Consulta: creatorFacets:"Chaparro, Cristian"
Registros recuperados: 18
Data/hora: 14/06/2024 03:22:53

A simple ATAC-seq protocol for population epigenetics
Provedor de dados: 5
Autores: De Carvalho Augusto, Ronaldo; Rey, Oliver; Cosseau, Céline; Chaparro, Cristian; Vidal-dupiol, Jeremie; Allienne, Jean-françois; Duval, David; Pinaud, Silvain; Tönges, Sina; Andriantsoa, Ranja; Luquet, Emilien; Aubret, Fabien; Dia Sow, Mamadou; David, Patrice; Thomson, Vicki; Joly, Dominique; Gomes Lima, Mariana; Federico, Déborah; Danchin, Etienne; Minoda, Aki; Grunau, Christoph.
We describe here a protocol for the generation of sequence-ready libraries for population epigenomics studies, and the analysis of alignment results. We show that the protocol can be used to monitor chromatin structure changes in populations when exposed to environmental cues. The protocol is a streamlined version of the Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) that provides a positive display of accessible, presumably euchromatic regions. The protocol is straightforward and can be used with small individuals such as daphnia and schistosome worms, and probably many other biological samples of comparable size (~10,000 cells), and it requires little molecular biology handling expertise.
Tipo: Text
Palavras-chave: Epigenetics; Epigenomics; ATAC-seq; Daphnia pulex; Schistosoma mansoni.
Ano: 2020
URL: https://archimer.ifremer.fr/doc/00681/79353/81859.pdf

A multistrain approach to studying the mechanisms underlying compatibility in the interaction between Biomphalaria glabrata and Schistosoma mansoni
Provedor de dados: 5
Autores: Galinier, Richard; Roger, Emmanuel; Mone, Yves; Duval, David; Portet, Anais; Pinaud, Silvain; Chaparro, Cristian; Grunau, Christoph; Genthon, Clemence; Dubois, Emeric; Rognon, Anne; Arancibia, Nathalie; Dejean, Bernard; Theron, Andre; Gourbal, Benjamin; Mitta, Guillaume.
In recent decades, numerous studies have sought to better understand the mechanisms underlying the compatibility between Biomphalaria glabrata and Schistosoma mansoni. The developments of comparative transcriptomics, comparative genomics, interactomics and more targeted approaches have enabled researchers to identify a series of candidate genes. However, no molecular comparative work has yet been performed on multiple populations displaying different levels of compatibility. Here, we seek to fill this gap in the literature. We focused on B. glabrata FREPs and S. mansoni SmPoMucs, which were previously demonstrated to be involved in snail/schistosome compatibility. We studied the expression and polymorphisms of these factors in combinations of snail and...
Tipo: Text
Ano: 2017
URL: https://archimer.ifremer.fr/doc/00388/49951/50515.pdf

Sympatric versus allopatric evolutionary contexts shape differential immune response in Biomphalaria / Schistosoma interaction
Provedor de dados: 5
Autores: Portet, Anais; Pinaud, Silvain; Chaparro, Cristian; Galinier, Richard; Dheilly, Nolwenn M.; Portela, Julien; Charriere, Guillaume; Allienne, Jean-francois; Duval, David; Gourbal, Benjamin.
Selective pressures between hosts and their parasites can result in reciprocal evolution or adaptation of specific life history traits. Local adaptation of resident hosts and parasites should lead to increase parasite infectivity/virulence (higher compatibility) when infecting hosts from the same location (in sympatry) than from a foreign location (in allopatry). Analysis of geographic variations in compatibility phenotypes is the most common proxy used to infer local adaptation. However, in some cases, allopatric host-parasite systems demonstrate similar or greater compatibility than in sympatry. In such cases, the potential for local adaptation remains unclear. Here, we study the interaction between Schistosoma and its vector snail Biomphalaria in which...
Tipo: Text
Ano: 2019
URL: https://archimer.ifremer.fr/doc/00488/59982/63214.pdf

