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2. Tissue Resources for the Functional Annotation of Animal Genomes

Author

Tixier-Boichard, Michèle, Fabre, Stéphane, Dhorne-Pollet, Sophie, Goubil, Adeline, Acloque, Hervé, Vincent-Naulleau, Silvia, Ross, Pablo, Wang, Ying, Chanthavixay, Ganrea, Cheng, Hans, Ernst, Catherine, Leesburg, Vicki, Giuffra, Elisabetta, Zhou, Huaijun, Group, Collaborative Working, Taragnat, Catherine, Berri, Cecile, Jardet, Déborah, Godet, Estelle, Laurent, Fabrice, Gomot, Gilles, Dardente, Hughes, Grasseau, Isabelle, Dubois, Jean-Philippe, Gautron, Joel, Gérard, Nadine, Quéré, Pascale, Lavocat, Roger-Paul, Dalbies-Tran, Rozenn, Métayer, Sonia, Marthey, Sylvain, Coustham, Vincent, and Druart, Xavier

Subjects
Biological Sciences, Genetics, tissue sampling, repository, mammals, bird, cryopreservation, genome, Collaborative Working Group, Clinical Sciences, Law
Abstract

In order to generate an atlas of the functional elements driving genome expression in domestic animals, the Functional Annotation of Animal Genome (FAANG) strategy was to sample many tissues from a few animals of different species, sexes, ages, and production stages. This article presents the collection of tissue samples for four species produced by two pilot projects, at INRAE (National Research Institute for Agriculture, Food and Environment) and the University of California, Davis. There were three mammals (cattle, goat, and pig) and one bird (chicken). It describes the metadata characterizing these reference sets (1) for animals with origin and selection history, physiological status, and environmental conditions; (2) for samples with collection site and tissue/cell processing; (3) for quality control; and (4) for storage and further distribution. Three sets are identified: set 1 comprises tissues for which collection can be standardized and for which representative aliquots can be easily distributed (liver, spleen, lung, heart, fat depot, skin, muscle, and peripheral blood mononuclear cells); set 2 comprises tissues requiring special protocols because of their cellular heterogeneity (brain, digestive tract, secretory organs, gonads and gametes, reproductive tract, immune tissues, cartilage); set 3 comprises specific cell preparations (immune cells, tracheal epithelial cells). Dedicated sampling protocols were established and uploaded in https://data.faang.org/protocol/samples. Specificities between mammals and chicken are described when relevant. A total of 73 different tissues or tissue sections were collected, and 21 are common to the four species. Having a common set of tissues will facilitate the transfer of knowledge within and between species and will contribute to decrease animal experimentation. Combining data on the same samples will facilitate data integration. Quality control was performed on some tissues with RNA extraction and RNA quality control. More than 5,000 samples have been stored with unique identifiers, and more than 4,000 were uploaded onto the Biosamples database, provided that standard ontologies were available to describe the sample. Many tissues have already been used to implement FAANG assays, with published results. All samples are available without restriction for further assays. The requesting procedure is described. Members of FAANG are encouraged to apply a range of molecular assays to characterize the functional status of collected samples and share their results, in line with the FAIR (Findable, Accessible, Interoperable, and Reusable) data principles.

Published
2021

8. Comparison of two molecular barcodes for the study of equine strongylid communities with amplicon sequencing

Author

Courtot, Élise, primary, Boisseau, Michel, additional, Dhorne-Pollet, Sophie, additional, Serreau, Delphine, additional, Gesbert, Amandine, additional, Reigner, Fabrice, additional, Basiaga, Marta, additional, Kuzmina, Tetiana, additional, Lluch, Jérôme, additional, Annonay, Gwenolah, additional, Kuchly, Claire, additional, Diekmann, Irina, additional, Krücken, Jürgen, additional, von Samson-Himmelstjerna, Georg, additional, Mach, Nuria, additional, and Sallé, Guillaume, additional

Published
2023
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9. Multi-species annotation of transcriptome and chromatin structure in domesticated animals

