@article {9558, title = {Ancestors{\textquoteright} 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}, journal = {Environmental Science \& Technology}, year = {2024}, issn = {0013-936X}, doi = {10.1021/acs.est.3c0820110}, url = {https://pubs.acs.org/doi/10.1021/acs.est.3c08201}, author = {Sol-Dourdin, Thomas and Guyomard, Killian and Rabiller, Manuella and Houssais, Nina and Cormier, Alexandre and Le Monier, Pauline and Sussarellu, Rossana and Guillaume Rivi{\`e}re} } @article {9557, title = {Structural and functional characterization of an egg-laying hormone signaling system in a lophotrochozoan {\textendash} The pacific oyster (Crassostrea gigas)}, journal = {General and Comparative Endocrinology}, volume = {346}, year = {2024}, month = {Jan-01-2024}, pages = {114417}, issn = {00166480}, doi = {10.1016/j.ygcen.2023.114417}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0016648023002228}, author = {Favrel, P. and Dubos, M.P. and Bernay, B. and Pasquier, J. and Schwartz, J. and Lefranc, B. and Mouret, L. and Guillaume Rivi{\`e}re and Leprince, J. and Bondon, A.} } @article {9559, title = {m6A Profile Dynamics Indicates Regulation of Oyster Development by m6A-RNA Epitranscriptomes}, journal = {Genomics, Proteomics \& Bioinformatics}, volume = {21}, year = {2023}, month = {Jan-08-2023}, pages = {742 - 755}, issn = {16720229}, doi = {10.1016/j.gpb.2022.12.002}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1672022922001516}, author = {Le Franc, Lorane and Petton, Bruno and Favrel, Pascal and Guillaume Rivi{\`e}re} } @article {9560, title = {Molecular and phenotypic effects of early exposure to an environmentally relevant pesticide mixture in the Pacific oyster, Crassostrea gigas.}, journal = {Environmental Pollution}, volume = {326}, year = {2023}, month = {Jan-06-2023}, pages = {121472}, issn = {02697491}, doi = {10.1016/j.envpol.2023.121472}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0269749123004748}, author = {Sol-Dourdin, Thomas and Guillaume Rivi{\`e}re and Cormier, Alexandre and Di Poi, Carole and Guyomard, Killian and Rabiller, Manuella and Akcha, Farida and Bah Sadialiou, Thierno and Le Monier, Pauline and Sussarellu, Rossana} } @article {9561, title = {Transcriptome Profiling of the Pacific Oyster Crassostrea gigas Visceral Ganglia over a Reproduction Cycle Identifies Novel Regulatory Peptides}, journal = {Marine Drugs}, volume = {19}, year = {2021}, month = {Jan-08-2021}, pages = {452}, doi = {10.3390/md19080452}, url = {https://www.mdpi.com/1660-3397/19/8/452}, author = {R{\'e}alis-Doyelle, Emilie and Schwartz, Julie and Cabau, C{\'e}dric and Le Franc, Lorane and Bernay, Beno{\^\i}t and Guillaume Rivi{\`e}re and Klopp, Christophe and Favrel, Pascal} } @article {8123, title = {Transcriptome Profiling of the Pacific Oyster Visceral Ganglia over a Reproduction Cycle Identifies Novel Regulatory Peptides.}, journal = {Mar Drugs}, volume = {19}, year = {2021}, month = {2021 Aug 07}, abstract = {

The neuropeptides involved in the regulation of reproduction in the Pacific oyster () are quite diverse. To investigate this diversity, a transcriptomic survey of the visceral ganglia (VG) was carried out over an annual reproductive cycle. RNA-seq data from 26 samples corresponding to VG at different stages of reproduction were de novo assembled to generate a specific reference transcriptome of the oyster nervous system and used to identify differentially expressed transcripts. Transcriptome mining led to the identification of novel neuropeptide precursors (NPPs) related to the bilaterian Eclosion Hormone (EH), crustacean female sex hormone/Interleukin 17, Nesfatin, neuroparsin/IGFBP, prokineticins, and urotensin I; to the protostome GNQQN, pleurin, prohormones 3 and 4, prothoracotropic hormones (PTTH), and QSamide/PXXXamide; to the lophotrochozoan CCWamide, CLCCY, HFAamide, and LXRX; and to the mollusk-specific NPPs CCCGS, clionin, FYFY, GNamide, GRWRN, GSWN, GWE, IWMPxxGYxx, LXRYamide, RTLFamide, SLRFamide, and WGAGamide. Among the complete repertoire of NPPs, no sex-biased expression was observed. However, 25 NPPs displayed reproduction stage-specific expression, supporting their involvement in the control of gametogenesis or associated metabolisms.

