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2. 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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3. The sheep genome illuminates biology of the rumen and lipid metabolism

Author

Jiang, Yu, Xie, Min, Chen, Wenbin, Talbot, Richard, Maddox, Jillian F., Faraut, Thomas, Wu, Chunhua, Muzny, Donna M., Li, Yuxiang, Zhang, Wenguang, Stanton, Jo-Ann, Brauning, Rudiger, Barris, Wesley C., Hourlier, Thibaut, Aken, Bronwen L., Searle, Stephen M. J., Adelson, David L., Bian, Chao, Cam, Graham R., Chen, Yulin, Cheng, Shifeng, DeSilva, Udaya, Dixen, Karen, Dong, Yang, Fan, Guangyi, Franklin, Ian R., Fu, Shaoyin, Fuentes-Utrilla, Pablo, Guan, Rui, Highland, Margaret A., Holder, Michael E., Huang, Guodong, Ingham, Aaron B., Jhangiani, Shalini N., Kalra, Divya, Kovar, Christie L., Lee, Sandra L., Liu, Weiqing, Liu, Xin, Lu, Changxin, Lv, Tian, Mathew, Tittu, McWilliam, Sean, Menzies, Moira, Pan, Shengkai, Robelin, David, Servin, Bertrand, Townley, David, Wang, Wenliang, Wei, Bin, White, Stephen N., Yang, Xinhua, Ye, Chen, Yue, Yaojing, Zeng, Peng, Zhou, Qing, Hansen, Jacob B., Kristiansen, Karsten, Gibbs, Richard A., Flicek, Paul, Warkup, Christopher C., Jones, Huw E., Oddy, V. Hutton, Nicholas, Frank W., McEwan, John C., Kijas, James W., Wang, Jun, Worley, Kim C., Archibald, Alan L., Cockett, Noelle, Xu, Xun, Wang, Wen, and Dalrymple, Brian P.

Published
2014

6. Major Reorganization of Chromosome Conformation During Muscle Development in Pig.

Author

Marti-Marimon, Maria, Vialaneix, Nathalie, Lahbib-Mansais, Yvette, Zytnicki, Matthias, Camut, Sylvie, Robelin, David, Yerle-Bouissou, Martine, and Foissac, Sylvain

Subjects
MUSCLE growth, CHROMOSOMES, CELL physiology, FLUORESCENCE in situ hybridization, DNA sequencing, CHROMATIN, HISTONES, EUKARYOTIC genomes
Abstract

The spatial organization of the genome in the nucleus plays a crucial role in eukaryotic cell functions, yet little is known about chromatin structure variations during late fetal development in mammals. We performed in situ high-throughput chromosome conformation capture (Hi-C) sequencing of DNA from muscle samples of pig fetuses at two late stages of gestation. Comparative analysis of the resulting Hi-C interaction matrices between both groups showed widespread differences of different types. First, we discovered a complex landscape of stable and group-specific Topologically Associating Domains (TADs). Investigating the nuclear partition of the chromatin into transcriptionally active and inactive compartments, we observed a genome-wide fragmentation of these compartments between 90 and 110 days of gestation. Also, we identified and characterized the distribution of differential cis - and trans -pairwise interactions. In particular, trans -interactions at chromosome extremities revealed a mechanism of telomere clustering further confirmed by 3D Fluorescence in situ Hybridization (FISH). Altogether, we report major variations of the three-dimensional genome conformation during muscle development in pig, involving several levels of chromatin remodeling and structural regulation. [ABSTRACT FROM AUTHOR]

Published
2021
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7. 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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8. 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

9. Characterization of 3D genomic interactions in fetal pig muscle

Author

Marti Marimon, Maria Eugenia, Acloque, Hervé, Zytnicki, Matthias, Robelin, David, Djebali Quelen, Sarah, Villa-Vialaneix, Nathalie, Madsen, Ole, Lahbib Mansais, Yvette, Esquerré, Diane, Mompart, Florence, Yerle-Bouissou, Martine, Groenen, Martien, Foissac, Sylvain, Ecole Nationale Vétérinaire de Toulouse - ENVT (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), Wageningen University & Research - WUR (NETHERLANDS), 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, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Wageningen University and Research [Wageningen] (WUR), Dynamiques Forestières dans l'Espace Rural (DYNAFOR), 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)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Wageningen University and Research Center (WUR), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Toulouse-Institut National Polytechnique (Toulouse) (Toulouse INP), and Institut National Polytechnique de Toulouse - INPT (FRANCE)