Author

Foissac, Sylvain, Djebali, Sarah, Munyard, Kylie, Vialaneix, Nathalie, Rau, Andrea, Muret, Kevin, Esquerré, Diane, Zytnicki, Matthias, Derrien, Thomas, Bardou, Philippe, Blanc, Fany, Cabau, Cédric, Crisci, Elisa, Dhorne-Pollet, Sophie, Drouet, Françoise, Faraut, Thomas, Gonzalez, Ignacio, Goubil, Adeline, Lacroix-Lamandé, Sonia, Laurent, Fabrice, Marthey, Sylvain, Marti-Marimon, Maria, Momal-Leisenring, Raphaelle, Mompart, Florence, Quéré, Pascale, Robelin, David, Cristobal, Magali San, Tosser-Klopp, Gwenola, Vincent-Naulleau, Silvia, Fabre, Stéphane, Pinard-Van der Laan, Marie-Hélène, Klopp, Christophe, Tixier-Boichard, Michèle, Acloque, Hervé, Lagarrigue, Sandrine, and Giuffra, Elisabetta

Published
2019
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15. Evaluation of the nemabiome approach for the study of equine strongylid communities

Author

Courtot, Élise, primary, Boisseau, Michel, additional, Dhorne-Pollet, Sophie, additional, Serreau, Delphine, additional, Gesbert, Amandine, additional, Reigner, Fabrice, additional, Basiaga, Marta, additional, Kuzmina, Tetiana, additional, Lluch, Jérôme, additional, Annonay, Gwenolah, additional, Kuchly, Claire, additional, Diekmann, Irina, additional, Krücken, Jürgen, additional, Samson-Himmelstjerna, Georg von, additional, Mach, Nuria, additional, and Sallé, Guillaume, additional

Published
2022
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16. Effect of sainfoin (Onobrychis viciifolia) on cyathostomin eggs excretion, larval development, larval community structure and efficacy of ivermectin treatment in horses

Author

Malsa, Joshua, primary, Courtot, Élise, additional, Boisseau, Michel, additional, Dumont, Bertrand, additional, Gombault, Pascale, additional, Kuzmina, Tetiana A., additional, Basiaga, Marta, additional, Lluch, Jérôme, additional, Annonay, Gwenolah, additional, Dhorne-Pollet, Sophie, additional, Mach, Nuria, additional, Sutra, Jean-François, additional, Wimel, Laurence, additional, Dubois, Cédric, additional, Guégnard, Fabrice, additional, Serreau, Delphine, additional, Lespine, Anne, additional, Sallé, Guillaume, additional, and Fleurance, Géraldine, additional

Published
2022
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18. Think Different with RNA Therapy: Can Antisense Oligonucleotides Be Used to Inhibit Replication and Transcription of SARS-Cov-2?

Author

Barrey, Eric, Burzio, Veronica, Dhorne-Pollet, Sophie, Eléouët, Jean-François, and Delmas, Bernard

Subjects
microbiology
Abstract

The severity of the global COVID-19 pandemic, with a high transmission rate, 2.6-4.7% lethality and a huge economic impact, poses an urgent need for efficient medical treatments and vaccines. Currently, there are only non-specific treatments to assist the patients in acute respiratory distress during the inflammatory step following the preliminary infection by SARS-CoV-2. Clinical trials of drug repurposing were quickly launched at the international level. Specific treatments such as the transfusion of plasma from patients who have recovered into infected patients or the use of specific inhibitors of the viral RNA-polymerase complex are promising strategies to block infection. To complete the therapeutic arsenal, we believe that the opportunity of targeting the SARS-CoV-2 genome by RNA therapy should be deeply investigated. In the present paper, we propose to design specific antisense oligonucleotides targeting transcripts encoding viral proteins associated to replication and transcription of SARS-CoV-2, aiming to block infection. We designed antisense oligonucleotides targeting the genomic 5’ untranslated region (5’-UTR), open reading frames 1a and 1b (ORF1a and ORF1b) governing expression of the replicase/transcriptase complex, and the gene N encoding the nucleoprotein that is genome-associated. To maximize the probability of efficiency, we predicted the antisense oligonucleotides by using two design methods: i) conventional antisense oligonucleotides with 100% phosphorothioate modifications (ASO); ii) antisense locked nucleic acids GapmeR. After binding the viral RNA target, the hetero-duplexes antisense oligonucleotide-RNA are cleaved by RNAse H1. Nine potent ASO candidates were found and we selected five of them targeting ORF1a (3), ORF1b (1) and N (1). Nine GapmeR candidates were predicted with excellent properties and we retained four of them targeting 5’-UTR (1), ORF1a (3), ORF1b (1) and N (1). The most potent GapmeR candidate targets the 5’-UTR, a key genomic domain with multiple functions in the viral cycle. By this open publication, we are pleased to share these in silico results with the scientific community in hopes of stimulating innovation in translational research in order to fight the unprecedented COVID-19 pandemic. These antisense oligonucleotide candidates should be now experimentally evaluated.