}, issn = {1660-3397}, doi = {10.3390/md19080452}, author = {R{\'e}alis-Doyelle, Emilie and Schwartz, Julie and Cabau, C{\'e}dric and Le Franc, Lorane and Bernay, Beno{\^\i}t and Riviere, Guillaume and Klopp, Christophe and Favrel, Pascal} } @article {7279, title = {A functional m6 A-RNA methylation pathway in the oyster Crassostrea gigas assumes epitranscriptomic regulation of lophotrochozoan development}, journal = {The FEBS Journal}, year = {2020}, month = {Jan-09-2020}, issn = {1742-464X}, doi = {10.1111/febs.15500}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/febs.15500}, author = {Le Franc, Lorane and Bernay, Beno{\^\i}t and Petton, Bruno and Since, Marc and Pascal Favrel and Guillaume Rivi{\`e}re} } @article {8155, title = {Data for evolutive analysis of insulin related peptides in bilaterian species}, journal = {Data in Brief}, volume = {22}, year = {2019}, month = {Jan-02-2019}, pages = {546 - 550}, issn = {23523409}, doi = {10.1016/j.dib.2018.12.050}, url = {https://linkinghub.elsevier.com/retrieve/pii/S2352340918315890}, author = {Cherif--Feildel, Ma{\"e}va and Clothilde Berthelin and Riviere, Guillaume and Favrel, Pascal and Kellner, Kristell} } @article {6849, title = {Histone Methylation Participates in Gene Expression Control during the Early Development of the Pacific Oyster Crassostrea gigas}, journal = {Genes}, volume = {10}, year = {2019}, month = {Jan-09-2019}, pages = {695}, doi = {10.3390/genes10090695}, url = {https://www.mdpi.com/2073-4425/10/9/695}, author = {Fellous, Alexandre and Le Franc, Lorane and Jouaux, Aude and Goux, Didier and Pascal Favrel and Guillaume Rivi{\`e}re} } @article {6117, title = {Histone Methylation Participates in Gene Expression Control during the Early Development of the Pacific Oyster .}, journal = {Genes (Basel)}, volume = {10}, year = {2019}, month = {2019 09 10}, abstract = {

Histone methylation patterns are important epigenetic regulators of mammalian development, notably through stem cell identity maintenance by chromatin remodeling and transcriptional control of pluripotency genes. But, the implications of histone marks are poorly understood in distant groups outside vertebrates and ecdysozoan models. However, the development of the Pacific oyster is under the strong epigenetic influence of DNA methylation, and histone-demethylase orthologues are highly expressed during . early life. This suggests a physiological relevance of histone methylation regulation in oyster development, raising the question of functional conservation of this epigenetic pathway in lophotrochozoan. Quantification of histone methylation using fluorescent ELISAs during oyster early life indicated significant variations in monomethyl histone H3 lysine 4 (H3K4me), an overall decrease in H3K9 mono- and tri-methylations, and in H3K36 methylations, respectively, whereas no significant modification could be detected in H3K27 methylation. Early in vivo treatment with the JmjC-specific inhibitor Methylstat induced hypermethylation of all the examined histone H3 lysines and developmental alterations as revealed by scanning electronic microscopy. Using microarrays, we identified 376 genes that were differentially expressed under methylstat treatment, which expression patterns could discriminate between samples as indicated by principal component analysis. Furthermore, Gene Ontology revealed that these genes were related to processes potentially important for embryonic stages such as binding, cell differentiation and development. These results suggest an important physiological significance of histone methylation in the oyster embryonic and larval life, providing, to our knowledge, the first insights into epigenetic regulation by histone methylation in lophotrochozoan development.

}, issn = {2073-4425}, doi = {10.3390/genes10090695}, author = {Alexandre Fellous and Lefranc, Lorane and Jouaux, Aude and Goux, Didier and Pascal Favrel and Riviere, Guillaume} } @article {5782, title = {Molecular evolution and functional characterisation of insulin related peptides in molluscs: Contributions of Crassostrea gigas genomic and transcriptomic-wide screening}, journal = {Journal of Comparative Endocrinology}, volume = {271}, year = {2019}, pages = {15-29}, type = {research}, abstract = {

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.