Subjects
Hi-C, [SDV]Life Sciences [q-bio], [SDV.BA]Life Sciences [q-bio]/Animal biology, Biologie animale, Biologie du développement, Nuclear architecture, Fetal development, Pig muscle, nuclear architecture, fetal development, pig muscle, CTCF, [SDV.BDD]Life Sciences [q-bio]/Development Biology
Abstract

Genome sequence alone is not sufficient to explain the overall coordination of nuclear activity in a particular tissue. The nuclear organisation and genomic long-range intra- and inter-chromosomal interactions play an important role in the regulation of gene expression and the activation of tissue- specific gene networks. Here we present an overview of the pig genome architecture in muscle at two late developmental stages. The muscle maturation process occurs between the 90th day and the end of gestation (114 days), a key period for survival at birth. To characterise this period we profiled chromatin interactions genome-wide with in situ Hi-C (High Throughput Chromosome Conformation Capture) in muscle samples collected at 90 and 110 days of gestation, specific moments where a drastic change in gene expression has been reported. About 200 million read pairs per library were generated (3 replicates per condition). This allowed: (a) the design of an experimental Hi-C protocol optimized for frozen fetal tissues, (b) the first Hi-C contact heatmaps in fetal porcine muscle cells, and (c) to profile Topologically Associated Domains (TADs) defined as genomic domains with high levels of chromatin interactions. Using the new assembly version Sus scrofa v11, we could map 82% of the Hi-C reads on the reference genome. After filtering, 49% of valid read pairs were used to infer the genomic interactions in both developmental stages. In addition, ChIP-seq experiments were performed to map the binding of the structural protein CTCF, known to regulate genome structure by promoting interactions between genes and distal enhancers. The Hi-C and ChIP-seq data were analysed in combination with the results of a previous transcriptome analysis, focusing on the hun-dreds of genes that were reported as differentially expressed during muscle maturation. We will report the observed general differences between both developmental stages in terms of transcription and structure.

Published
2017

10. Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples

Author

Boitard, Simon, Kofler, Robert, Francoise, Pierre, Robelin, David, Schlötterer, Christian, Futschik, Andreas, Laboratoire de Génétique Cellulaire (LGC), 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, Vetmeduni Vienna, University of Vienna [Vienna], and Christian Schlötterer is supported by grants of the Austrian Science Fund (FWF, P19467). Travels between France and Austria were funded by the PHC Amadeus grant 25154QH.

Subjects
next generation sequencing, hidden markov model, Internet, newt generation sequencing, Models, Genetic, hidden Markov models, [SDV]Life Sciences [q-bio], genetic processes, High-Throughput Nucleotide Sequencing, Genomics, Sequence Analysis, DNA, pooled DNA, Polymorphism, Single Nucleotide, Quail, selective sweep, allele frequency spectrum, Gene Frequency, selective sweeps, Resource Articles, Animals, natural sciences, Software
Abstract

Chantier qualité GA; International audience; Due to its cost effectiveness, next generation sequencing of pools of individuals (Pool-Seq) is becoming a popular strategy for genome-wide estimation of allele frequencies in population samples. As the allele frequency spectrum provides information about past episodes of selection, Pool-seq is also a promising design for genomic scans for selection. However, no software tool has yet been developed for selection scans based on Pool-Seq data. We introduce Pool-hmm, a Python program for the estimation of allele frequencies and the detection of selective sweeps in a Pool-Seq sample. Pool-hmm includes several options that allow a flexible analysis of Pool-Seq data, and can be run in parallel on several processors. Source code and documentation for Pool-hmm is freely available at https://qgsp.jouy.inra.fr/.

Published
2013
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11. 3D nuclear positioning of IGF2 alleles and trans interactions with imprinted genes

Author

Lahbib Mansais, Yvette, Marti-Marimon, Maria, Voillet, Valentin, Barasc, Harmonie, Mompart, Florence, Riquet, Juliette, Foissac, Sylvain, Robelin, David, ACLOQUE, Hervé, Billon, Yvon, Villa-Vialaneix, Nathalie, Liaubet, Laurence, Yerle-Bouissou, Martine, 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, Expérimentation et Système Innovants (GenESI), Institut National de la Recherche Agronomique (INRA), and Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], interaction, [INFO]Computer Science [cs], genetic, [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2016

12. 3D nuclear positioning of IGF2 alleles and trans interactions with imprinted genes in pig fetal cells