Published
2020

26. Using direct long RNA sequencing to explore transcriptome and long non-coding RNA in equine muscle

Author

Dhorne-Pollet, Sophie, Robert, Céline, Pollet, Nicolas, Barrey, Eric, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Université Paris Saclay (COmUE), École nationale vétérinaire d'Alfort (ENVA), Évolution, génomes, comportement et écologie (EGCE), Centre National de la Recherche Scientifique (CNRS)-IRD-Université Paris-Sud - Paris 11 (UP11), European Molecular Biology Laboratory (EMBL). DEU., Pollet, Nicolas, Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris-Sud - Paris 11 (UP11)-IRD-Centre National de la Recherche Scientifique (CNRS), and ProdInra, Migration

Subjects
[SDV] Life Sciences [q-bio], [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV]Life Sciences [q-bio], [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.GEN] Life Sciences [q-bio]/Genetics, [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

27. Test de génotypage du caractère frisé chez le cheval Curly

Author

Dhorne-Pollet, Sophie, Morgenthaler, Caroline, Debus, Alexia, Robert, Céline, Barrey, Eric, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Université Paris Saclay (COmUE), École nationale vétérinaire d'Alfort (ENVA), and Institut Français du Cheval et de l'Equitation (IFCE). FRA.

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], cheval, test de genotypage, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2019

28. MOESM1 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals

Author

Foissac, Sylvain, Djebali, Sarah, Munyard, Kylie, Vialaneix, Nathalie, Rau, Andrea, Muret, Kevin, Esquerré, Diane, Zytnicki, Matthias, Derrien, Thomas, Bardou, Philippe, Blanc, Fany, Cabau, Cédric, Crisci, Elisa, Dhorne-Pollet, Sophie, Drouet, Françoise, Faraut, Thomas, Gonzalez, Ignacio, Goubil, Adeline, Lacroix-Lamandé, Sonia, Laurent, Fabrice, Marthey, Sylvain, Marti-Marimon, Maria, Raphaelle Momal-Leisenring, Mompart, Florence, Quéré, Pascale, Robelin, David, Cristobal, Magali, Tosser-Klopp, Gwenola, Vincent-Naulleau, Silvia, Fabre, Stéphane, Marie-Hélène Pinard-Van Der Laan, Klopp, Christophe, Tixier-Boichard, Michèle, Acloque, Hervé, Lagarrigue, Sandrine, and Giuffra, Elisabetta

Abstract

Additional file 1 Additional file 1: Supplementary figures (S1-S26) and tables (S1-S15).

Published
2019
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31. A new method adapted for sequencing mitochondrial genomes

Author

Dhorne-Pollet, Sophie, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), and International Society of Antioxidant in Nutrition and Health (ISANH). INT.

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

32. MicroRNA profiling of synovial fluid of horses reveals potential biomarkers of Osteochondrosis

Author

Dhorne-Pollet, Sophie, Riousset, Isabelle, Robert, Céline, Le Moyec, Laurence, Barrey, Eric, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), SERVIER, École nationale vétérinaire d'Alfort (ENVA), Université d'Évry-Val-d'Essonne (UEVE), Dorothy Russell Havemeyer Foundation, Inc.. USA., and École nationale vétérinaire - Alfort (ENVA)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

33. Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig

Author

Foissac, Sylvain, Djebali, Sarah, Munyard, Kylie, Vialaneix, Nathalie, Rau, Andrea, Muret, Kévin, Esquerré, Diane, Zytnicki, Matthias, Derrien, Thomas, Bardou, Philippe, Blanc, Fany, Cabau, Cédric, CRISCI, Elisa, Dhorne-Pollet, Sophie, Drouet, Françoise, González, Ignacio, Goubil, Adeline, Lacroix-Lamandé, Sonia, Laurent, Fabrice, Marthey, Sylvain, Marti-Marimon, Maria, Momal-Leisenring, Raphaëlle, Mompart, Florence, Quéré, Pascale, Robelin, David, San Cristobal, Magali, Tosser-Klopp, Gwenola, Vincent-Naulleau, Silvia, Fabre, Stéphane, Pinard - Van Der Laan, Marie-Helene, Klopp, Christophe, Tixier-Boichard, Michele, ACLOQUE, Hervé, Lagarrigue, Sandrine, Giuffra, Elisabetta, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Curtin University [Perth], Planning and Transport Research Centre (PATREC), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), iRCM, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), and Institut National de la Recherche Agronomique (INRA)-Université de Tours

