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Leemans M, Spirhanzlova P, Couderq S, Le Mével S, Grimaldi A, Duvernois-Berthet E, Demeneix B, Fini JB. A Mixture of Chemicals Found in Human Amniotic Fluid Disrupts Brain Gene Expression and Behavior in Xenopus laevis. Int J Mol Sci 2023; 24:ijms24032588. [PMID: 36768911 PMCID: PMC9916464 DOI: 10.3390/ijms24032588] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/31/2023] Open
Abstract
Thyroid hormones (TH) are essential for normal brain development, influencing neural cell differentiation, migration, and synaptogenesis. Multiple endocrine-disrupting chemicals (EDCs) are found in the environment, raising concern for their potential effects on TH signaling and the consequences on neurodevelopment and behavior. While most research on EDCs investigates the effects of individual chemicals, human health may be adversely affected by a mixture of chemicals. The potential consequences of EDC exposure on human health are far-reaching and include problems with immune function, reproductive health, and neurological development. We hypothesized that embryonic exposure to a mixture of chemicals (containing phenols, phthalates, pesticides, heavy metals, and perfluorinated, polychlorinated, and polybrominated compounds) identified as commonly found in the human amniotic fluid could lead to altered brain development. We assessed its effect on TH signaling and neurodevelopment in an amphibian model (Xenopus laevis) highly sensitive to thyroid disruption. Fertilized eggs were exposed for eight days to either TH (thyroxine, T4 10 nM) or the amniotic mixture (at the actual concentration) until reaching stage NF47, where we analyzed gene expression in the brains of exposed tadpoles using both RT-qPCR and RNA sequencing. The results indicate that whilst some overlap on TH-dependent genes exists, T4 and the mixture have different gene signatures. Immunohistochemistry showed increased proliferation in the brains of T4-treated animals, whereas no difference was observed for the amniotic mixture. Further, we demonstrated diminished tadpoles' motility in response to T4 and mixture exposure. As the individual chemicals composing the mixture are considered safe, these results highlight the importance of examining the effects of mixtures to improve risk assessment.
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Rigolet M, Buisine N, Scharwatt M, Duvernois-Berthet E, Buchholz DR, Sachs LM. Crosstalk between Thyroid Hormone and Corticosteroid Signaling Targets Cell Proliferation in Xenopus tropicalis Tadpole Liver. Int J Mol Sci 2022; 23:ijms232213715. [PMID: 36430192 PMCID: PMC9692397 DOI: 10.3390/ijms232213715] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022] Open
Abstract
Thyroid hormones (TH) and glucocorticoids (GC) are involved in numerous developmental and physiological processes. The effects of individual hormones are well documented, but little is known about the joint actions of the two hormones. To decipher the crosstalk between these two hormonal pathways, we conducted a transcriptional analysis of genes regulated by TH, GC, or both hormones together in liver of Xenopus tropicalis tadpoles using RNA-Seq. Among the differentially expressed genes (DE), 70.5% were regulated by TH only, 0.87% by GC only, and 15% by crosstalk between the two hormones. Gene ontology analysis of the crosstalk-regulated genes identified terms referring to DNA replication, DNA repair, and cell-cycle regulation. Biological network analysis identified groups of genes targeted by the hormonal crosstalk and corroborated the gene ontology analysis. Specifically, we found two groups of functionally linked genes (chains) mainly composed of crosstalk-regulated hubs (highly interactive genes), and a large subnetwork centred around the crosstalk-regulated genes psmb6 and cdc7. Most of the genes in the chains are involved in cell-cycle regulation, as are psmb6 and cdc7, which regulate the G2/M transition. Thus, the biological action of these two hormonal pathways acting together in the liver targets cell-cycle regulation.
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Affiliation(s)
- Muriel Rigolet
- UMR PhyMA CNRS, Muséum National d’Histoire Naturelle, 75005 Paris, France
| | - Nicolas Buisine
- UMR PhyMA CNRS, Muséum National d’Histoire Naturelle, 75005 Paris, France
| | - Marylou Scharwatt
- UMR PhyMA CNRS, Muséum National d’Histoire Naturelle, 75005 Paris, France
| | | | - Daniel R. Buchholz
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Laurent M. Sachs
- UMR PhyMA CNRS, Muséum National d’Histoire Naturelle, 75005 Paris, France
- UMR7221 CNRS, Muséum National d’Histoire Naturelle, CP32, 7 Rue Cuvier, CEDEX 05, 75231 Paris, France
- Correspondence: ; Tel.: +33-1-40-79-36-17
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Boisard J, Duvernois-Berthet E, Duval L, Schrével J, Guillou L, Labat A, Le Panse S, Prensier G, Ponger L, Florent I. Marine gregarine genomes reveal the breadth of apicomplexan diversity with a partially conserved glideosome machinery. BMC Genomics 2022; 23:485. [PMID: 35780080 PMCID: PMC9250747 DOI: 10.1186/s12864-022-08700-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Received: 02/10/2022] [Accepted: 06/13/2022] [Indexed: 12/29/2022] Open
Abstract
Our current view of the evolutionary history, coding and adaptive capacities of Apicomplexa, protozoan parasites of a wide range of metazoan, is currently strongly biased toward species infecting humans, as data on early diverging apicomplexan lineages infecting invertebrates is extremely limited. Here, we characterized the genome of the marine eugregarine Porospora gigantea, intestinal parasite of Lobsters, remarkable for the macroscopic size of its vegetative feeding forms (trophozoites) and its gliding speed, the fastest so far recorded for Apicomplexa. Two highly syntenic genomes named A and B were assembled. Similar in size (~ 9 Mb) and coding capacity (~ 5300 genes), A and B genomes are 10.8% divergent at the nucleotide level, corresponding to 16-38 My in divergent time. Orthogroup analysis across 25 (proto)Apicomplexa species, including Gregarina niphandrodes, showed that A and B are highly divergent from all other known apicomplexan species, revealing an unexpected breadth of diversity. Phylogenetically these two species branch sisters to Cephaloidophoroidea, and thus expand the known crustacean gregarine superfamily. The genomes were mined for genes encoding proteins necessary for gliding, a key feature of apicomplexans parasites, currently studied through the molecular model called glideosome. Sequence analysis shows that actin-related proteins and regulatory factors are strongly conserved within apicomplexans. In contrast, the predicted protein sequences of core glideosome proteins and adhesion proteins are highly variable among apicomplexan lineages, especially in gregarines. These results confirm the importance of studying gregarines to widen our biological and evolutionary view of apicomplexan species diversity, and to deepen our understanding of the molecular bases of key functions such as gliding, well known to allow access to the intracellular parasitic lifestyle in Apicomplexa.