Effects of a parental exposure to diuron on Pacific oyster spat methylome
Provedor de dados: 5
Autores: Rondon Sallan, Rodolfo; Grunau, Christoph; Fallet, Manon; Charlemagne, Nicolas; Sussarellu, Rossana; Chaparro, Cristian; Montagnani, Caroline; Mitta, Guillaume; Bachere, Evelyne; Akcha, Farida; Cosseau, Celine.
Environmental epigenetic is an emerging field that studies the cause-effect relationship between environmental factors and heritable trait via an alteration in epigenetic marks. This field has received much attentions since the impact of environmental factors on different epigenetic marks have been shown to be associated with a broad range of phenotypic disorders in natural ecosystems. Chemical pollutants have been shown to affect immediate epigenetic information carriers of several aquatic species but the heritability of the chromatin marks and the consequences for long term adaptation remain open questions. In this work, we investigated the impact of the diuron herbicide on the DNA methylation pattern of spat from exposed Crassotrea gigas genitors. This...
Tipo: Text
Palavras-chave: Crassostrea gigas; Mollusk; DNA methylation; Herbicide; Epigenetic.
Ano: 2017
URL: https://archimer.ifremer.fr/doc/00602/71413/69895.pdf

Immune-suppression by OsHV-1 viral infection causes fatal bacteraemia in Pacific oysters
Provedor de dados: 5
Autores: De Lorgeril, Julien; Lucasson, Aude; Petton, Bruno; Toulza, Eve; Montagnani, Caroline; Clerissi, Camille; Vidal-dupiol, Jeremie; Chaparro, Cristian; Galinier, Richard; Escoubas, Jean Michel; Haffner, Philippe; Degremont, Lionel; Charriere, Guillaume; Lafont, Maxime; Delort, Abigail; Vergnes, Agnes; Chiarello, Marlene; Faury, Nicole; Rubio, Tristan; Leroy, Marc; Perignon, Adeline; Regler, Denis; Morga, Benjamin; Alunno-bruscia, Marianne; Boudry, Pierre; Le Roux, Frederique; Destoumieux-garzon, Delphine; Gueguen, Yannick; Mitta, Guillaume.
Infectious diseases are mostly explored using reductionist approaches despite repeated evidence showing them to be strongly in fluenced by numerous interacting host and environmental factors. Many diseases with a complex aetiology therefore remain misunderstood. By developing a holistic approach to tackle the complexity of interactions, we decipher the complex intra-host interactions underlying Pacific oyster mortality syndrome affecting juveniles of Crassostrea gigas, the main oyster species exploited worldwide. Using experimental infections reproducing the natural route of infection and combining thorough molecular analyses of oyster families with contrasted susceptibilities, we demonstrate that the disease is caused by multiple infection with an initial...
Tipo: Text
Ano: 2018
URL: https://archimer.ifremer.fr/doc/00461/57234/59228.pdf

On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses
Provedor de dados: 5
Autores: Lerat, Emmanuelle; Casacuberta, Josep; Chaparro, Cristian; Vieira, Cristina.
Eukaryotic genomes comprise a large proportion of repeated sequences, an important fraction of which are transposable elements (TEs). TEs are mobile elements that have a significant impact on genome evolution and on gene functioning. Although some TE insertions could provide adaptive advantages to species, transposition is a highly mutagenic event that has to be tightly controlled to ensure its viability. Genomes have evolved sophisticated mechanisms to control TE activity, the most important being epigenetic silencing. However, the epigenetic control of TEs can also affect genes located nearby that can become epigenetically regulated. It has been proposed that the combination of TE mobilization and the induced changes in the epigenetic landscape could...
Tipo: Text
Palavras-chave: Transposable element; Epigenomics; Bioinformatic tools.
Ano: 2019
URL: https://archimer.ifremer.fr/doc/00487/59900/63082.pdf