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Livestock, Hi-C, [SDV]Life Sciences [q-bio], Functional annotation, [INFO]Computer Science [cs], ATAC-seq, RNA-seq, [MATH]Mathematics [math]
Abstract

Article publié dans BMC Biology. Disponible ici : https://prodinra.inra.fr/record/491694; Functional annotation of livestock genomes is a critical step to decipher the genotype-to-phenotype relationship underlying complex traits. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aims at profiling the landscape of transcription (RNA-seq) and chromatin accessibility and conformation (ATAC-seq and Hi-C) in four livestock species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells). Standardized protocols were applied to produce transcriptome and chromatin datasets for the four species. RNA-seq assays allowed to considerably extend the available catalog of protein-coding and non-coding transcripts. Gene expression profiles were consistent with known metabolic/immune functions and revealed differentially expressed transcripts with unknown function, including new lncRNAs in syntenic regions. The majority of ATAC-seq peaks of chromatin accessibility mapped to putative regulatory regions, with an enrichment of predicted transcription factor binding sites in differentially accessible peaks. Hi-C provided the first set of genome-wide maps of three-dimensional interactions across livestock and showed consistency with results from gene expression and chromatin accessibility in topological compartments of the genomes. We report the first multi-species and multi-assay genome annotation results obtained by a FAANG pilot project. The global consistency between gene expression and chromatin structure data in these four livestock species adds up to previous findings in model animals. Overall, these results emphasize the value of FAANG for the research on domesticated animals and strengthen the importance of future meta-analyses of the reference datasets being generated by this community on different species.

Published
2018
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35. Profiling the landscape of transcription, chromatin accessibility and chromosome conformation of cattle, pig, chicken and goat genomes [FAANG pilot project]

Author

Foissac, Sylvain, Djebali Quelen, Sarah, ACLOQUE, Hervé, Bardou, Philippe, Blanc, Fany, Cabau, Cédric, Derrien, Thomas, Drouet, Françoise, Esquerre, Diane, Fabre, Stéphane, Gaspin, Christine, GONZALEZ, Ignacio, Goubil, Adeline, Klopp, Christophe, Laurent, Fabrice, Marthey, Sylvain, Marti-Marimon, Maria, Mompart, Florence, Munyard, Kylie, Muret, Kévin, Pollet, Sophie, Quéré, Pascale, Rau, Andrea, Robelin, David, San Cristobal, Magali, Tixier-Boichard, Michele, Tosser-Klopp, Gwenola, Villa-Vialaneix, Nathalie, Vincent-Naulleau, Silvia, Zytnicki, Matthias, Pinard - Van Der Laan, Marie-Helene, Lagarrigue, Sandrine, Giuffra, Elisabetta, Institut National de la Recherche Agronomique - INRA (FRANCE), Institut National Polytechnique de Toulouse - INPT (FRANCE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Infectiologie Animale et Santé Publique - IASP (Nouzilly, France), Institut National de la Recherche Agronomique (INRA), Dynamiques Forestières dans l'Espace Rural (DYNAFOR), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Toulouse-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), FR-AgENCODE, Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Institut National de la Recherche Agronomique (INRA)-Université de Tours

Subjects
multispecies, Hi-C, [SDV]Life Sciences [q-bio], Multispecies, Biologie animale, Functional annotation of animal genome (FAANG), functional annotation of animal genome (FAANG), ATAC-seq, RNA-seq
Abstract