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Affiliation(s)
- Julie Boisard
- Département Adaptations du Vivant (AVIV), Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245 CNRS), Muséum National d'Histoire Naturelle, CNRS, CP 52, 57 rue Cuvier, 75231 Cedex 05, Paris, France. .,Département Adaptations du Vivant (AVIV), Structure et instabilité des génomes (STRING UMR 7196 CNRS/INSERM U1154), Muséum National d'Histoire Naturelle, CNRS, INSERM, CP 26, 57 rue Cuvier, 75231 Cedex 05, Paris, France. .,Department of Biology, Lund University, Sölvegatan 35, 223 62, Lund, Sweden.
| | - Evelyne Duvernois-Berthet
- Département Adaptations du Vivant (AVIV), Physiologie Moléculaire et Adaptation (PhyMA UMR 7221 CNRS), Muséum national d'Histoire naturelle, CNRS, CP 32, 7 rue Cuvier, 75005, Paris, France
| | - Linda Duval
- Département Adaptations du Vivant (AVIV), Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245 CNRS), Muséum National d'Histoire Naturelle, CNRS, CP 52, 57 rue Cuvier, 75231 Cedex 05, Paris, France
| | - Joseph Schrével
- Département Adaptations du Vivant (AVIV), Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245 CNRS), Muséum National d'Histoire Naturelle, CNRS, CP 52, 57 rue Cuvier, 75231 Cedex 05, Paris, France
| | - Laure Guillou
- CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, Sorbonne Université, 29680, Roscoff, France
| | - Amandine Labat
- Département Adaptations du Vivant (AVIV), Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245 CNRS), Muséum National d'Histoire Naturelle, CNRS, CP 52, 57 rue Cuvier, 75231 Cedex 05, Paris, France
| | - Sophie Le Panse
- Plateforme d'Imagerie Merimage, FR2424, Centre National de la Recherche Scientifique, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Gérard Prensier
- Cell biology and Electron Microscopy Laboratory, François Rabelais University, 10 Boulevard Tonnellé, 3223 Cedex, Tours, BP, France
| | - Loïc Ponger
- Département Adaptations du Vivant (AVIV), Structure et instabilité des génomes (STRING UMR 7196 CNRS/INSERM U1154), Muséum National d'Histoire Naturelle, CNRS, INSERM, CP 26, 57 rue Cuvier, 75231 Cedex 05, Paris, France.
| | - Isabelle Florent
- Département Adaptations du Vivant (AVIV), Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245 CNRS), Muséum National d'Histoire Naturelle, CNRS, CP 52, 57 rue Cuvier, 75231 Cedex 05, Paris, France.