Developmental Methylome of the Medicinal Plant Catharanthus roseus Unravels the Tissue-Specific Control of the Monoterpene Indole Alkaloid Pathway by DNA Methylation
Provedor de dados: 5
Autores: Dugé De Bernonville, Thomas; Maury, Stéphane; Delaunay, Alain; Daviaud, Christian; Chaparro, Cristian; Tost, Jörg; O’connor, Sarah Ellen; Courdavault, Vincent.
Catharanthus roseus produces a wide spectrum of monoterpene indole alkaloids (MIAs). MIA biosynthesis requires a tightly coordinated pathway involving more than 30 enzymatic steps that are spatio-temporally and environmentally regulated so that some MIAs specifically accumulate in restricted plant parts. The first regulatory layer involves a complex network of transcription factors from the basic Helix Loop Helix (bHLH) or AP2 families. In the present manuscript, we investigated whether an additional epigenetic layer could control the organ-, developmental- and environmental-specificity of MIA accumulation. We used Whole-Genome Bisulfite Sequencing (WGBS) together with RNA-seq to identify differentially methylated and expressed genes among nine samples...
Tipo: Text
Palavras-chave: Alkaloids; DNA methylation; Epigenetics; Folivory; Organs; Plant specialized metabolism.
Ano: 2020
URL: https://archimer.ifremer.fr/doc/00652/76453/77543.pdf

Natural resistance to Fasciola hepatica (Trematoda) in Pseudosuccinea columella snails: A review from literature and insights from comparative “omic” analyses
Provedor de dados: 5
Autores: Alba, Annia; Tetreau, Guillaume; Chaparro, Cristian; Sánchez, Jorge; Vázquez, Antonio A.; Gourbal, Benjamin.
The snail Pseudosuccinea columella is one of the main vectors of the medically-important trematode Fasciola hepatica. In Cuba, the existence of natural P. columella populations that are either susceptible or resistant to F. hepatica infection offers a unique snail-parasite for study of parasite-host compatibility and immune function in gastropods. Here, we review all previous literature on this system and present new “omic” data that provide a molecular baseline of both P. columella phenotypes from naïve snails. Comparison of whole snail transcriptomes (RNAseq) and the proteomes of the albumen gland (2D-electrophoresis, MS) revealed that resistant and susceptible strains differed mainly in an enrichment of particular biological processes/functions and a...
Tipo: Text
Palavras-chave: Transcriptome; Albumen gland; Allocation of resources; Response to stress; Immune defense; Cost of resistance.
Ano: 2019
URL: https://archimer.ifremer.fr/doc/00509/62039/66180.pdf

No pre-zygotic isolation mechanisms between Schistosoma haematobium and Schistosoma bovis parasites: From mating interactions to differential gene expression
Provedor de dados: 5
Autores: Kincaid-smith, Julien; Mathieu-bégné, Eglantine; Chaparro, Cristian; Reguera-gomez, Marta; Mulero, Stephen; Allienne, Jean-francois; Toulza, Eve; Boissier, Jérôme; Lamberton, Poppy H. L.
Species usually develop reproductive isolation mechanisms allowing them to avoid interbreeding. These preventive barriers can act before reproduction, “pre-zygotic barriers”, or after reproduction, “post-zygotic barriers”. Pre-zygotic barriers prevent unfavourable mating, while post-zygotic barriers determine the viability and selective success of the hybrid offspring. Hybridization in parasites and the underlying reproductive isolation mechanisms maintaining their genetic integrity have been overlooked. Using an integrated approach this work aims to quantify the relative importance of pre-zygotic barriers in Schistosoma haematobium x S. bovis crosses. These two co-endemic species cause schistosomiasis, one of the major debilitating parasitic diseases...
Tipo: Text
Ano: 2021
URL: https://archimer.ifremer.fr/doc/00693/80481/83621.pdf