Functional annotation of livestock genomes is a critical and obvious next step to derive maximum benefit for agriculture, animal science, animal welfare and human health. The aim of the Fr-AgENCODE project is to generate multi-species functional genome annotations by applying high-throughput molecular assays on three target tissues/cells relevant to the study of immune and metabolic traits. An extensive collection of stored samples from other tissues is available for further use (FAANG Biosamples ‘FR-AGENCODE’). From each of two males and two females per species (pig, cattle, goat, chicken), strand-oriented RNA-seq and chromatin accessibility ATAC-seq assays were performed on liver tissue and on two T-cell types (CD3+CD4+&CD3+CD8+) sorted from blood (mammals) or spleen (chicken). Chromosome Conformation Capture (in situ Hi-C) was also carried out on liver. Sequencing reads from the 3 assays were processed using standard processing pipelines. While most (50–70%) RNA-seq reads mapped to annotated exons, thousands of novel transcripts and genes were found, including extensions of annotated protein-coding genes and new lncRNAs (see abstract #69857). Consistency of ATAC-seq results was confirmed by the significant proportion of called peaks in promoter regions (36–66%) and by the specific accumulation pattern of peaks around gene starts (TSS) v. gene ends (TTS). Principal Component Analyses for RNA-seq (based on quantified gene expression) and ATAC-seq (based on quantified chromatin accessibility) highlighted clusters characterised by cell type and sex in all species. From Hi-C data, we generated 40kb-resolution interaction maps, profiled a genome-wide Directionality Index and identified from 4,100 (chicken) to 12,100 (pig) topologically-associating do- mains (TADs). Correlations were reported between RNA-seq and ATAC-seq results (see abstract #71581). In summary, we present here an overview of the first multi-species and -tissue annotations of chromatin accessibility and genome architecture related to gene expression for farm animals.

Published
2017

36. Transcriptome and chromatin structure annotation of liver, CD4+ and CD8+ T cells from four livestock species

Author

Foissac, Sylvain, primary, Djebali, Sarah, additional, Munyard, Kylie, additional, Vialaneix, Nathalie, additional, Rau, Andrea, additional, Muret, Kevin, additional, Esquerré, Diane, additional, Zytnicki, Matthias, additional, Derrien, Thomas, additional, Bardou, Philippe, additional, Blanc, Fany, additional, Cabau, Cèdric, additional, Crisci, Elisa, additional, Dhorne-Pollet, Sophie, additional, Drouet, Françoise, additional, Faraut, Thomas, additional, Gonzalez, Ignacio, additional, Goubil, Adeline, additional, Lacroix-Lamandé, Sonia, additional, Laurent, Fabrice, additional, Marthey, Sylvain, additional, Marti-Marimon, Maria, additional, Momal-Leisenring, Raphaelle, additional, Mompart, Florence, additional, Quéré, Pascale, additional, Robelin, David, additional, Cristobal, Magali San, additional, Tosser-Klopp, Gwenola, additional, Vincent-Naulleau, Silvia, additional, Fabre, Stéphane, additional, der Laan, Marie-Hélène Pinard-Van, additional, Klopp, Christophe, additional, Tixier-Boichard, Michelè, additional, Acloque, Hervé, additional, Lagarrigue, Sandrine, additional, and Giuffra, Elisabetta, additional

Published
2018
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39. RNA silencing-targeted transcriptome of porcine alveolar macrophages upon infection with porcine reproductive and respiratory syndrome viruses (PRRSV) of different virulence

Author

Dhorne-Pollet, Sophie, Renson, Patricia, Jaffrézic, Florence, Marot, Guillemette, Moroldo, Marco, Lecardonnel, Jerôme, Bourry, Olivier, Giuffra, Elisabetta, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Inria Lille - Nord Europe, and Institut National de Recherche en Informatique et en Automatique (Inria)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2016

40. Functional Analysis of microRNAs:mRNA Interactions Between Pseudorabies Virus (PrV) and Its Natural Pig Host

Author

Pollet, Sophie, Marot, Guillemette, Lecardonnel, Jerôme, Moroldo, Marco, Jaffrezic, Florence, Giuffra, Elisabetta, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech

Subjects
nervous system, viruses, [SDV]Life Sciences [q-bio]
Abstract

Poster et abstract; Functional Analysis of microRNAs:mRNA Interactions Between Pseudorabies Virus (PrV) and Its Natural Pig Host. 24. Plant and Animal Genome Conference (PAG)

Published
2016

41. Sampling tissue for FAANG: the example of cattle and chickens in France

Author

Tixier-Boichard, Michèle, Fabre, Stéphane, Dhorne-Pollet, Sophie, Rebours, Emmanuelle, Goubil, Adeline, ACLOQUE, HERVE, Druart, Xavier, Dardente, Hugues, Berri, Cécile, Gautron, Joël, Laurent, Fabrice, Quéré, Pascale, Gallard, Yves, Baumard, Yannick, Giuffra, Elisabetta, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Unité de Recherches Avicoles (URA), Institut National de la Recherche Agronomique (INRA), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Domaine expérimental animal du Pin (SEA), Pôle d'Expérimentation Avicole de Tours (UE PEAT), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Recherche Agronomique (INRA)-Université de Tours

