8 results on '"FR-AgENCODE"'
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2. Watch out for a second SNP: focus on multi-nucleotide variants in coding regions and rescued stop-gained
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Fabien Degalez, Frédéric Jehl, Kévin Muret, Maria Bernard, Frédéric Lecerf, Laetitia Lagoutte, Colette Désert, Frédérique Pitel, Christophe Klopp, Sandrine Lagarrigue, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Animale et Biologie Intégrative (GABI), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), 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]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), French institutions Institut Agro (AGROCAMPUS OUEST) and INRAE [Fr-AgENCODE project (2015–2017) and ELASTICe project (2012)]. FJ, FD, and KM were Ph.D. fellows supported by the Brittany region (France) and the INRAE Animal Genetics division. These funding bodies had no role in the design of the study, in the collection, analysis, and interpretation of data, or in the writing of the manuscript., ANR-11-BSV7-0004,FatInteger,Recherche de régulateurs clefs de la plasticité lipidique chez deux espèces monogastriques majeures (porc et poule) en combinant des données haut débit et des approches statistique, bioinformatique et phylogénique.(2011), ANR-13-ADAP-0014,ChickStress,Mécanismes d'adaptation à la chaleur et à un aliment suboptimal chez la poule pondeuse(2013), ANR-09-GENM-0004,EpiBird,Analyse Epigénétique chez les Oiseaux(2009), European Project: 633531,H2020,H2020-SFS-2014-2,Feed-a-Gene(2015), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO 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), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
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SNP ,MNV ,Single-nucleotide polymorphism ,Computational biology ,QH426-470 ,Biology ,03 medical and health sciences ,0302 clinical medicine ,FATP4 ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,SLC27A4 ,rescued stop-gained ,Genetics ,Coding region ,Missense mutation ,Gene ,Genetics (clinical) ,Original Research ,030304 developmental biology ,0303 health sciences ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,multi-nucleotide variants (MNV) ,Potential effect ,Molecular Medicine ,variation ,030217 neurology & neurosurgery - Abstract
Most single-nucleotide polymorphisms (SNPs) are located in non-coding regions, but the fraction usually studied is harbored in protein-coding regions because potential impacts on proteins are relatively easy to predict by popular tools such as the Variant Effect Predictor. These tools annotate variants independently without considering the potential effect of grouped or haplotypic variations, often called “multi-nucleotide variants” (MNVs). Here, we used a large RNA-seq dataset to survey MNVs, comprising 382 chicken samples originating from 11 populations analyzed in the companion paper in which 9.5M SNPs— including 3.3M SNPs with reliable genotypes—were detected. We focused our study on in-codon MNVs and evaluate their potential mis-annotation. Using GATK HaplotypeCaller read-based phasing results, we identified 2,965 MNVs observed in at least five individuals located in 1,792 genes. We found 41.1% of them showing a novel impact when compared to the effect of their constituent SNPs analyzed separately. The biggest impact variation flux concerns the originally annotated stop-gained consequences, for which around 95% were rescued; this flux is followed by the missense consequences for which 37% were reannotated with a different amino acid. We then present in more depth the rescued stop-gained MNVs and give an illustration in the SLC27A4 gene. As previously shown in human datasets, our results in chicken demonstrate the value of haplotype-aware variant annotation, and the interest to consider MNVs in the coding region, particularly when searching for severe functional consequence such as stop-gained variants.