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Buffet JP, Corre E, Duvernois-Berthet E, Fournier J, Lopez PJ. Adhesive gland transcriptomics uncovers a diversity of genes involved in glue formation in marine tube-building polychaetes. Acta Biomater 2018; 72:316-328. [PMID: 29597026 DOI: 10.1016/j.actbio.2018.03.037] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 03/16/2018] [Accepted: 03/20/2018] [Indexed: 11/30/2022]
Abstract
Tube-building sabellariid polychaetes are hermatypic organisms capable of forming vast reefs in highly turbulent marine habitats. Sabellariid worms assemble their tube by gluing together siliceous and calcareous clastic particles using a polyelectrolytic biocement. Here, we performed transcriptomic analyses to investigate the genes that are differentially expressed in the parathorax region, which contains the adhesive gland and tissues, from the rest of the body. We found a large number of candidate genes to be involved in the composition and formation of biocement in two species: Sabellaria alveolata and Phragmatopoma caudata. Our results indicate that the glue is likely to be composed by a large diversity of cement-related proteins, including Poly(S), GY-rich, H-repeat and miscellaneous categories. However, sequences divergence and differences in expression profiles between S. alveolata and P. caudata of cement-related proteins may reflect adaptation to the type of substratum used to build their tube, and/or to their habitat (temperate vs tropical, amplitude of pH, salinity …). Related to the L-DOPA metabolic pathways and linked with the genes that were differentially expressed in the parathorax region, we found that tyrosinase and peroxidase gene families may have undergone independent expansion in the two Sabellariidae species investigated. Our data also reinforce the importance of protein modifications in cement formation. Altogether these new genomic resources help to identify novel transcripts encoding for cement-related proteins, but also important enzymes putatively involved in the chemistry of the adhesion process, such as kinases, and may correspond to new targets to develop biomimetic approaches. STATEMENTS OF SIGNIFICANCE The diversity of bioadhesives elaborated by marine invertebrates is a tremendous source of inspiration to develop biomimetic approaches for biomedical and technical applications. Recent studies on the adhesion system of mussel, barnacle and sea star had highlighted the usefulness of high-throughput RNA sequencing in accelerating the development of biomimetic adhesives. Adhesion in sandcastle worms, which involves catechol and phosphate chemistries, polyelectrolyte complexes, supramolecular architectures, and a coacervation process, is a useful model to develop multipurpose wet adhesives. Using transcriptomic tools, we have explored the diversity of genes encoding for structural and catalytic proteins involved in cement formation of two sandcastle worm species, Sabellaria alveolata and Phragmatopoma caudata. The important genomic resource generated should help to design novel "blue" adhesives.
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Affiliation(s)
- Jean-Philippe Buffet
- UMR Biologie des Organismes et des Ecosystèmes Aquatiques, MNHN/CNRS-7208 Sorbonne Université/IRD-207/UCN /UA, 43 rue Cuvier, Paris 75005, France
| | - Erwan Corre
- Station Biologique - FR 2424, CNRS/Sorbonne Université, ABiMS, Roscoff 29680, France
| | | | - Jérôme Fournier
- UMR Biologie des Organismes et des Ecosystèmes Aquatiques, MNHN/CNRS-7208 Sorbonne Université/IRD-207/UCN /UA, 43 rue Cuvier, Paris 75005, France
| | - Pascal Jean Lopez
- UMR Biologie des Organismes et des Ecosystèmes Aquatiques, MNHN/CNRS-7208 Sorbonne Université/IRD-207/UCN /UA, 43 rue Cuvier, Paris 75005, France.
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Bellessort B, Bachelot A, Grouthier V, De Lombares C, Narboux-Neme N, Garagnani P, Pirazzini C, Astigiano S, Mastracci L, Fontaine A, Alfama G, Duvernois-Berthet E, Levi G. Comparative analysis of molecular signatures suggests the use of gabapentin for the management of endometriosis-associated pain. J Pain Res 2018; 11:715-725. [PMID: 29692624 PMCID: PMC5903492 DOI: 10.2147/jpr.s163611] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 11/30/2022] Open
Abstract
Background It has been repetitively shown that the transcription factors DLX5 and DLX6 are drastically downregulated in endometriotic lesions when compared with eutopic endometrium. These findings suggest that regulatory cascades involving DLX5/6 might be at the origin of endometriosis symptoms such as chronic pelvic pain (CPP). We have shown that inactivation of Dlx5 and Dlx5/6 in the mouse uterus results in an endometrial phenotype reminiscent of endometriosis. Methods We focused on genes that present a similar deregulation in endometriosis and in Dlx5/6-null mice in search of new endometriosis targets. Results We confirmed a strong reduction of DLX5 expression in endometriosis implants. We identified a signature of 30 genes similarly deregulated in human endometriosis implants and in Dlx5/6-null mouse uteri, reinforcing the notion that the downregulation of Dlx5/6 is an early event in the progress of endometriosis. CACNA2D3, a component of the α2δ family of voltage-dependent calcium channel complex, was strongly overexpressed both in mutant mouse uteri and in endometriosis implants, were also CACNA2D1 and CACNA2D2, other members of the α2δ family involved in nociception, are upregulated. Conclusion Comparative analysis of gene expression signatures from endometriosis and mouse models showed that calcium channel subunits α2δ involved in nociception can be targets for the treatment of endometriosis-associated pain. CACNA2D3 has been associated with pain sensitization and heat nociception in animal models. In patients, CACNA2D3 variants were associated with reduced sensitivity to acute noxious stimuli. As α2δs were targets of gabapentinoid analgesics, the results suggested the use of these drugs for the treatment of endometriosis-associated pain. Indeed, recent small-scale clinical studies have shown that gabapentin could be effective in women with CPP. The findings of this study reinforce the need for a large definitive trial.