Subjects
[SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2015

42. Les microARN circulants : de nouveaux biomarqueurs pour des caractères économiquement importants chez les poules ?

Author

Zerjal, Tatiana, Endale Ahanda, Marie-Laure, Pollet, Sophie, Rau, Andrea, Giuffra, Elisabetta, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and AgroParisTech-Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV]Life Sciences [q-bio]
Abstract

Les microARN (miARN) représentent une classe importante de petits ARN non codants chez les organismes eucaryotes et sont des régulateurs puissants d'un large éventail de processus biologiques. Grâce à leur présence dans le flux sanguin et leur grande stabilité, les miARN circulants font l’objet de nombreuses études chez l’homme en vue d’identifier leur potentiel en tant que biomarqueurs pour la détection précoce de nombreuses maladies. Des applications plus larges pourraient être envisagées dans d'autres domaines tels que la génétique végétale ou animale pour identifier des miARN qui seraient associés à des caractères économiquement importants. Pour explorer cette possibilité nous avons réalisé une étude pilote afin d’identifier des miARN circulants répondant à un stress abiotique (la mise à jeun pour un temps limité). Deux lignées de poules sélectionnées pour être divergentes en terme de consommation alimentaire résiduelle (les lignées R + et R-) ont été choisies pour les différences extrêmes qu’elles présentent dans la prise alimentaire et le métabolisme énergétique. Le séquençage des miARN plasmatiques a permis d’identifier 148 miARN, dont 23 présentaient des différences significatives d’abondance entre les conditions « à jeun » et « nourri », et 19 entre les lignées R+ et R-. Notre étude montre que, chez la poule, le profil plasmatique des miARN réagit rapidement à la modification de l'état physiologique de l'animal, et ceci avec une forte influence du fond génétique de l’animal. Dans notre cas, nous pouvons y voir le reflet de la divergence génétique due à la sélection à long terme., MicroRNAs (miRNAs) are an important class of small non-coding RNAs in eukaryotic organisms and are potent regulators of a wide range of biological processes. With their presence in the blood stream and their high stability, circulating miRNAs are the subject of many studies in humans to identify their potential as biomarkers for early detection of many diseases. Broader applications could be considered in other areas such as plant or animal genetics to identify miRNAs that might be associated with economically important traits. To explore this possibility we conducted a pilot study to identify plasmatic miRNAs responding to an abiotic stress (fasting condition for a limited time). Two chickens lines divergently selected for residual feed intake (R+ and R- chicken lines) were chosen because of their extreme differences in food intake and energy metabolism. Sequencing of plasma miRNAs allowed us to identify 148 miRNAs, of which 23 were significantly different between feeding conditions ("fasted" versus "fed") and 19 differed between lines (R+ versus R-). Our study shows that in the miRNA chicken plasma profile reacts quickly to changes in the physiological state of the animal, but it is strongly influenced by the genetic background of the animal which in our case reflects genetic divergence acquired by the long-term selection.

Published
2015

43. Functional analysis of candidate interactions between miRNAs encoded by the pseudorabies virus (PrV) and pig genes

Author

Mahjoub, Nada, Pollet, Sophie, Sherba, Gail, Mettenleiter, Thomas, Giuffra, Elisabetta, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, University of Illinois at Urbana-Champaign [Urbana], University of Illinois System, Fredrich-Loeffler-Institut (FLI), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech

Subjects
viruses, [SDV]Life Sciences [q-bio], education
Abstract

Functional analysis of candidate interactions between miRNAs encoded by the pseudorabies virus (PrV) and pig genes.. 34. International Society for Animal Genetics Conference (ISAG)

Published
2014

44. Understanding the complex interaction between pseudorabies virus (PrV) and its natural host using RIP-Chip enrichment analysis

Author

Pollet, Sophie, Lecardonnel, Jerôme, Jaffrezic, Florence, Moroldo, Marco, Giuffra, Elisabetta, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris-Saclay, Target-MI (GA Div.), and INRA Package

Subjects
miRNA, PrV, viruses, [SDV]Life Sciences [q-bio]
Abstract

Understanding the complex interaction between pseudorabies virus (PrV) and its natural host using RIP-Chip enrichment analysis. 34. International Society for Animal Genetics Conference (ISAG)