Author

Lahbib Mansais, Yvette, Marti-Marimon, Maria, Voillet, Valentin, Barasc, Harmonie, Mompart, Florence, Riquet, Juliette, Foissac, Sylvain, Robelin, David, ACLOQUE, Hervé, Billon, Yvon, Villa-Vialaneix, Nathalie, Liaubet, Laurence, Yerle- Bouissou, Martine, 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, Expérimentation et Système Innovants (GenESI), Institut National de la Recherche Agronomique (INRA), and Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA)

Subjects
genomic, pig, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], interaction, [INFO]Computer Science [cs], 3D nuclear, genetic, [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS, génétique
Abstract

International audience

Published
2016

13. 3D nuclear organization of theCMHcomplex in control and LPS-activated porcine and human macrophages

Author

Mompart, Florence, Robelin, David, Gaillard, Claire, Bouissou-Matet Yerle, Martine, 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, 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], education, macrophage
Abstract

3D nuclear organization of theCMHcomplex in control and LPS-activated porcine and human macrophages. 22. International Colloquim on Animal Cytogenetics and Genomics (ICACG)

Published
2016

14. 3D nuclear organization of the CMH complex in control and LPS-activated porcine and human macrophages

Author

Mompart, Florence, Robelin, David, Gaillard, Claire, Bouissou-Matet Yerle, Martine, 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), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
pig, human macrophage, [SDV]Life Sciences [q-bio], education, 3d nuclear, respiratory system, genetic
Abstract

3D nuclear organization of the CMH complex in control and LPS-activated porcine and human macrophages. 22. International Colloquim on Animal Cytogenetics and Genomics (ICACG)

Published
2016

15. Construction of whole genome interaction maps and study of correlation with gene expression level in fetal muscle cells

Author

Marti-Marimon, Maria, ACLOQUE, Hervé, Robelin, David, Zytnicki, Matthias, Djebali, Sarah, Lahbib Mansais, Yvette, Esquerré, Diane, Mompart, Florence, Yerle-Bouissou, Martine, Foissac, Sylvain, 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, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), and Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, correlation, [SDV]Life Sciences [q-bio], interaction, [INFO]Computer Science [cs], genetic, [MATH]Mathematics [math], genome, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2016

16. Investigating the nuclear spatial conformation of livestock genomes using Hi-C

Author

Foissac, Sylvain, ACLOQUE, Herve, Mompart, Florence, Esquerre, Diane, Robelin, David, San Cristobal, Magali, Djebali Quelen, Sarah, Zytnicki, Matthias, 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, 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, ProdInra, Archive Ouverte, 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
[SDV] Life Sciences [q-bio], livestock, [SDV]Life Sciences [q-bio], parasitic diseases, genome
Abstract

Investigating the nuclear spatial conformation of livestock genomes using Hi-C. NGS'16 Genome Annotation

Published
2016

17. Profiling the Nuclear Spatial Conformation of Livestock Genomes in Cell Lines and Liver Cells

Author

Foissac, Sylvain, Acloque, Hervé, Mompart, Florence, Esquerre, Diane, Robelin, David, San Cristobal, Magali, Zytnicki, Matthias, Giuffra, Elisabetta, Djebali Quelen, Sarah, 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, Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, 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], and ProdInra, Archive Ouverte

Subjects
[SDV] Life Sciences [q-bio], livestock, nervous system, [SDV]Life Sciences [q-bio], nuclear spatial, genome
Abstract

Profiling the Nuclear Spatial Conformation of Livestock Genomes in Cell Lines and Liver Cells. PAG XXIV - Plant and Animal Genome Conference

Published
2016

18. A new local score based method applied to behavior-divergent quail lines sequenced in pools precisely detects selection signatures on genes related to autism

Author

Fariello Rico, Maria Inès, Boitard, Simon, Mercier, Sabine, Robelin, David, Faraut, Thomas, Arnould, Cécile, Recoquillay, Julien, Bouchez, Olivier, Salin, Gérald, Dehais, Patrice, Gourichon, David, Leroux, Sophie, Pitel, Frédérique, Leterrier, Christine, and San Cristobal, Magali

Subjects
Autre (Sciences du Vivant), quantitative biology, population and evolution, genomic
Abstract

Detecting genomic footprints of selection is an important step in the understanding of evolution. Accounting for linkage disequilibrium in genome scans allows increasing the detection power, but haplotype-based methods require individual genotypes and are not applicable on pool-sequenced samples. We propose to take advantage of the local score approach to account for linkage disequilibrium, accumulating (possibly small) signals from single markers over a genomic segment, to clearly pinpoint a selection signal, avoiding windowing methods. This method provided results similar to haplotype-based methods on two benchmark data sets with individual genotypes. Results obtained for a divergent selection experiment on behavior in quail, where two lines were sequenced in pools, are precise and biologically coherent, while competing methods failed: our approach led to the detection of signals involving genes known to act on social responsiveness or autistic traits. This local score approach is general and can be applied to other genome-wide analyzes such as GWAS or genome scans for selection.