}, author = {Ma{\"e}va Cherif{\textendash}Feildel and Clothilde Berthelin and B{\'e}atrice Adeline and Guillaume Rivi{\`e}re and Pascal Favrel and Kristell Kellner-Cousin} } @article {5779, title = {Copper induces expression and methylation changes of early development genes in Crassostrea gigas embryos}, journal = {Aquat Toxicol}, volume = {196}, year = {2018}, pages = {70-78}, keywords = {Oyster Embryotoxicity Copper Gene expression DNA methylation}, doi = {doi: 10.1016/j.aquatox.2018.01.001}, url = {https://www.sciencedirect.com/science/article/pii/S0166445X18300018?via\%3Dihub}, author = {Sussarellu, Rossana and Lebreton Morgane and Rouxel Julien and Akcha Farida and Guillaume Rivi{\`e}re} } @article {5031, title = {Dynamics of DNA methylomes underlie oyster development}, journal = {PLoS Genetics}, volume = {13}, year = {2017}, month = {06/2017}, pages = {e1006807}, type = {Research Paper}, url = {https:// doi.org/10.13 71/journal.p gen.1006807}, author = {Guillaume Rivi{\`e}re and Yan He and Samuele Tecchio and Elizabeth Crowell and Micha{\"e}l Gras and Pascal Sourdaine and Guo, Ximing and Pascal Favrel} } @article {4419, title = {GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas.}, journal = {BMC Bioinformatics}, volume = {16}, year = {2015}, month = {2015}, pages = {401}, abstract = {

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.

}, keywords = {Animals, Base Sequence, Computational Biology, Crassostrea, Databases, Genetic, Gene Library, Gene Ontology, Genome, High-Throughput Nucleotide Sequencing, Molecular Sequence Data, Sequence Analysis, RNA, Software, Transcriptome}, issn = {1471-2105}, doi = {10.1186/s12859-015-0833-4}, author = {Guillaume Rivi{\`e}re and Klopp, Christophe and Ibouniyamine, Nabihoudine and Huvet, Arnaud and Boudry, Pierre and Pascal Favrel} } @article {4418, title = {Regulation of Hox orthologues in the oyster Crassostrea gigas evidences a functional role for promoter DNA methylation in an invertebrate.}, journal = {FEBS Lett}, volume = {589}, year = {2015}, month = {2015 Jun 4}, pages = {1459-66}, abstract = {

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.

}, keywords = {Animals, Azacitidine, CHO Cells, Crassostrea, Cricetinae, Cricetulus, DNA (Cytosine-5-)-Methyltransferase, DNA Methylation, Embryo, Nonmammalian, Enzyme Inhibitors, Gene Expression Regulation, Developmental, Homeodomain Proteins, Invertebrates, Promoter Regions, Genetic, Transfection}, issn = {1873-3468}, doi = {10.1016/j.febslet.2015.04.043}, author = {Saint-Carlier, Emma and Guillaume Rivi{\`e}re} } @article {3399, title = {Epigenetic features in the oyster Crassostrea gigas suggestive of functionally relevant promoter DNA methylation in invertebrates.}, journal = {Frontiers in Physiology}, volume = {5}, year = {2014}, month = {04/2014}, type = {Research Perspective}, abstract = {

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{\textquoteright}s developmental and reproductive stage. We discuss the perspective that oyster DNA methylation could be biased toward the 5{\textquoteright}-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.

}, doi = {10.3389/fphys.2014.00129}, author = {Guillaume Rivi{\`e}re} } @article {3394, title = {The Jumonji gene family in Crassostrea gigas suggests evolutionary conservation of Jmj-C histone demethylases orthologues in the oyster gametogenesis and development.}, journal = {Gene}, volume = {538}, year = {2014}, month = {2014 Mar 15}, pages = {164-75}, abstract = {

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{\textquoteright}-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: {\textquoteright}single-domain Jmj{\textquoteright} and {\textquoteright}multi-domain Jmj{\textquoteright}, 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.

}, keywords = {Animals, Base Sequence, Conserved Sequence, Crassostrea, Evolution, Molecular, Gametogenesis, Gene Expression Regulation, Developmental, Jumonji Domain-Containing Histone Demethylases, Molecular Sequence Data, Multigene Family, RNA, Messenger}, issn = {1879-0038}, doi = {10.1016/j.gene.2013.12.016}, author = {Alexandre Fellous and Pascal Favrel and Guo, Ximing and Guillaume Rivi{\`e}re} } @article {3396, title = {Temperature influences histone methylation and mRNA expression of the Jmj-C histone-demethylase orthologues during the early development of the oyster Crassostrea gigas.}, journal = {Mar Genomics}, year = {2014}, month = {2014 Sep 16}, abstract = {

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{\textdegree}C, 25{\textdegree}C and 32{\textdegree}C). Histone methylation levels were investigated using fluorescent ELISA at 6 and 24h post-fertilization. When compared to the 25{\textdegree}C group, at 18{\textdegree}C H3K4, H3K9 and H3K27 residues were hypomethylated at 6h post fertilization (hpf) and hypermethylated at 24hpf. In contrast, at 32{\textdegree}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.

}, issn = {1876-7478}, doi = {10.1016/j.margen.2014.09.002}, author = {Alexandre Fellous and Pascal Favrel and Guillaume Rivi{\`e}re} }