Published
2014

45. In vitro maturation of oocytes alters gene expression and signaling pathways in bovine cumulus cells

Author

Salhab, Mohamad, Pollet, Sophie, Auclair, Sylvain, Guyader-Joly, Catherine, Brisard, Daphné, Dalbies Tran, Rozenn, Dupont, Joëlle, Ponsart, Claire, Mermillod, Pascal, Uzbekova, Svetlana, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Union nationale des coopératives d’élevage et d’insémination animale (UNCEIA), French National Research Agency and Apisgen (OSCILE ANR-08-GENM-033 and OVOGENAE2 ANR-07-GANI-004 programs), Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Union Nationale des Coopératives Agricoles d'Elevage et d'Insémination Animale, Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)

Subjects
signaling pathway, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], ivm, urogenital system, embryonic structures, cow, cumulus transcriptome, oocyte quality
Abstract

Chantier qualité GA; In vitro maturation (IVM) of immature oocytes is widely used in assisted reproduction technologies in cattle, and is increasingly used to treat human infertility. The development competence of IVM oocytes, however, is lower than preovulatory, in vivo-matured oocytes. During maturation, cumulus cells (CC) are metabolically coupled with an oocyte and support the acquisition of its developmental potential. Our objective was to identify genes and pathways that were affected by IVM in bovine CC. Microarray transcriptomic analysis of CC enclosing in vitro- or in vivo-mature oocytes revealed 472 differentially expressed genes, including 28% related to apoptosis, correlating with twofold higher cell death after IVM than in vivo, as detected by TUNEL. Genes overexpressed after IVM were significantly enriched in functions involved in cell movement, focal adhesion, extracellular matrix function, and TGF-beta signaling, whereas under-expressed genes were enriched in regulating gene expression, energy metabolism, stress response, and MAP kinases pathway functions. Differential expression of 15 genes, including PAG11 (increased) and TXNIP (decreased), which were never detected in CC before, was validated by real-time RT-PCR. Moreover, protein quantification confirmed the lower abundance of glutathione S-transferase A1 and prostaglandin G/H synthase 2, and the higher abundance of hyaluronan synthase 2 and SMAD4, a member of TGF-beta pathway, in CC after IVM. Phosphorylation levels of SMAD2, MAPK3/1, and MAPK14, but not MAPK8, were higher after IVM that in vivo. In conclusion, IVM provokes the hyper-activation of TGF-beta and MAPK signaling components, modifies gene expression, leads to increased apoptosis in CC, and thus affects oocyte quality.

Published
2013
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46. Validation of novel reference genes for RT-qPCR studies of gene expression in Xenopus tropicalis during embryonic and post-embryonic development

Author

Dhorne-Pollet, Sophie, Thélie, Aurore, Pollet, Nicolas, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut de biologie systémique et synthétique (ISSB), Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), CNRS, Genopole, Universite d'Evry, AFM (Amphigenetools), Association Francaise contre les Myopathies, AgroParisTech-Institut National de la Recherche Agronomique (INRA), and Université d'Évry-Val-d'Essonne (UEVE)-Génopole-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, DNA, Complementary, Time Factors, Reverse Transcriptase Polymerase Chain Reaction, Gene Expression Profiling, Xenopus, reference gene, Gene Expression Regulation, Developmental, rt-qpcr, qrt-pcr, Xenopus laevis, Animals, RNA, amphibian, transcriptome, development, DNA Primers, Developmental Biology
Abstract

Chantier qualité GA; Background: Accurate interpretation of transcriptome profiling by quantitative PCR requires the establishment of species-specific standards. However, the selection of reference genes for assessing RNA expression profiles in Xenopus laevis and Xenopus tropicalis was mostly based on historical reasons and they often only reflect the traditions of a laboratory. Results: We investigated the expression stability of 10 genes (dicer1, drosha, eef1a1, elavl3, gsc, h4, odc1, rpl8, smn2, tbp), 8 of which are commonly used as internal controls in published RT-qPCR experiments. We defined specific primer pairs and evaluated their suitability as reference genes by performing RT-qPCR expression profiling in Xenopus tropicalis. Gene expression stability was assayed in a set of 15 developmental stages from the egg to the froglet, and in dissected embryos. Conclusions: Overall, we determined a set of qualified reference genes for distinct developmental periods. We recommend the use of dicer1, drosha, eef1a1, and smn2 from early embryonic development up to the end of metamorphosis. During early embryogenesis drosha, eef1a1, smn2 are suitable. For the whole post-embryonic development and for metamorphic stages including pro-metamorphosis and metamorphic climax, we recommend the use of drosha and smn2. These reference genes should prove their usefulness for data comparison across studies.