Terminal-Repeat Retrotransposons with GAG Domain in Plant Genomes: A New Testimony on the Complex World of Transposable Elements
Provedor de dados: 5
Autores: Chaparro, Cristian; Gayraud, Thomas; De Souza, Rogerio Fernandes; Domingues, Douglas Silva; Akaffou, Selastique; Laforga Vanzela, Andre Luis; De Kochko, Alexandre; Rigoreau, Michel; Crouzillat, Dominique; Hamon, Serge; Hamon, Perla; Guyot, Romain.
A novel structure of nonautonomous long terminal repeat (LTR) retrotransposons called terminal repeat with GAG domain (TR-GAG) has been described in plants, both in monocotyledonous, dicotyledonous and basal angiosperm genomes. TR-GAGs are relatively short elements in length (&lt;4 kb) showing the typical features of LTR-retrotransposons. However, they carry only one open reading frame coding for the GAG precursor protein involved for instance in transposition, the assembly, and the packaging of the element into the virus-like particle. GAG precursors show similarities with both Copia and Gypsy GAG proteins, suggesting evolutionary relationships of TR-GAG elements with both families. Despite the lack of the enzymatic machinery required for their mobility,...
Tipo: Text
Palavras-chave: Nonautonomous elements; LTR-retrotransposons; GAG; Conservation in plant genomes.
Ano: 2015
URL: https://archimer.ifremer.fr/doc/00615/72715/71715.pdf

Species-specific mechanisms of cytotoxicity toward immune cells determine the successful outcome of Vibrio infections
Provedor de dados: 5
Autores: Rubio, Tristan; Oyanedel, Daniel; Labreuche, Yannick; Toulza, Eve; Luo, Xing; Bruto, Maxime; Chaparro, Cristian; Torres, Marta; De Lorgeril, Julien; Haffner, Philippe; Vidal-dupiol, Jeremie; Lagorce, Arnaud; Petton, Bruno; Mitta, Guillaume; Jacq, Annick; Le Roux, Frederique; Charriere, Guillaume; Destoumieux-garzon, Delphine.
Vibrio species cause infectious diseases in humans and animals, but they can also live as commensals within their host tissues. How Vibrio subverts the host defenses to mount a successful infection remains poorly understood, and this knowledge is critical for predicting and managing disease. Here, we have investigated the cellular and molecular mechanisms underpinning infection and colonization of 2 virulent Vibrio species in an ecologically relevant host model, oyster, to study interactions with marine Vibrio species. All Vibrio strains were recognized by the immune system, but only nonvirulent strains were controlled. We showed that virulent strains were cytotoxic to hemocytes, oyster immune cells. By analyzing host and bacterial transcriptional...
Tipo: Text
Palavras-chave: T6SS; Toxin; Dual RNA-seq; Cytolysis; Pathogenesis.
Ano: 2019
URL: https://archimer.ifremer.fr/doc/00507/61837/65900.pdf

Notos - a galaxy tool to analyze CpN observed expected ratios for inferring DNA methylation types
Provedor de dados: 5
Autores: Bulla, Ingo; Aliaga, Benoit; Lacal, Virginia; Bulla, Jan; Grunau, Christoph; Chaparro, Cristian.
Background: DNA methylation patterns store epigenetic information in the vast majority of eukaryotic species. The relatively high costs and technical challenges associated with the detection of DNA methylation however have created a bias in the number of methylation studies towards model organisms. Consequently, it remains challenging to infer kingdom-wide general rules about the functions and evolutionary conservation of DNA methylation. Methylated cytosine is often found in specific CpN dinucleotides, and the frequency distributions of, for instance, CpG observed/expected (CpG o/e) ratios have been used to infer DNA methylation types based on higher mutability of methylated CpG. Results: Predominantly model-based approaches essentially founded on...
Tipo: Text
Palavras-chave: Epigenetics; DNA methylation; Kernel density estimation; CpG o/e ratio; CpN o/e ratio.
Ano: 2018
URL: https://archimer.ifremer.fr/doc/00437/54816/71790.pdf