Published
2015

19. Local Score Based Method On Pool-Sequenced Behavior-Divergent Quail Lines Precisely Detected Selection Signatures Related To Autism

Author

Fariello Rico, Maria Inès, Arnould, Cécile, Boitard, Simon, Dehais, Patrice, Faraut, Thomas, Duval, Elisabeth, Leterrier, Christine, Mercier, Sylvie, Pitel, Frederique, Recoquillay, Julien, Robelin, David, Salin, Gerald, San Cristobal, Magali, 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, Institut Pasteur de Montevideo, Réseau International des Instituts Pasteur (RIIP), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Toulouse - Jean Jaurès (UT2J), 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), Unité de Recherches Avicoles (URA), 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 (UT)-Centre National de la Recherche Scientifique (CNRS), Unité de Nutrition Humaine (UNH), Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université-Institut National de la Recherche Agronomique (INRA), Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), 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), Recherches Avicoles (SRA), Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], AgroParisTech-Institut National de la Recherche Agronomique (INRA), 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), and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
autisme, behavior-divergent, quail lines, [SDV]Life Sciences [q-bio], séquençage, comportement, selection, pool-sequenced, [INFO]Computer Science [cs], caille, bioinformatique, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2014

20. Meiotic recombination analysis for individual chromosomes in male pigs

Author

Mary, Nicolas, Barasc, Harmonie, Ferchaud, Stéphane, Billon, Yvon, Meslier, Frederic, Robelin, David, Calgaro, Anne, Dudez, Anne-Marie, Bonnet, Nathalie, Yerle, Martine, Ducos, Alain, Pinton, Alain, 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, Expérimentation et Système Innovants (GenESI), Institut National de la Recherche Agronomique (INRA), and Centre National de la Recherche Scientifique (CNRS)

Subjects
pig, [SDV]Life Sciences [q-bio], meiotic, [INFO]Computer Science [cs], genetic, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2014
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21. 3D nuclear organization of the CMH complex in control and LPS-activated porcine macrophages

Author

Mompart, Florence, Robelin, David, Gaillard, Claire, Bouissou-Matet Yerle, Martine, 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), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
pig, [SDV]Life Sciences [q-bio], 3d nuclear
Abstract

absent

Published
2014
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22. Arcitecture nucléaire 3D et expression du génome

Author

Yerle-Bouissou, Martine, Lahbib Mansais, Yvette, Mompart, Florence, ACLOQUE, HERVE, Robelin, David, Laboratoire de Génétique Cellulaire (LGC), 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), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
génome, [SDV]Life Sciences [q-bio], architecture nucléaire, 3d, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2014

23. 3D organization of telomeres in control and LPS-activated neutrophils

Author

Mompart, Florence, Robelin, David, Delcros, Chantal, Bouissou-Matet Yerle, Martine, Laboratoire de Génétique Cellulaire (LGC), 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), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
[SDV]Life Sciences [q-bio], telomeres, neutrophils, 3D FISH, LPS-activation, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2012

24. QGP: Quantitative Genetics Platform. A high performance computing solution for quantitative genetics software

Author

Monsoor, Misharl, Neau, Andre, Souchal, Martin, Nugier, Sylvie, Laperruque, Francois, Iannuccelli, Eddie, Le Roy, Pascale, Ricard, Edmond, Robelin, David, Filangi, Olivier, 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), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Centre de Traitement de l'Information Génétique (CTIG), Institut National de la Recherche Agronomique (INRA), Station d'Amélioration Génétique des Animaux (SAGA), Laboratoire de Génétique Cellulaire (LGC), 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), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
analyse de données, Bioinformatics, génotypage, plateforme informatique, Bio-informatique, biologie intégrative, animal, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2012

25. 3D organization of telomeres in control and LPS-activated porcine neutrophils

Author

Mompart, Florence, Robelin, David, Delcros, Chantal, Bouissou-Matet Yerle, Martine, Laboratoire de Génétique Cellulaire (LGC), 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), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

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

International audience

Published
2012

26. Pool-HMM & Freq-HMM

Author

Boitard, Simon, Robelin, David, Koffler, Robert, and ProdInra, Migration

Subjects
[SDV] Life Sciences [q-bio], estimation, Quantitative Biology::Populations and Evolution, pool-hmm, freq-hmm, Quantitative Biology::Genomics, allele frequency
Abstract

Freq-hmm estimates the allele frequency spectrum and detects selective sweeps using allele frequency data for a sample of individuals from the same population. It implements the HMM method of Boitard et al (2009). - Pool-hmm extends this approach to the use of NGS data obtained from pooled DNA. It estimates allele frequencies at each position from NGS data and accounts for the uncertainty of this estimation when computing the allele frequency spectrum and detecting sweeps. It implements the HMM method of Boitard et al (2012).