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Affiliation(s)
- Brice Bellessort
- Evolution of Endocrine Regulations, Department AVIV, National Museum of Natural History, Paris, France
| | - Anne Bachelot
- Evolution of Endocrine Regulations, Department AVIV, National Museum of Natural History, Paris, France.,AP-HP, Department of Endocrinology and Reproductive Medicine, Reference Center for Rare Endocrine Diseases, Pitié-Salpêtrière Hospital, UPMC, Paris, France
| | - Virginie Grouthier
- AP-HP, Department of Endocrinology and Reproductive Medicine, Reference Center for Rare Endocrine Diseases, Pitié-Salpêtrière Hospital, UPMC, Paris, France
| | - Camille De Lombares
- Evolution of Endocrine Regulations, Department AVIV, National Museum of Natural History, Paris, France
| | - Nicolas Narboux-Neme
- Evolution of Endocrine Regulations, Department AVIV, National Museum of Natural History, Paris, France
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna, Italy
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna, Italy
| | - Simonetta Astigiano
- Department of Integrated Oncological Therapies, San Martino Hospital, Genova, Italy
| | - Luca Mastracci
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genoa, Genova, Italy.,Division of Anatomic Pathology, Department of Surgical Science and Integrated Diagnostics, University of Genoa, Genova, Italy
| | - Anastasia Fontaine
- Evolution of Endocrine Regulations, Department AVIV, National Museum of Natural History, Paris, France
| | - Gladys Alfama
- Evolution of Endocrine Regulations, Department AVIV, National Museum of Natural History, Paris, France
| | - Evelyne Duvernois-Berthet
- Evolution of Endocrine Regulations, Department AVIV, National Museum of Natural History, Paris, France
| | - Giovanni Levi
- Evolution of Endocrine Regulations, Department AVIV, National Museum of Natural History, Paris, France
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Abstract
Bivalves have evolved a range of complex shell forming mechanisms that are reflected by their incredible diversity in shell mineralogy and microstructures. A suite of proteins exported to the shell matrix space plays a significant role in controlling these features, in addition to underpinning some of the physical properties of the shell itself. Although, there is a general consensus that a minimum basic protein tool kit is required for shell construction, to date, this remains undefined. In this study, the shell matrix proteins (SMPs) of four highly divergent bivalves (The Pacific oyster, Crassostrea gigas; the blue mussel, Mytilus edulis; the clam, Mya truncata, and the king scallop, Pecten maximus) were analyzed in an identical fashion using proteomics pipeline. This enabled us to identify the critical elements of a "basic tool kit" for calcification processes, which were conserved across the taxa irrespective of the shell morphology and arrangement of the crystal surfaces. In addition, protein domains controlling the crystal layers specific to aragonite and calcite were also identified. Intriguingly, a significant number of the identified SMPs contained domains related to immune functions. These were often are unique to each species implying their involvement not only in immunity, but also environmental adaptation. This suggests that the SMPs are selectively exported in a complex mix to endow the shell with both mechanical protection and biochemical defense.
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Affiliation(s)
- Jaison Arivalagan
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France
- UMR 7208 CNRS/MNHN/UPMC/IRD Biologie des Organismes Aquatiques et Ecosystèmes, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France
| | - Tejaswi Yarra
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, United Kingdom
- University of Edinburgh, Institute of Evolutionary Biology, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, United Kingdom
| | - Benjamin Marie
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France
| | - Victoria A Sleight
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, United Kingdom
| | - Evelyne Duvernois-Berthet
- UMR 7221 CNRS/MNHN Evolution des Régulations Endocriniennes, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France
| | - Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, United Kingdom
| | - Arul Marie
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France
| | - Sophie Berland
- UMR 7208 CNRS/MNHN/UPMC/IRD Biologie des Organismes Aquatiques et Ecosystèmes, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France
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Qiao Q, Le Manach S, Huet H, Duvernois-Berthet E, Chaouch S, Duval C, Sotton B, Ponger L, Marie A, Mathéron L, Lennon S, Bolbach G, Djediat C, Bernard C, Edery M, Marie B. An integrated omic analysis of hepatic alteration in medaka fish chronically exposed to cyanotoxins with possible mechanisms of reproductive toxicity. Environ Pollut 2016; 219:119-131. [PMID: 27814527 DOI: 10.1016/j.envpol.2016.10.029] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [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: 08/04/2016] [Revised: 09/27/2016] [Accepted: 10/09/2016] [Indexed: 05/22/2023]
Abstract
Cyanobacterial blooms threaten human health as well as the population of other living organisms in the aquatic environment, particularly due to the production of natural toxic components, the cyanotoxin. So far, the most studied cyanotoxins are microcystins (MCs). In this study, the hepatic alterations at histological, proteome and transcriptome levels were evaluated in female and male medaka fish chronically exposed to 1 and 5 μg L-1 microcystin-LR (MC-LR) and to the extract of MC-producing Microcystis aeruginosa PCC 7820 (5 μg L-1 of equivalent MC-LR) by balneation for 28 days, aiming at enhancing our understanding of the potential reproductive toxicity of cyanotoxins in aquatic vertebrate models. Indeed, both MC and Microcystis extract adversely affect reproductive parameters including fecundity and egg hatchability. The liver of toxin treated female fish present glycogen storage loss and cellular damages. The quantitative proteomics analysis revealed that the quantities of 225 hepatic proteins are dysregulated. In particular, a notable decrease in protein quantities of vitellogenin and choriogenin was observed, which could explain the decrease in reproductive output. Liver transcriptome analysis through Illumina RNA-seq reveals that over 100-400 genes are differentially expressed under 5 μg L-1 MC-LR and Microcystis extract treatments, respectively. Ingenuity pathway analysis of the omic data attests that various metabolic pathways, such as energy production, protein biosynthesis and lipid metabolism, are disturbed by both MC-LR and the Microcystis extract, which could provoke the observed reproductive impairment. The transcriptomics analysis also constitutes the first report of the impairment of circadian rhythm-related gene induced by MCs. This study contributes to a better understanding of the potential consequences of chronic exposure of fish to environmental concentrations of cyanotoxins, suggesting that Microcystis extract could impact a wider range of biological pathways, compared with pure MC-LR, and even 1 μg L-1 MC-LR potentially induces a health risk for aquatic organisms.
