CONCLUSIONS: The GigaTON database provides a convenient, potent and versatile interface to browse, retrieve, confront and compare massive transcriptomic information in an extensive range of conditions, tissues and developmental stages in Crassostrea gigas. To our knowledge, the GigaTON database constitutes the most extensive transcriptomic database to date in marine invertebrates, thereby a new reference transcriptome in the oyster, a highly valuable resource to physiologists and evolutionary biologists.

%B BMC Bioinformatics %V 16 %P 401 %8 2015 %G eng %R 10.1186/s12859-015-0833-4 %0 Journal Article %J FEBS Lett %D 2015 %T Regulation of Hox orthologues in the oyster Crassostrea gigas evidences a functional role for promoter DNA methylation in an invertebrate. %A Saint-Carlier, Emma %A Guillaume Rivière %K Animals %K Azacitidine %K CHO Cells %K Crassostrea %K Cricetinae %K Cricetulus %K DNA (Cytosine-5-)-Methyltransferase %K DNA Methylation %K Embryo, Nonmammalian %K Enzyme Inhibitors %K Gene Expression Regulation, Developmental %K Homeodomain Proteins %K Invertebrates %K Promoter Regions, Genetic %K Transfection %X

DNA methylation within promoter regions (PRDM) controls vertebrate early gene transcription and thereby development, but is neglected outside this group. However, epigenetic features in the oyster Crassostrea gigas suggest functional significance of PDRM in invertebrates. To investigate this, reporter constructs containing in vitro methylated oyster Hox gene promoters were transfected into oyster embryos. The influence of in vivo methylation was studied using bisulfite sequencing and DNA methyltransferase inhibition during development. Our results demonstrate that methylation controls the transcriptional activity of the promoters investigated, unraveling a functional role for PRDM in a lophotrochozoan, an important finding regarding the evolution of epigenetic regulation.

%B FEBS Lett %V 589 %P 1459-66 %8 2015 Jun 4 %G eng %N 13 %R 10.1016/j.febslet.2015.04.043 %0 Journal Article %J Frontiers in Physiology %D 2014 %T Epigenetic features in the oyster Crassostrea gigas suggestive of functionally relevant promoter DNA methylation in invertebrates. %A Guillaume Rivière %X

DNA methylation is evolutionarily conserved. Vertebrates exhibit high, widespread DNA methylation whereas invertebrate genomes are less methylated, predominantly within gene bodies. DNA methylation in invertebrates is associated with transcription level, alternative splicing and genome evolution, but functional outcomes of DNA methylation remain poorly described in lophotrochozoans. Recent genome-wide approaches improve understanding in distant taxa such as molluscs, where the phylogenetic position and life traits of Crassostrea gigas make this bivalve an ideal model to study the physiological and evolutionary implications of DNA methylation. We review the literature about DNA methylation in invertebrates and focus on DNA methylation features in the oyster. Indeed, though our MeDIP-seq results confirm predominant intragenic methylation, the profiles depend on the oyster’s developmental and reproductive stage. We discuss the perspective that oyster DNA methylation could be biased toward the 5’-end of some genes, depending on physiological status, suggesting important functional outcomes of putative promoter methylation from cell differentiation during early development to sustained adaptation of the species to the environment.

%B Frontiers in Physiology %V 5 %8 04/2014 %G eng %9 Research Perspective %R 10.3389/fphys.2014.00129 %0 Journal Article %J Gene %D 2014 %T The Jumonji gene family in Crassostrea gigas suggests evolutionary conservation of Jmj-C histone demethylases orthologues in the oyster gametogenesis and development. %A Alexandre Fellous %A Pascal Favrel %A Guo, Ximing %A Guillaume Rivière %K Animals %K Base Sequence %K Conserved Sequence %K Crassostrea %K Evolution, Molecular %K Gametogenesis %K Gene Expression Regulation, Developmental %K Jumonji Domain-Containing Histone Demethylases %K Molecular Sequence Data %K Multigene Family %K RNA, Messenger %X

Jumonji (Jmj) proteins are histone demethylases, which control the identity of stem cells. Jmj genes were characterized from plants to mammals where they have been implicated in the epigenetic regulation of development. Despite the Pacific oyster Crassostrea gigas representing one of the most important aquaculture resources worldwide, the molecular mechanisms governing the embryogenesis and reproduction of this lophotrochozoan species remain poorly understood. However, annotations in the C. gigas EST library suggested the presence of putative Jumonji genes, raising the question of the conservation of this family of histone demethylases in the oyster. Using Primer walking, 5'-RACE PCR and in silico analyses, we characterized nine Jumonji orthologues in the oyster, called Cg-Jmj, bearing conserved domains critical for putative histone demethylase activity. Phylogenic analyses revealed that oyster Jumonji cluster into two distinct groups: 'single-domain Jmj' and 'multi-domain Jmj', and define 8 subgroups corresponding to each cognate orthologues in metazoans. RT-qPCR investigations showed specific regulations of Cg-Jmj mRNAs during the early development and along the reproduction cycle. Furthermore, in situ and in toto hybridizations indicate that oyster Jumonji genes are transcribed mostly within the gonad in adult oysters whereas they display a ubiquitous expression during embryonic and larval development. Our study demonstrates the presence of nine Jumonji orthologues in the oyster C. gigas. Their domain conservation and their expression profile suggest an implication during reproduction and development, questioning about the epigenetic regulation by histone methylation in lophotrochozoans.

%B Gene %V 538 %P 164-75 %8 2014 Mar 15 %G eng %N 1 %R 10.1016/j.gene.2013.12.016 %0 Journal Article %J Mar Genomics %D 2014 %T Temperature influences histone methylation and mRNA expression of the Jmj-C histone-demethylase orthologues during the early development of the oyster Crassostrea gigas. %A Alexandre Fellous %A Pascal Favrel %A Guillaume Rivière %X

In many groups, epigenetic mechanisms influence developmental gene regulation under environmental inputs. The Pacific oyster Crassostrea gigas belongs to lophotrochozoans and its larval development is highly dependent on temperature, but the role of epigenetic mechanisms in this context is unknown despite high levels of the recently characterized Jumonji histone demethylase (JHDM) orthologues (Cg_Jumonji) suggesting a physiological relevance of histone methylation in the oyster development. Because in other species alterations of the histone methylation pattern have deleterious outcomes, we investigated the influence of temperature during the oyster larval life on histone methylation and JHDM expression. To shed light on this point, oyster embryonic and early larval development experiments were carried out at different temperatures (18°C, 25°C and 32°C). Histone methylation levels were investigated using fluorescent ELISA at 6 and 24h post-fertilization. When compared to the 25°C group, at 18°C H3K4, H3K9 and H3K27 residues were hypomethylated at 6h post fertilization (hpf) and hypermethylated at 24hpf. In contrast, at 32°C, 6hpf animals present a dramatic hypermethylation (ca. 4-fold) of all examined residues, which is minored but sustained at 24hpf. RT-qPCR investigations of the mRNA expression of the nine oyster JHDMs, showed gene- and stage-specific temperature sensitivities throughout the early life of oysters. This study provides evidence of the biological significance of histone methylation during development in a lophotrochozoan species. Our results also indicate that temperature influences histone methylation, possibly through the expression level of putative actors of its regulation, which might participate in developmental control. To our knowledge, this is the first report indicating a direct relationship between an epigenetic mark and an environmental parameter in marine molluscs. Such investigations could help better understand the molecular mechanisms of development and adaptation in lophotrochozoans.

%B Mar Genomics %8 2014 Sep 16 %G eng %R 10.1016/j.margen.2014.09.002