Published
2012

27. QTLMAP, a software for QTL detection in outbred populations

Author

Gilbert, Hélène, Le Roy, Pascale, Moreno, C., Robelin, David, Elsen, J.M., ProdInra, Migration, Station de Génétique Quantitative et Appliquée (SGQA), Institut National de la Recherche Agronomique (INRA), Génétique Animale (GARen), 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)-Ecole Nationale Supérieure Agronomique de Rennes, Laboratoire de Génétique Cellulaire (LGC), 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), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
[SDV] Life Sciences [q-bio], QTL, [SDV]Life Sciences [q-bio], SOFTWARE, OUTBRED POPULATION, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2008

28. QTLMAP : a large possibility software to detect QTL in outbred populations

Author

Gilbert, Hélène, Le Roy, Pascale, Moreno, Carole, Robelin, David, Boichard, Didier, Elsen, Jean Michel, Station de Génétique Quantitative et Appliquée (SGQA), Institut National de la Recherche Agronomique (INRA), Génétique Animale (GARen), 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)-Ecole Nationale Supérieure Agronomique de Rennes, and Station d'Amélioration Génétique des Animaux (SAGA)

Subjects
QTL, QTLMAP, software, [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2007

29. DNA sequence drives nucleosome occupancy of yeast promoters

Author

Miele, V., Vaillant, C., d'Aubenton, Y., Robelin, David, Prum, B., Thermes, C., Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT]
Published
2006

30. Accounting for linkage disequilibrium in genome scans for selection without individual genotypes: The local score approach.

Author

Fariello, María Inés, Boitard, Simon, Mercier, Sabine, Robelin, David, Faraut, Thomas, Arnould, Cécile, Recoquillay, Julien, Bouchez, Olivier, Salin, Gérald, Dehais, Patrice, Gourichon, David, Leroux, Sophie, Pitel, Frédérique, Leterrier, Christine, and SanCristobal, Magali

Subjects
LINKAGE disequilibrium, GENOTYPE-environment interaction, COMPUTER simulation, HAPLOTYPE statistics, POPULATION genetics
Abstract

Detecting genomic footprints of selection is an important step in the understanding of evolution. Accounting for linkage disequilibrium in genome scans increases detection power, but haplotype-based methods require individual genotypes and are not applicable on pool-sequenced samples. We propose to take advantage of the local score approach to account for linkage disequilibrium in genome scans for selection, cumulating (possibly small) signals from single markers over a genomic segment, to clearly pinpoint a selection signal. Using computer simulations, we demonstrate that this approach detects selection with higher power than several state-of-the-art single-marker, windowing or haplotype-based approaches. We illustrate this on two benchmark data sets including individual genotypes, for which we obtain similar results with the local score and one haplotype-based approach. Finally, we apply the local score approach to Pool-Seq data obtained from a divergent selection experiment on behaviour in quail and obtain precise and biologically coherent selection signals: while competing methods fail to highlight any clear selection signature, our method detects several regions involving genes known to act on social responsiveness or autistic traits. Although we focus here on the detection of positive selection from multiple population data, the local score approach is general and can be applied to other genome scans for selection or other genomewide analyses such as GWAS. [ABSTRACT FROM AUTHOR]

Published
2017
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31. Expressed alleles of imprinted IGF2, DLK1 and MEG3 colocalize in 3D-preserved nuclei of porcine fetal cells.