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Affiliation(s)
- Qin Qiao
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France.
| | - Séverine Le Manach
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Hélène Huet
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France; Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, BioPôle Alfort, 94700 Maisons-Alfort, France
| | - Evelyne Duvernois-Berthet
- UMR 7221 CNRS/MNHN, Évolution des Régulations Endocriniennes, Sorbonne Universités, Muséum Nationale d'Histoire Naturelle, Paris, France
| | - Soraya Chaouch
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Charlotte Duval
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Benoit Sotton
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Loïc Ponger
- UMR 7196 MNHN/CNRS, INSERM U1154, Sorbonne Universités, Museum National d'Histoire Naturelle, Paris, France
| | - Arul Marie
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Lucrèce Mathéron
- Institut de Biologie Paris Seine/FR 3631, Plateforme Spectrométrie de masse et Protéomique, Institut de Biologie Intégrative IFR 83, Sorbonne Universités, Université Pierre et Marie Curie, 75005 Paris, France
| | | | - Gérard Bolbach
- Institut de Biologie Paris Seine/FR 3631, Plateforme Spectrométrie de masse et Protéomique, Institut de Biologie Intégrative IFR 83, Sorbonne Universités, Université Pierre et Marie Curie, 75005 Paris, France
| | - Chakib Djediat
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Cécile Bernard
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Marc Edery
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Benjamin Marie
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France.
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Qiao Q, Le Manach S, Sotton B, Huet H, Duvernois-Berthet E, Paris A, Duval C, Ponger L, Marie A, Blond A, Mathéron L, Vinh J, Bolbach G, Djediat C, Bernard C, Edery M, Marie B. Deep sexual dimorphism in adult medaka fish liver highlighted by multi-omic approach. Sci Rep 2016; 6:32459. [PMID: 27561897 PMCID: PMC5000296 DOI: 10.1038/srep32459] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/09/2016] [Indexed: 02/05/2023] Open
Abstract
Sexual dimorphism describes the features that discriminate between the two sexes at various biological levels. Especially, during the reproductive phase, the liver is one of the most sexually dimorphic organs, because of different metabolic demands between the two sexes. The liver is a key organ that plays fundamental roles in various physiological processes, including digestion, energetic metabolism, xenobiotic detoxification, biosynthesis of serum proteins, and also in endocrine or immune response. The sex-dimorphism of the liver is particularly obvious in oviparous animals, as the female liver is the main organ for the synthesis of oocyte constituents. In this work, we are interested in identifying molecular sexual dimorphism in the liver of adult medaka fish and their sex-variation in response to hepatotoxic exposures. By developing an integrative approach combining histology and different high-throughput omic investigations (metabolomics, proteomics and transcriptomics), we were able to globally depict the strong sexual dimorphism that concerns various cellular and molecular processes of hepatocytes comprising protein synthesis, amino acid, lipid and polysaccharide metabolism, along with steroidogenesis and detoxification. The results of this work imply noticeable repercussions on the biology of oviparous organisms environmentally exposed to chemical or toxin issues.
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Affiliation(s)
- Qin Qiao
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Séverine Le Manach
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Benoit Sotton
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Hélène Huet
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France.,Université Paris-Est, Ecole Nationale Vétérinaire d'Alfort, BioPôle Alfort, Maisons-Alfort, France
| | - Evelyne Duvernois-Berthet
- UMR 7221 CNRS/MNHN, Évolution des Régulations Endocriniennes, Sorbonne Universités, Muséum Nationale d'Histoire Naturelle, Paris, France
| | - Alain Paris
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Charlotte Duval
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Loïc Ponger
- UMR 7196 MNHN/CNRS, INSERM U1154, Sorbonne Universités, Museum National d'Histoire Naturelle, Paris, France
| | - Arul Marie
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Alain Blond
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Lucrèce Mathéron
- Institut de Biologie Paris Seine/FR 3631, Plateforme Spectrométrie de masse et Protéomique, Institut de Biologie Intégrative IFR 83, Sorbonne Universités, Université Pierre et Marie Curie, Paris, France
| | - Joelle Vinh
- USR 3149 ESPCI/CNRS SMPB, Laboratory of Biological Mass Spectrometry and Proteomics, ESPCI Paris, PSL Research University, Paris, France
| | - Gérard Bolbach
- Institut de Biologie Paris Seine/FR 3631, Plateforme Spectrométrie de masse et Protéomique, Institut de Biologie Intégrative IFR 83, Sorbonne Universités, Université Pierre et Marie Curie, Paris, France
| | - Chakib Djediat
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Cécile Bernard
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Marc Edery