Diverging patterns of introgression from Schistosoma bovis across S. haematobium African lineages
Provedor de dados: 5
Autores: Rey, Olivier; Toulza, Eve; Chaparro, Cristian; Allienne, Jean-françois; Kincaid-smith, Julien; Mathieu-begné, Eglantine; Allan, Fiona; Rollinson, David; Webster, Bonnie L.; Boissier, Jérôme.
Hybridization is a fascinating evolutionary phenomenon that raises the question of how species maintain their integrity. Inter-species hybridization occurs between certain Schistosoma species that can cause important public health and veterinary issues. In particular hybrids between Schistosoma haematobium and S. bovis associated with humans and animals respectively are frequently identified in Africa. Recent genomic evidence indicates that some S. haematobium populations show signatures of genomic introgression from S. bovis. Here, we conducted a genomic comparative study and investigated the genomic relationships between S. haematobium, S. bovis and their hybrids using 19 isolates originating from a wide geographical range over Africa, including samples...
Tipo: Text
Ano: 2021
URL: https://archimer.ifremer.fr/doc/00678/79020/81421.pdf

The anti-fecundity effect of 5-azacytidine (5-AzaC) on Schistosoma mansoni is linked to dis-regulated transcription, translation and stem cell activities
Provedor de dados: 5
Autores: Geyer, Kathrin K.; Munshi, Sabrina E.; Vickers, Martin; Squance, Michael; Wilkinson, Toby J.; Berrar, Daniel; Chaparro, Cristian; Swain, Martin T.; Hoffmann, Karl F.
Uncontrolled host immunological reactions directed against tissue-trapped eggs precipitate a potentially lethal, pathological cascade responsible for schistosomiasis. Blocking schistosome egg production, therefore, presents a strategy for simultaneously reducing immunopathology as well as limiting disease transmission in endemic or emerging areas. We recently demonstrated that the ribonucleoside analogue 5-azacytidine (5-AzaC) inhibited Schistosoma mansoni oviposition, egg maturation and ovarian development. While these anti-fecundity effects were associated with a loss of DNA methylation, other molecular processes affected by 5-AzaC were not examined at the time. By comparing the transcriptomes of 5-AzaC-treated females to controls, we provide evidence...
Tipo: Text
Palavras-chave: Schistosoma mansoni; Epigenetics; 5-Azacytidine; Fecundity; RNA-Seq; Protein synthesis; Stem cells.
Ano: 2018
URL: https://archimer.ifremer.fr/doc/00615/72703/71747.pdf

Contribution of Viral Genomic Diversity to Oyster Susceptibility in the Pacific Oyster Mortality Syndrome
Provedor de dados: 5
Autores: Delmotte, Jean; Chaparro, Cristian; Galinier, Richard; De Lorgeril, Julien; Petton, Bruno; Stenger, Pierre-louis; Vidal-dupiol, Jeremie; Destoumieux-garzon, Delphine; Gueguen, Yannick; Montagnani, Caroline; Escoubas, Jean Michel; Mitta, Guillaume.
Juvenile Pacific oysters (Crassostrea gigas) are subjected to recurrent episodes of mass mortalities that constitute a threat for the oyster industry. This mortality syndrome named “Pacific Oyster Mortality Syndrome” (POMS) is a polymicrobial disease whose pathogenesis is initiated by a primary infection by a variant of an Ostreid herpes virus named OsHV-1 μVar. The characterization of the OsHV-1 genome during different disease outbreaks occurring in different geographic areas has revealed the existence of a genomic diversity for OsHV-1 μVar. However, the biological significance of this diversity is still poorly understood. To go further in understanding the consequences of OsHV-1 diversity on POMS, we challenged five biparental families of oysters to two...
Tipo: Text
Palavras-chave: Crassostrea gigas; Herpesvirus diversity; Genotype-genotype interactions; Oyster genetic background; Viral populations.
Ano: 2020
URL: https://archimer.ifremer.fr/doc/00643/75533/76414.pdf