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- 2021
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3. Multi-species annotation of transcriptome and chromatin structure in domesticated animals
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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, der Laan, Marie-Hélène Pinard-Van, Klopp, Christophe, Tixier-Boichard, Michèle, 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, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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 ), Université de Rennes (UR), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Paris Saclay (COMUE), INRA 'SelGen metaprogramme', grant 'FR-AgENCODE: A French pilot project to enrich the annotation of livestock genomes' (2015-2017), Animal Health and Welfare ERA-Net (anihwa) -project KILLeuPRRSV, ANR-11-INBS-0003,CRB-Anim,Réseau de Centres de Ressources Biologiques pour les animaux domestiques(2011), European Project: FP7-609398, 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], Curtin University, GeT PlaGe, Genotoul, 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 ), Université de Rennes (UNIV-RENNES), Infectiologie Animale et Santé Publique - IASP (Nouzilly, France), CEA Paris Saclay, AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), 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, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech-Institut National de la Recherche Agronomique (INRA), 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), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), 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
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Livestock ,Goats ,[SDV]Life Sciences [q-bio] ,Sus scrofa ,Molecular Sequence Annotation ,Functional annotation ,ATAC-seq ,Chromatin ,lcsh:Biology (General) ,Hi-C ,Animals, Domestic ,[SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies ,Animals ,Cattle ,RNA-seq ,Transcriptome ,Chickens ,lcsh:QH301-705.5 ,Phylogeny ,Research Article - Abstract
Background Comparative genomics studies are central in identifying the coding and non-coding elements associated with complex traits, and the functional annotation of genomes is a critical step to decipher the genotype-to-phenotype relationships in livestock animals. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aimed to create reference functional maps of domesticated animals by profiling the landscape of transcription (RNA-seq), chromatin accessibility (ATAC-seq) and conformation (Hi-C) in 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). Results RNA-seq assays considerably extended the available catalog of annotated transcripts and identified differentially expressed genes with unknown function, including new syntenic lncRNAs. ATAC-seq highlighted an enrichment for transcription factor binding sites in differentially accessible regions of the chromatin. Comparative analyses revealed a core set of conserved regulatory regions across species. Topologically associating domains (TADs) and epigenetic A/B compartments annotated from Hi-C data were consistent with RNA-seq and ATAC-seq data. Multi-species comparisons showed that conserved TAD boundaries had stronger insulation properties than species-specific ones and that the genomic distribution of orthologous genes in A/B compartments was significantly conserved across species. Conclusions We report the first multi-species and multi-assay genome annotation results obtained by a FAANG project. Beyond the generation of reference annotations and the confirmation of previous findings on model animals, the integrative analysis of data from multiple assays and species sheds a new light on the multi-scale selective pressure shaping genome organization from birds to mammals. Overall, these results emphasize the value of FAANG for research on domesticated animals and reinforces the importance of future meta-analyses of the reference datasets being generated by this community on different species.
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- 2019
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4. Profiling the landscape of transcription, chromatin accessibility and chromosome conformation of cattle, pig, chicken and goat genomes [FAANG pilot project]
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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
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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.
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- 2017
5. Long-non coding RNAs repertoires in liver and two T lymphocyte cell types in four livestock species
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Muret, Kévin, Djebali Quelen, Sarah, Derrien, Thomas, Cabau, Cédric, Klopp, Christophe, Esquerre, Diane, Munyard, Kylie, Tosser-Klopp, Gwenola, Acloque, Hervé, Giuffra, Elisabetta, Foissac, Sylvain, Lagarrigue, Sandrine, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, 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], Institut de Génétique et Développement de Rennes (IGDR), 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 ), Université de Rennes (UNIV-RENNES), Sigenae, Institut National de la Recherche Agronomique (INRA), Plateforme Genotoul, Curtin University [Perth], Planning and Transport Research Centre (PATREC), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Fr-Agencode, 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), 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, 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), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), 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 ), Université de Rennes (UR), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), and Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
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Animal biology ,Multispecies ,Comparative genomics ,[SDV.BA]Life Sciences [q-bio]/Animal biology ,Biologie animale ,Functional Annotation of Animal Genomes (FAANG) ,RNA-seq ,Long non-coding RNAs - Abstract
Understanding genome-to-phenome relationships requires deep and cross-disciplinary genetic analyses among which functional annotation provides crucial insights. The development of High Throughput Sequencing and RNA-seq now help us to find a large number of heterogeneous and low-expressed transcripts known to be long non-coding RNAs (lncRNAs). One of the aims of the FAANG pilot project ‘FR-AgENCODE’ is to identify and characterise the long non-coding RNAs of multiple tissues and cell lines in 4 farm animals (chicken, bovine, pig and goat) of both sexes. Here, we focus our analysis on the liver tissue and two blood T-cell types (CD3+CD4+, CD3+CD8+) where samples were collected through 4 biological replicates (2 males and 2 females). It allows us to compare lncRNA repertoires between tissues, sex and species in relation with fundamental biological functions like energy storage and immunity. High depth strand-specific RNA-seq produced ~200M paired-end reads for each of the 16 RNA-seq datasets. After transcriptome reconstruction, we used the recently published FEELnc program (Wucher et al., 2017, Nucleic Acid Research) to identify lncRNAs longer than 200 bp and without protein-coding capabilities. FEELnc also classifies lncRNAs based on their genomic localizations with respect to the ENSEMBL protein-coding annotation: intergenic lncRNAs are categorized depending on the distance and orientation with respect to the closest mRNAs and the intragenic lncRNAs are extracted based on their overlap with mRNAs exons and introns. We will report these lncRNA repertoires in terms of intergenic/ intragenic lncRNA class, structure and expression and comparing these features between livestock species, tissues and sexes. By profiling the transcriptional landscape of lncRNAs in these 4 species, this data will further contribute to the global action for annotating functional elements of livestock genomes.