Author

Lahbib-Mansais, Yvette, Barasc, Harmonie, Marti-Marimon, Maria, Mompart, Florence, Iannuccelli, Eddie, Robelin, David, Riquet, Juliette, and Yerle-Bouissou, Martine

Subjects
ALLELES, SOMATOMEDIN A, GENE expression in mammals, GENOMIC imprinting, SWINE genetics, FLUORESCENCE in situ hybridization, CELL nuclei, CHROMATIN, MAMMALS
Abstract

Background: To explore the relationship between spatial genome organization and gene expression in the interphase nucleus, we used a genomic imprinting model, which offers parental-specific gene expression. Using 3D FISH in porcine fetal liver cells, we compared the nuclear organization of the two parental alleles (expressed or not) of insulin-like growth factor 2 (IGF2), a paternally imprinted gene located on chromosome 2. We investigated whether its nuclear positioning favors specific locus associations. We also tested whether IGF2 is implicated in long-range chromatin trans-associations as previously shown in the mouse model species for its reciprocal imprinted gene H19. Results: We focused on the 3D position of IGF2 alleles, with respect to their individual chromosome 2 territories. The paternally expressed allele was tagged with nascent RNA. There were no significant differences in the position of the two alleles (p = 0.06). To determine long-range chromatin trans-interactions, we chose 12 genes, some of which are known to be imprinted in mammalian model species and belong to a network of imprinted genes (i.e. SLC38A4, DLK1, MEG3, and ZAC1). We screened them and ABCG2, OSBP2, OSBPL1, RPL32, NF1, ZAR1, SEP15, GPC3 for associations with IGF2 in liver cells. All imprinted genes tested showed an association with IGF2. The DLK1/MEG3 locus showed the highest rate of colocalization. This gene association was confirmed by 3D FISH (in 20 % of the nuclei analyzed), revealing also the close proximity of chromosomes 2 and 7 (in 60 % of nuclei). Furthermore, our observations showed that the expressed paternal IGF2 allele is involved in this association. This IGF2-(DLK1/MEG3) association also occurred in a high percentage of fetal muscle cells (36 % of nuclei). Finally, we showed that nascent IGF2, DLK1 and MEG3 RNAs can associate in pairs or in a three-way combination. Conclusion: Our results show that trans-associations occur between three imprinted genes IGF2, DLK1 and MEG3 both in fetal liver and muscle cells. All three expressed alleles associated in muscle cells. Our findings suggest that the 3D nuclear organization is linked to the transcriptional state of these genes. [ABSTRACT FROM AUTHOR]

Published
2016
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32. Meiotic Recombination Analyses of Individual Chromosomes in Male Domestic Pigs (Sus scrofa domestica).

Author

Mary, Nicolas, Barasc, Harmonie, Ferchaud, Stéphane, Billon, Yvon, Meslier, Frédéric, Robelin, David, Calgaro, Anne, Loustau-Dudez, Anne-Marie, Bonnet, Nathalie, Yerle, Martine, Acloque, Hervé, Ducos, Alain, and Pinton, Alain

Subjects
MEIOSIS, RECOMBINANT DNA, TELOMERES, SEX chromosomes, HOMOLOGOUS chromosomes, CELL cycle, SYNAPTONEMAL complexes
Abstract

For the first time in the domestic pig, meiotic recombination along the 18 porcine autosomes was directly studied by immunolocalization of MLH1 protein. In total, 7,848 synaptonemal complexes from 436 spermatocytes were analyzed, and 13,969 recombination sites were mapped. Individual chromosomes for 113 of the 436 cells (representing 2,034 synaptonemal complexes) were identified by immunostaining and fluorescence in situ hybridization (FISH). The average total length of autosomal synaptonemal complexes per cell was 190.3 µm, with 32.0 recombination sites (crossovers), on average, per cell. The number of crossovers and the lengths of the autosomal synaptonemal complexes showed significant intra- (i.e. between cells) and inter-individual variations. The distributions of recombination sites within each chromosomal category were similar: crossovers in metacentric and submetacentric chromosomes were concentrated in the telomeric regions of the p- and q-arms, whereas two hotspots were located near the centromere and in the telomeric region of acrocentrics. Lack of MLH1 foci was mainly observed in the smaller chromosomes, particularly chromosome 18 (SSC18) and the sex chromosomes. All autosomes displayed positive interference, with a large variability between the chromosomes. [ABSTRACT FROM AUTHOR]

Published
2014
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33. 3D organization of telomeres in porcine neutrophils and analysis of LPS-activation effect.