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Benjamin Marie
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
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Bussard A, Corre E, Hubas C, Duvernois-Berthet E, Le Corguillé G, Jourdren L, Coulpier F, Claquin P, Lopez PJ. Physiological adjustments and transcriptome reprogramming are involved in the acclimation to salinity gradients in diatoms. Environ Microbiol 2016; 19:909-925. [DOI: 10.1111/1462-2920.13398] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adrien Bussard
- UMR Biologie des Organismes et des Ecosystèmes Aquatiques, CNRS 7208-MNHN-UPMC-IRD 207-UCN-UA; 43 rue Cuvier Paris 75005 France
| | - Erwan Corre
- CNRS, UPMC, FR2424, ABiMS, Station Biologique; Roscoff 29680 France
| | - Cédric Hubas
- UMR Biologie des Organismes et des Ecosystèmes Aquatiques, CNRS 7208-MNHN-UPMC-IRD 207-UCN-UA; 43 rue Cuvier Paris 75005 France
| | | | | | - Laurent Jourdren
- Ecole Normale Supérieure, PSL Research University, CNRS, Inserm, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Plateforme Génomique; Paris 75005 France
| | - Fanny Coulpier
- Ecole Normale Supérieure, PSL Research University, CNRS, Inserm, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Plateforme Génomique; Paris 75005 France
| | - Pascal Claquin
- UMR Biologie des Organismes et des Ecosystèmes Aquatiques, CNRS 7208-MNHN-UPMC-IRD 207-UCN-UA, Esplanade de la paix; Caen 14032 France
| | - Pascal Jean Lopez
- UMR Biologie des Organismes et des Ecosystèmes Aquatiques, CNRS 7208-MNHN-UPMC-IRD 207-UCN-UA; 43 rue Cuvier Paris 75005 France
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10
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Renaud JB, Boix C, Charpentier M, De Cian A, Cochennec J, Duvernois-Berthet E, Perrouault L, Tesson L, Edouard J, Thinard R, Cherifi Y, Menoret S, Fontanière S, de Crozé N, Fraichard A, Sohm F, Anegon I, Concordet JP, Giovannangeli C. Improved Genome Editing Efficiency and Flexibility Using Modified Oligonucleotides with TALEN and CRISPR-Cas9 Nucleases. Cell Rep 2016; 14:2263-2272. [PMID: 26923600 DOI: 10.1016/j.celrep.2016.02.018] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/16/2015] [Accepted: 01/28/2016] [Indexed: 01/08/2023] Open
Abstract
Genome editing has now been reported in many systems using TALEN and CRISPR-Cas9 nucleases. Precise mutations can be introduced during homology-directed repair with donor DNA carrying the wanted sequence edit, but efficiency is usually lower than for gene knockout and optimal strategies have not been extensively investigated. Here, we show that using phosphorothioate-modified oligonucleotides strongly enhances genome editing efficiency of single-stranded oligonucleotide donors in cultured cells. In addition, it provides better design flexibility, allowing insertions more than 100 bp long. Despite previous reports of phosphorothioate-modified oligonucleotide toxicity, clones of edited cells are readily isolated and targeted sequence insertions are achieved in rats and mice with very high frequency, allowing for homozygous loxP site insertion at the mouse ROSA locus in particular. Finally, when detected, imprecise knockin events exhibit indels that are asymmetrically positioned, consistent with genome editing taking place by two steps of single-strand annealing.
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Affiliation(s)
- Jean-Baptiste Renaud
- INSERM U1154, CNRS UMR7196, Museum National d'Histoire Naturelle, Paris 75005, France
| | - Charlotte Boix
- INSERM U1154, CNRS UMR7196, Museum National d'Histoire Naturelle, Paris 75005, France
| | - Marine Charpentier
- INSERM U1154, CNRS UMR7196, Museum National d'Histoire Naturelle, Paris 75005, France
| | - Anne De Cian
- INSERM U1154, CNRS UMR7196, Museum National d'Histoire Naturelle, Paris 75005, France
| | - Julien Cochennec
- INSERM U1154, CNRS UMR7196, Museum National d'Histoire Naturelle, Paris 75005, France
| | | | - Loïc Perrouault
- INSERM U1154, CNRS UMR7196, Museum National d'Histoire Naturelle, Paris 75005, France
| | - Laurent Tesson
- INSERM U1064, CHU de Nantes, Nantes 44093, France; Platform Rat Transgenesis Immunophenomic, CNRS UMS3556, Nantes 44093, France
| | - Joanne Edouard
- Amagen, CNRS UMS 3504, INRA UMS 1374, Institut de Neurobiologie A. Fessard, Gif-sur-Yvette 91198, France
| | - Reynald Thinard
- INSERM U1064, CHU de Nantes, Nantes 44093, France; Platform Rat Transgenesis Immunophenomic, CNRS UMS3556, Nantes 44093, France
| | | | - Séverine Menoret
- INSERM U1064, CHU de Nantes, Nantes 44093, France; Platform Rat Transgenesis Immunophenomic, CNRS UMS3556, Nantes 44093, France
| | | | - Noémie de Crozé
- Amagen, CNRS UMS 3504, INRA UMS 1374, Institut de Neurobiologie A. Fessard, Gif-sur-Yvette 91198, France
| | | | - Frédéric Sohm
- Amagen, CNRS UMS 3504, INRA UMS 1374, Institut de Neurobiologie A. Fessard, Gif-sur-Yvette 91198, France
| | - Ignacio Anegon
- INSERM U1064, CHU de Nantes, Nantes 44093, France; Platform Rat Transgenesis Immunophenomic, CNRS UMS3556, Nantes 44093, France
| | - Jean-Paul Concordet
- INSERM U1154, CNRS UMR7196, Museum National d'Histoire Naturelle, Paris 75005, France.
| | - Carine Giovannangeli
- INSERM U1154, CNRS UMR7196, Museum National d'Histoire Naturelle, Paris 75005, France.