Published
2012
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47. A functional genomic approach to the study of the milking ability in dairy sheep

Author

Dhorne-Pollet, Sophie, Robert-Granié, C., Aurel, M., Marie-Etancelin, C., Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Station d'Amélioration Génétique des Animaux (SAGA), Institut National de la Recherche Agronomique (INRA), Domaine expérimental de La Fage (LA FAGE), AgroParisTech-Institut National de la Recherche Agronomique (INRA), and European Project: QLK5-2000-00656,GENESHEEPSAFETY

Subjects
collagen, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, animal structures, [SDV]Life Sciences [q-bio], Gene Expression Profiling, food and beverages, dairy sheep, Dairying, fluids and secretions, Milk, cdna array, udder, gene expression, Animals, Lactation, Female, milking ability, Sheep, Domestic
Abstract

International audience; To understand the mechanisms underlying milk ability and more precisely the kinetics of milk emission, we compared teat transcriptome profiles from Lacaune ewes in the tails of the milk flow phenotypic distribution. Two different arrays containing respectively 1896 and 13 168 PCR products selected from several tissue-specific cDNA libraries, including mammary gland, allowed the identification of 73 differentially expressed genes between teats from high and low milk flow ewes. Genes involved in muscle contraction were identified as over-expressed, and genes encoding collagen were found to be under-expressed in teats from low milk flow ewes. We confirmed this underexpression of COL1A1 and COL1A2 in low-milk flow ewes using RT-qPCR. These results suggest that milking ability may be due to the capacity of the teat sphincter to relax during mechanical milking. We propose that an optimal condition for mechanical milking may require proper relaxation of the teats. To our knowledge, this is the first transcriptomic analysis studying milking ability, using udder tissue for gene expression profiling, which demonstrates that mechanical milking ability is not only determined by morphological features but also by tissue composition.

Published
2012
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48. Cumulus cells transcriptomics revealed the potential biomarkers of oocyte development competence and differences in signaling pathways during in vitro and in vivo maturation bovine

Author

Uzbekova, Svetlana, Pollet, Sophie, Salhab, Mohamad, Auclair, Sylvain, Dalbies Tran, Rozenn, Mermillod, Pascal, Ponsart, Claire, Dupont, Joëlle, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Biologie du développement et reproduction (BDR), Centre National de la Recherche Scientifique (CNRS)-École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Union nationale des coopératives d’élevage et d’insémination animale (UNCEIA), Rheinische Friedrich-Wilhelms-Universität Bonn. Labo/service de l'auteur, Bonn, DEU., ProdInra, Archive Ouverte, Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Biologie du Développement et Reproduction (BDR), Institut National de la Recherche Agronomique (INRA), Union Nationale des Coopératives Agricoles d'Elevage et d'Insémination Animale, and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], [SDV.OT] Life Sciences [q-bio]/Other [q-bio.OT]
Abstract

absent

Published
2011

49. Potential markers of oocyte developmental competence in cumulus cells: comparative analysis of in vitro and in vivo maturation in bovine (Bos taurus)

Author

Salhab, Mohamad, Pollet, Sophie, Auclair, Sylvain, Dupont, Joëlle, Perreau, Christine, Mermillod, Pascal, HUMBLOT, P., Uzbekova, Svetlana, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Union nationale des coopératives d’élevage et d’insémination animale (UNCEIA), ProdInra, Archive Ouverte, Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Union Nationale des Coopératives Agricoles d'Elevage et d'Insémination Animale, and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV] Life Sciences [q-bio], TECHNOLOGIE DE LA REPRODUCTION ASSISTEE, [SDV]Life Sciences [q-bio], education, human activities, health care economics and organizations
Abstract

Poster 23; absent

Published
2010

50. Potential markers of oocyte developmental competence revealed by transcriptome analysis of cumulus cells in bovine (Bos taurus)

Author

Salhab, Mohamad, Auclair, Sylvain, Pollet, Sophie, Hennequet-Antier, Christelle, Guyader-Joly, C., Humblot, P., Dalbies-Tran, Rozenn, Mermillod, Pascal, Uzbekova, Svetlana, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Biologie du développement et reproduction (BDR), Centre National de la Recherche Scientifique (CNRS)-École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Unité de Recherches Avicoles (URA), Institut National de la Recherche Agronomique (INRA), Union nationale des coopératives d’élevage et d’insémination animale (UNCEIA), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), and ProdInra, Migration

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], [INFO] Computer Science [cs], TECHNOLOGIE DE LA REPRODUCTION, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2010

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