Author

Mompart, Florence, Robelin, David, Delcros, Chantal, and Yerle-Bouissou, Martine

Subjects
*NEUTROPHILS, *IMMUNE system, *CELL determination, *MEDICAL research, *CHROMOSOMES
Abstract

Background: While the essential role of 3D nuclear architecture on nuclear functions has been demonstrated for various cell types, information available for neutrophils, essential components of the immune system, remains limited. In this study, we analysed the spatial arrangements of telomeres which play a central role in cell fate. Our studies were carried out in swine, which is an excellent model organism for both biomedical research and agronomic applications. We isolated bacterial artificial chromosome (BAC)-containing subtelomeric p and q sequences specific to each porcine chromosome. This allowed us to study the behaviour of p and q telomeres of homologous chromosomes for seven pairs chosen for their difference in length and morphology. This was performed using 3D-FISH on structurally preserved neutrophils, and confocal microscopy. Resting and lipopolysaccharide (LPS)-activated states were investigated to ascertain whether a response to a pathogen aggression modifies this organization. Results: The positions of the p and q telomeres relative to the nuclear outer border were determined in the two states. All p telomeres changed their position significantly during the activation process, although the effect was less pronounced for the q telomeres. The patterns of telomeric associations between homologs and their frequencies were analysed for 7 pairs of chromosomes. This analysis revealed that the distribution of pp, qq and pq associations differs significantly among the 7 chromosomes. This distribution does not fit with the theoretical distribution for each chromosome, suggesting that preferential associations occur between subtelomeres. Conclusions: The percentage of nuclei harbouring at least one telomeric association between homologs varies significantly among the chromosomes, the smallest metacentric chromosome SSC12, which is also the richest in gene-density, harbouring the highest value. The distribution of types of telomeric associations is highly dependent on the chromosomes and is not affected by the activation process. The frequencies of telomeric associations are also highly dependent on the type of association and the type of chromosome. Overall, the LPS-activation process induces only minor changes in these patterns of associations. When telomeric associations occur, the associations of p and q arms from the same chromosome are the most frequent, suggesting that "chromosome bending" occurs in neutrophils as previously observed in gametes. [ABSTRACT FROM AUTHOR]

Published
2013
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34. Transcriptomic and nuclear architecture of immune cells after LPS activation.

Author

Solinhac, Romain, Mompart, Florence, Martin, Pascal, Robelin, David, Pinton, Philippe, Iannuccelli, Eddie, Lahbib-Mansais, Yvette, Oswald, Isabelle, and Yerle-Bouissou, Martine

Subjects
CELLULAR immunity, GENE expression, NEUTROPHILS, BIODIVERSITY, GENETIC regulation, FLUORESCENCE in situ hybridization, MACROPHAGES
Abstract

Changes in the nuclear positioning of specific genes, depending on their expression status, have been observed in a large diversity of physiological processes. However, gene position is poorly documented for immune cells which have been subjected to activation following bacterial infection. Using a pig model, we focused our study on monocyte-derived macrophages and neutrophils, as they are the first lines of defence against pathogens. We examined whether changes in gene expression due to LPS activation imply that genes have repositioned in the nuclear space. We first performed a transcriptomic analysis to identify the differentially expressed genes and then analysed the networks involved during lypopolysaccharide/interferon gamma activation in monocyte-derived macrophages. This allowed us to select four up-regulated (IL1β, IL8, CXCL10 and TNFα) and four down-regulated (VIM, LGALS3, TUBA3 and IGF2) genes. Their expression statuses were verified by quantitative real-time RT-PCR before studying their behaviour in the nuclear space during macrophage activation by means of 3D fluorescence in situ hybridization. No global correlation was found between gene activity and radial positioning. Only TNFα belonging to the highly transcribed MHC region on chromosome 7 became more peripherally localized in relation to the less decondensed state of its chromosome territory (CT) in activated macrophages. The analysis of gene positioning towards their CT revealed that IL8 increases significantly its tendency to be outside its CT during the activation process. In addition, the gene to CT edge distances increase for the three up-regulated genes (IL8, CXCL10 and TNFα) among the four analysed. Contrarily, the four down-regulated genes did not change their position. The analysis of gene behaviour towards their CT was extended to include neutrophils for three (TNFα, IL8 and IL1β) up- and two (IGF2 and TUBA3) down-regulated genes, and similar results were obtained. The analysis was completed by studying the four up-regulated genes in fibroblasts, not involved in immune response. Our data suggest that relocation in the nuclear space of genes that are differentially expressed in activated immune cells is gene and cell type specific but also closely linked to the entire up-regulation status of their chromosomal regions. [ABSTRACT FROM AUTHOR]

Published
2011
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35. Detecting Local High-Scoring Segments: a First-Stage Approach for Genome-Wide Association Studies.