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11
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Bellessort B, Le Cardinal M, Bachelot A, Narboux-Nême N, Garagnani P, Pirazzini C, Barbieri O, Mastracci L, Jonchere V, Duvernois-Berthet E, Fontaine A, Alfama G, Levi G. Dlx5 and Dlx6 control uterine adenogenesis during post-natal maturation: possible consequences for endometriosis. Hum Mol Genet 2016; 25:97-108. [PMID: 26512061 DOI: 10.1093/hmg/ddv452] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 10/25/2015] [Indexed: 09/19/2023] Open
Abstract
Dlx5 and Dlx6 are two closely associated homeobox genes which code for transcription factors involved in the control of steroidogenesis and reproduction. Inactivation of Dlx5/6 in the mouse results in a Leydig cell defect in the male and in ovarian insufficiency in the female. DLX5/6 are also strongly expressed by the human endometrium but their function in the uterus is unknown. The involvement of DLX5/6 in human uterine pathology is suggested by their strong downregulation in endometriotic lesions and upregulation in endometrioïd adenocarcinomas. We first show that Dlx5/6 expression begins in Müllerian ducts epithelia and persists then in the uterine luminal and glandular epithelia throughout post-natal maturation and in the adult. We then use a new mouse model in which Dlx5 and Dlx6 can be simultaneously inactivated in the endometrium using a Pgr(cre/+) allele. Post-natal inactivation of Dlx5/6 in the uterus results in sterility without any obvious ovarian involvement. The uteri of Pgr(cre/+); Dlx5/6(flox/flox) mice present very few uterine glands and numerous abnormally large and branched invaginations of the uterine lumen. In Dlx5/6 mutant uteri, the expression of genes involved in gland formation (Foxa2) and in epithelial remodelling during implantation (Msx1) is significantly reduced. Furthermore, we show that DLX5 is highly expressed in human endometrial glandular epithelium and that its expression is affected in endometriosis. We conclude that Dlx5 and Dlx6 expression determines uterine architecture and adenogenesis and is needed for implantation. Given their importance for female reproduction, DLX5 and DLX6 must be regarded as interesting targets for future clinical research.
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Affiliation(s)
- Brice Bellessort
- Évolution des Régulations Endocriniennes, CNRS UMR 7221, Muséum Nationale d'Histoire Naturelle, Paris 75005, France
| | - Marine Le Cardinal
- Évolution des Régulations Endocriniennes, CNRS UMR 7221, Muséum Nationale d'Histoire Naturelle, Paris 75005, France
| | - Anne Bachelot
- Évolution des Régulations Endocriniennes, CNRS UMR 7221, Muséum Nationale d'Histoire Naturelle, Paris 75005, France, AP-HP, Department of Endocrinology and Reproductive Medicine, Centre de Référence des Maladies Endocriniennes Rares de la Croissance, Pitié-Salpêtrière Hospital (Groupe Hospitalier Pitié-Salpêtrière), Université Pierre et Marie Curie, Site Pitié, 75013 Paris, France
| | - Nicolas Narboux-Nême
- Évolution des Régulations Endocriniennes, CNRS UMR 7221, Muséum Nationale d'Histoire Naturelle, Paris 75005, France
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy, Interdepartmental Center 'L. Galvani', University of Bologna, Bologna 40126, Italy
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy, Interdepartmental Center 'L. Galvani', University of Bologna, Bologna 40126, Italy
| | - Ottavia Barbieri
- Department of Experimental Medicine (DIMES) and, IRCCS AOU San Martino-IST, National Institute for Cancer Research, Genova, Italy and
| | - Luca Mastracci
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, Division of Anatomic Pathology, Department of Surgical Science and Integrated Diagnostics (DISC), University of Genoa, Genova, Italy
| | - Vincent Jonchere
- Évolution des Régulations Endocriniennes, CNRS UMR 7221, Muséum Nationale d'Histoire Naturelle, Paris 75005, France
| | - Evelyne Duvernois-Berthet
- Department of Régulations, Développement et Diversité Moléculaire, Muséum National d'Histoire Naturelle, Paris 75005, France
| | - Anastasia Fontaine
- Évolution des Régulations Endocriniennes, CNRS UMR 7221, Muséum Nationale d'Histoire Naturelle, Paris 75005, France
| | - Gladys Alfama
- Évolution des Régulations Endocriniennes, CNRS UMR 7221, Muséum Nationale d'Histoire Naturelle, Paris 75005, France
| | - Giovanni Levi
- Évolution des Régulations Endocriniennes, CNRS UMR 7221, Muséum Nationale d'Histoire Naturelle, Paris 75005, France,
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Ito T, Tarutani Y, To TK, Kassam M, Duvernois-Berthet E, Cortijo S, Takashima K, Saze H, Toyoda A, Fujiyama A, Colot V, Kakutani T. Genome-wide negative feedback drives transgenerational DNA methylation dynamics in Arabidopsis. PLoS Genet 2015; 11:e1005154. [PMID: 25902052 PMCID: PMC4406451 DOI: 10.1371/journal.pgen.1005154] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 03/18/2015] [Indexed: 12/12/2022] Open
Abstract