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- 2017
6. Integrative and differential analysis of transcriptomes and chromatin accessibility regions reveals regulatory mechanisms involved in pig immune and metabolic functions
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Djebali Quelen, Sarah, Munyard, Kylie, Villa-Vialaneix, Nathalie, Cabau, Cédric, Rau, Andrea, CRISCI, Elisa, Derrien, Thomas, Klopp, Christophe, Zytnicki, Matthias, Lagarrigue, Sandrine, ACLOQUE, Hervé, Foissac, Sylvain, Giuffra, Elisabetta, 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, 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), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), 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), Fr-Agencode, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)
- Subjects
Pigs and related species ,Hi-C ,[SDV]Life Sciences [q-bio] ,Functional Annotation of Animal Genomes (FAANG) ,ATAC-seq ,RNA-seq - Abstract
In the context of the FAANG pilot project ‘FR-AgENCODE’ to improve the functional annotation of livestock genomes, we characterised the transcriptome and the chromatin accessibility of pig hepatocytes and two types of lymphocytes. More specifically, CD3+CD4+ (‘CD4’) and CD3+CD8+ (‘CD8’) T-cells were sorted from the blood of two male and two female Large White adult pigs. These samples, along with liver samples from the same animals, were processed by strand-oriented RNA-seq and ATAC-seq experiments. Principal Component Analyses on log-transformed TMM-normalized read counts in genes (from RNA-seq) and regions of chromatin accessibility (from ATAC-seq) consistently highlighted the variability between liver and the T-cells, and to a lesser extent within T-cells (CD4 v. CD8), as well as between the male and female samples. Comparative analyses identified differentially expressed genes between cell types as well as potential regulatory sites from differentially accessible chromatin regions. As expected, ontology annotations of differentially expressed genes were enriched for either immunity- or metabolism-related terms. Interestingly, correlations between gene expression and promoter accessibility across samples were enriched for both extreme positive and negative values, which suggests that ATAC-seq can efficiently capture distinct regulatory mechanisms of gene expression. Candidate enhancers and repressors were identified by comparing ATAC-seq regions with predicted binding sites of 500+ transcription factors. By integrating these results with those from Hi-C chromosome con-formation capture on the liver samples, we further characterised the differences between ‘active’ and ‘repressed’ topological domains in terms of functional features, including gene density and general chromatin accessibility. Altogether, these results lead to a better un-derstanding of the molecular mechanisms involved in pig immune and metabolic functions, and illustrate a useful contribution to the functional annotation effort of the FAANG initiative.
- Published
- 2017
7. Profiling the landscape of transcription and chromatin conformation reveals regulatory mechanisms involved in immune and metabolic functions
- Author
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Sylvain Foissac, Sarah Djebali Quelen, Hervé Acloque, Marie-Helene Pinard - van der Laan, Sandrine Lagarrigue, Elisabetta Giuffra, ProdInra, Archive Ouverte, 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, 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), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), FAANG pilot project 'FR-AgENCODE', AgroParisTech-Institut National de la Recherche Agronomique (INRA), 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), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]
- Subjects
pig ,[SDV]Life Sciences [q-bio] ,chicken ,génome ,goat ,animal de rente ,T cells ,functional annotation ,liver ,cash cattle ,[SDV] Life Sciences [q-bio] ,cattle ,chromatin ,annotation fonctionnelle ,chromatine - 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. Here we present on-going results on gene expression and chromatin conformation in hepatocytes and CD3+CD4+ (“CD4”) and CD3+CD8+ (“CD8”) T cells with a focus on the pig species (two male and two female Large White adult pigs). These samples were processed by strand-oriented RNA-seq and ATAC-seq experiments. Principal Component Analyses on log-transformed TMM-normalized read counts in genes (from RNA-seq) and regions of chromatin accessibility (from ATAC-seq) consistently highlighted the variability between liver and the T cells, and to a lesser extent within T cells (CD4 vs. CD8), as well as between the male and female samples. Comparative analyses identified differentially expressed genes between cell types as well as potential regulatory sites from differentially accessible chromatin regions. As expected, ontology annotations of differentially expressed genes were enriched for either immunity- or metabolism-related terms. Interestingly, correlations between gene expression and promoter accessibility across samples were enriched for both extreme positive and negative values, which suggests that ATAC-seq can efficiently capture distinct regulatory mechanisms of gene expression. Candidate enhancers and repressors were identified by comparing ATAC-seq regions with predicted binding sites of 500+ transcription factors. By integrating these results with those from Hi-C chromosome conformation capture on the liver samples, we investigated differences between “active” and “repressed” topological domains in terms of functional features, including gene density and general chromatin accessibility. Altogether, these results lead to a better understanding of the molecular mechanisms involved in pig immune and metabolic functions, and illustrate a useful contribution to the functional annotation effort of the FAANG initiative.