Author

Guedj, Mickael, Robelin, David, Hoebeke, Mark, Lamarine, Marc, Wojcik, Jerome, and Nuel, Gregory

Subjects
*GENETICS, *EPIDEMIOLOGY, *DISEASES, *GENOMES, *STATISTICS
Abstract

Genetic epidemiology aims at identifying biological mechanisms responsible for human diseases. Genome-wide association studies, made possible by recent improvements in genotyping technologies, are now promisingly investigated. In these studies, common first-stage strategies focus on marginal effects but lead to multiple-testing and are unable to capture the possibly complex interplay between genetic factors. We have adapted the use of the local score statistic, already successfully applied to analyse long molecular sequences. Via sum statistics, this method captures local and possible distant dependences between markers. Dedicated to genome-wide association studies, it is fast to compute, able to handle large datasets, circumvents the the multiple-testing problem and outlines a set of genomic regions (segments) for further analyses. Applied to simulated and real data, our approach outperforms classical Bonferroni and FDR corrections for multiple-testing. It is implemented in a software termed LHiSA for Local High-scoring Segments for Association and available at: http://stat.genopole.cnrs.fr/software/lhisa. [ABSTRACT FROM AUTHOR]

Published
2006
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37. Meiotic Recombination Analyses of Individual Chromosomes in Male Domestic Pigs (Sus scrofa domestica).

Author

Mary, Nicolas, Barasc, Harmonie, Ferchaud, Stéphane, Billon, Yvon, Meslier, Frédéric, Robelin, David, Calgaro, Anne, Loustau-Dudez, Anne-Marie, Bonnet, Nathalie, Yerle, Martine, Acloque, Hervé, Ducos, Alain, and Pinton, Alain

Subjects
*MEIOSIS, *RECOMBINANT DNA, *TELOMERES, *SEX chromosomes, *HOMOLOGOUS chromosomes, *CELL cycle, *SYNAPTONEMAL complexes
Abstract

For the first time in the domestic pig, meiotic recombination along the 18 porcine autosomes was directly studied by immunolocalization of MLH1 protein. In total, 7,848 synaptonemal complexes from 436 spermatocytes were analyzed, and 13,969 recombination sites were mapped. Individual chromosomes for 113 of the 436 cells (representing 2,034 synaptonemal complexes) were identified by immunostaining and fluorescence in situ hybridization (FISH). The average total length of autosomal synaptonemal complexes per cell was 190.3 µm, with 32.0 recombination sites (crossovers), on average, per cell. The number of crossovers and the lengths of the autosomal synaptonemal complexes showed significant intra- (i.e. between cells) and inter-individual variations. The distributions of recombination sites within each chromosomal category were similar: crossovers in metacentric and submetacentric chromosomes were concentrated in the telomeric regions of the p- and q-arms, whereas two hotspots were located near the centromere and in the telomeric region of acrocentrics. Lack of MLH1 foci was mainly observed in the smaller chromosomes, particularly chromosome 18 (SSC18) and the sex chromosomes. All autosomes displayed positive interference, with a large variability between the chromosomes. [ABSTRACT FROM AUTHOR]

Published
2014
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38. Meiotic recombination analyses of individual chromosomes in male domestic pigs (Sus scrofa domestica).

Author

Mary N, Barasc H, Ferchaud S, Billon Y, Meslier F, Robelin D, Calgaro A, Loustau-Dudez AM, Bonnet N, Yerle M, Acloque H, Ducos A, and Pinton A

Subjects
Animals, Male, Chromosomes, Meiosis, Recombination, Genetic, Swine genetics
Abstract

For the first time in the domestic pig, meiotic recombination along the 18 porcine autosomes was directly studied by immunolocalization of MLH1 protein. In total, 7,848 synaptonemal complexes from 436 spermatocytes were analyzed, and 13,969 recombination sites were mapped. Individual chromosomes for 113 of the 436 cells (representing 2,034 synaptonemal complexes) were identified by immunostaining and fluorescence in situ hybridization (FISH). The average total length of autosomal synaptonemal complexes per cell was 190.3 µm, with 32.0 recombination sites (crossovers), on average, per cell. The number of crossovers and the lengths of the autosomal synaptonemal complexes showed significant intra- (i.e. between cells) and inter-individual variations. The distributions of recombination sites within each chromosomal category were similar: crossovers in metacentric and submetacentric chromosomes were concentrated in the telomeric regions of the p- and q-arms, whereas two hotspots were located near the centromere and in the telomeric region of acrocentrics. Lack of MLH1 foci was mainly observed in the smaller chromosomes, particularly chromosome 18 (SSC18) and the sex chromosomes. All autosomes displayed positive interference, with a large variability between the chromosomes.

Published
2014
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