Epigenetic variations of phenotypes, especially those associated with DNA methylation, are often inherited over multiple generations in plants. The active and inactive chromatin states are heritable and can be maintained or even be amplified by positive feedback in a transgenerational manner. However, mechanisms controlling the transgenerational DNA methylation dynamics are largely unknown. As an approach to understand the transgenerational dynamics, we examined long-term effect of impaired DNA methylation in Arabidopsis mutants of the chromatin remodeler gene DDM1 (Decrease in DNA Methylation 1) through whole genome DNA methylation sequencing. The ddm1 mutation induces a drastic decrease in DNA methylation of transposable elements (TEs) and repeats in the initial generation, while also inducing ectopic DNA methylation at hundreds of loci. Unexpectedly, this ectopic methylation can only be seen after repeated self-pollination. The ectopic cytosine methylation is found primarily in the non-CG context and starts from 3’ regions within transcription units and spreads upstream. Remarkably, when chromosomes with reduced DNA methylation were introduced from a ddm1 mutant into a DDM1 wild-type background, the ddm1-derived chromosomes also induced analogous de novo accumulation of DNA methylation in trans. These results lead us to propose a model to explain the transgenerational DNA methylation redistribution by genome-wide negative feedback. The global negative feedback, together with local positive feedback, would ensure robust and balanced differentiation of chromatin states within the genome. DNA methylation is important for controlling activity of transposable elements and genes. An intriguing feature of DNA methylation in plants is that its pattern can be inherited over multiple generations at high fidelity in a Mendelian manner. However, mechanisms controlling the trans-generational DNA methylation dynamics are largely unknown. Arabidopsis mutants of a chromatin remodeler gene DDM1 (Decrease in DNA Methylation 1) show drastic reduction of DNA methylation in transposons and repeats, and also show progressive changes in developmental phenotypes during propagation through self-pollination. We now show using whole genome DNA methylation sequencing that upon repeated selfing, the ddm1 mutation induces an ectopic accumulation of DNA methylation at hundreds of loci. Remarkably, even in the wild type background, the analogous de novo increase of DNA methylation can be induced in trans by chromosomes with reduced DNA methylation. Collectively, our findings support a model to explain the transgenerational DNA methylation redistribution by genome-wide negative feedback, which should be important for balanced differentiation of DNA methylation states within the genome.
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Affiliation(s)
- Tasuku Ito
- Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
- * E-mail: (TI); (TK)
| | - Yoshiaki Tarutani
- Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Yata, Shizuoka, Japan
| | - Taiko Kim To
- Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Mohamed Kassam
- Ecole Normale Supérieure, Institut de Biologie (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR8197, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, Paris, France
| | - Evelyne Duvernois-Berthet
- Ecole Normale Supérieure, Institut de Biologie (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR8197, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, Paris, France
| | - Sandra Cortijo
- Ecole Normale Supérieure, Institut de Biologie (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR8197, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, Paris, France
| | - Kazuya Takashima
- Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hidetoshi Saze
- Okinawa Institute of Science and Technology, Onna-son, Okinawa, Japan
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics, Yata, Shizuoka, Japan
| | - Asao Fujiyama
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Yata, Shizuoka, Japan
- Center for Information Biology, National Institute of Genetics, Yata, Shizuoka, Japan
| | - Vincent Colot
- Ecole Normale Supérieure, Institut de Biologie (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR8197, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, Paris, France
| | - Tetsuji Kakutani
- Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Yata, Shizuoka, Japan
- * E-mail: (TI); (TK)
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Chica C, Szarzynska B, Chen-Min-Tao R, Duvernois-Berthet E, Kassam M, Colot V, Roudier F. Profiling spatial enrichment of chromatin marks suggests an additional epigenomic dimension in gene regulation. Frontiers in Life Science 2013. [DOI: 10.1080/21553769.2013.844734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Chen CJ, Servant N, Toedling J, Sarazin A, Marchais A, Duvernois-Berthet E, Cognat V, Colot V, Voinnet O, Heard E, Ciaudo C, Barillot E. ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data. Bioinformatics 2012; 28:3147-9. [PMID: 23044543 DOI: 10.1093/bioinformatics/bts587] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
SUMMARY Non-coding RNA (ncRNA) PROfiling in small RNA (sRNA)-seq (ncPRO-seq) is a stand-alone, comprehensive and flexible ncRNA analysis pipeline. It can interrogate and perform detailed profiling analysis on sRNAs derived from annotated non-coding regions in miRBase, Rfam and RepeatMasker, as well as specific regions defined by users. The ncPRO-seq pipeline performs both gene-based and family-based analyses of sRNAs. It also has a module to identify regions significantly enriched with short reads, which cannot be classified under known ncRNA families, thus enabling the discovery of previously unknown ncRNA- or small interfering RNA (siRNA)-producing regions. The ncPRO-seq pipeline supports input read sequences in fastq, fasta and color space format, as well as alignment results in BAM format, meaning that sRNA raw data from the three current major platforms (Roche-454, Illumina-Solexa and Life technologies-SOLiD) can be analyzed with this pipeline. The ncPRO-seq pipeline can be used to analyze read and alignment data, based on any sequenced genome, including mammals and plants. AVAILABILITY Source code, annotation files, manual and online version are available at http://ncpro.curie.fr/. CONTACT bioinfo.ncproseq@curie.fr or cciaudo@ethz.ch SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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