- Published
- 2017
8. GO-FAANG meeting: a Gathering On Functional Annotation of Animal Genomes
- Author
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Tuggle, Christopher, Giuffra, Elisabetta, White, Stephen, Clarke, Laura, Zhou, Huaijun, Ross, Pablo, Finno, Carrie, Acloque, H., Reecy, James, Archibald, Alan, Bellone ¶ ¶, Rebecca, Boichard, Michèle, Chamberlain, Amanda, Cheng, Hans, Crooijmans, Richard, Delany, Mary, Finno, Carrie J., Groenen, Martien, Hayes, Ben, Lunney, Joan, Petersen, Jessica, Plastow, Graham, Schmidt, Carl, Song, Jiuzhou, Watson, Mick, Iowa State University (ISU), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, USDA-ARS : Agricultural Research Service, Center for Reproductive Biology, Washington State University (WSU), Department of Veterinary Microbiology and Pathology, European Molecular Biology Laboratory, European Bioinformatics Institute, Department of Animal Science, University of California, Department of Population Health and Reproduction, 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, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Department of Population Health and Reproduction, School of Veterinary Medicine, Department of Economic Development, Jobs, Transport and Resources (DEDJTR), Avian Disease and Oncology Laboratory, 4279 E Mount Hope Road, Animal Breeding and Genomics Centre, Wageningen University and Research [Wageningen] (WUR), Centre for Nutrition and Food Sciences - Queensland Alliance for Agriculture and Food Innovation, University of Southern Queensland (USQ), Animal Parasitic Diseases Laboratory [Beltsville, USA], United States Department of Agriculture (USDA)-USDA Agricultural Research Service [Beltsville, Maryland], USDA-ARS : Agricultural Research Service-USDA-ARS : Agricultural Research Service, Department of Agricultural, Food & Nutritional Science, University of Alberta, Department of Animal & Food Sciences, University of Delaware [Newark], Department of Animal and Avian Sciences, University of Maryland [College Park], University of Maryland System-University of Maryland System, National Science Foundation (NSF) NSF-IOS-1548275, United States Department of Agriculture (USDA) USDA-NIFA-AFRI, 2015-68004-24104, Illumina, Inc, Iowa State University, USDA-NRSP-8 Bioinformatics, United States Department of Agriculture (USDA) 2016-67015-24579, Genome Canada, Affymetrix, Inc, Geneseek, Inc, Biotechnology and Biological Sciences Research Council including Institute Strategic Programme and National Capability Grants (BBSRC) BBS/E/D/20310000 BB/J004243/1, INRA through the SelGen metaprogramme (Fr-AgENCODE project), Biotechnology and Biological Sciences Research Council (BBSRC) : BBS/E/D/20211551, BBS/E/D/20211550, BBS/E/D/20310000, BB/M01844X/1., United States Department of Agriculture (USDA), European Molecular Biology Laboratory European Bioinformatics Institute, University of California [Davis] (UC Davis), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT], Roslin Institute, Wageningen University and Research Centre (WUR), University of Queensland [Brisbane], Dept Anim & Food Sci, and University of Maryland System
- Subjects
data coordination centre (DCC) ,Dairy & Animal Science ,[SDV]Life Sciences [q-bio] ,International Cooperation ,data sharing ,[SDV.SA.ZOO]Life Sciences [q-bio]/Agricultural sciences/Zootechny ,dna ,Animal Breeding and Genomics ,metanalysis ,genomic ,Genetics ,Animals ,[INFO]Computer Science [cs] ,Fokkerij en Genomica ,Veterinary Sciences ,Domestic ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,regulatory variation ,Genome ,Genomics ,Articles ,Congresses as Topic ,Reference Standards ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics ,reveal principle ,data coordination centre ,Animals, Domestic ,District of Columbia ,WIAS ,chromatin ,Original Article ,Zoology - Abstract
International audience; The Functional Annotation of Animal Genomes (FAANG) Consortium recently held a Gathering On FAANG (GO-FAANG) Workshop in Washington, DC on October 7-8, 2015. This consortium is a grass-roots organization formed to advance the annotation of newly assembled genomes of domesticated and non-model organisms (www.faang.org). The workshop gathered together from around the world a group of 100+ genome scientists, administrators, representatives of funding agencies and commodity groups to discuss the latest advancements of the consortium, new perspectives, next steps and implementation plans. The workshop was streamed live and recorded, and all talks, along with speaker slide presentations, are available at www.faang.org. In this report, we describe the major activities and outcomes of this meeting. We also provide updates on ongoing efforts to implement discussions and decisions taken at GO-FAANG to guide future FAANG activities. In summary, reference datasets are being established under pilot projects; plans for tissue sets, morphological classification and methods of sample collection for different tissues were organized; and core assays and data and meta-data analysis standards were established.
- Published
- 2016
- Full Text
- View/download PDF
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