A Sustained Immune Response Supports Long-Term Antiviral Immune Priming in the Pacific Oyster,  Crassostrea gigas
Provedor de dados: 5
Autores: Lafont, Maxime; Vergnes, Agnes; Vidal-dupiol, Jeremie; De Lorgeril, Julien; Gueguen, Yannick; Haffner, Philippe; Petton, Bruno; Chaparro, Cristian; Barrachina, Celia; Destoumieux-garzon, Delphine; Mitta, Guillaume; Gourbal, Benjamin; Montagnani, Caroline.
Over the last decade, innate immune priming has been evidenced in many invertebrate phyla. If mechanistic models have been proposed, molecular studies aiming to substantiate these models have remained scarce. We reveal here the transcriptional signature associated with immune priming in the oyster Crassostrea gigas. Oysters were fully protected against Ostreid herpesvirus 1 (OsHV-1), a major oyster pathogen, after priming with poly(I·C), which mimics viral double-stranded RNA. Global analysis through RNA sequencing of oyster and viral genes after immune priming and viral infection revealed that poly(I·C) induces a strong antiviral response that impairs OsHV-1 replication. Protection is based on a sustained upregulation of immune genes, notably genes...
Tipo: Text
Palavras-chave: Innate immunity; Priming; OsHV-1; Antiviral response; Immune memory; Oyster; POMS; Poly(I·C); Interferon; Transcriptomic.
Ano: 2020
URL: https://archimer.ifremer.fr/doc/00614/72580/71541.pdf

New Insights Into Biomphalysin Gene Family Diversification in the Vector Snail Biomphalaria glabrata
Provedor de dados: 5
Autores: Pinaud, Silvain; Tetreau, Guillaume; Poteaux, Pierre; Galinier, Richard; Chaparro, Cristian; Lassalle, Damien; Portet, Anaïs; Simphor, Elodie; Gourbal, Benjamin; Duval, David.
Aerolysins initially characterized as virulence factors in bacteria are increasingly found in massive genome and transcriptome sequencing data from metazoans. Horizontal gene transfer has been demonstrated as the main way of aerolysin-related toxins acquisition in metazoans. However, only few studies have focused on their potential biological functions in such organisms. Herein, we present an extensive characterization of a multigene family encoding aerolysins - named biomphalysin - in Biomphalaria glabrata snail, the intermediate host of the trematode Schistosoma mansoni. Our results highlight that duplication and domestication of an acquired bacterial toxin gene in the snail genome result in the acquisition of a novel and diversified toxin family....
Tipo: Text
Palavras-chave: Biomphalaria; Biomphalysin; Aerolysin; Invertebrate immunity; Pore-forming toxin (PFT); Structure.
Ano: 2021
URL: https://archimer.ifremer.fr/doc/00687/79909/82814.pdf

Histone methylation changes are required for life cycle progression in the human parasite Schistosoma mansoni
Provedor de dados: 5
Autores: Roquis, David; Taudt, Aaron; Geyer, Kathrin K.; Padalino, Gilda; Hoffmann, Karl F.; Holroyd, Nancy; Berriman, Matt; Aliaga, Benoit; Chaparro, Cristian; Grunau, Christoph; De Carvalho Augusto, Ronaldo.
Epigenetic mechanisms and chromatin structure play an important role in development. Their impact is therefore expected to be strong in parasites with complex life cycles and multiple, strikingly different, developmental stages, i.e. developmental plasticity. Some studies have already described how the chromatin structure, through histone modifications, varies from a developmental stage to another in a few unicellular parasites. While H3K4me3 profiles remain relatively constant, H3K27 trimethylation and bivalent methylation show strong variation. Inhibitors (A366 and GSK343) of H3K27 histone methyltransferase activity in S. mansoni efficiently blocked miracidium to sporocyst transition indicating that H3K27 trimethylation is required for life cycle...
Tipo: Text
Ano: 2018
URL: https://archimer.ifremer.fr/doc/00445/55690/71773.s001