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Poster communications
Profiling the landscape of transcription, chromatin accessibility and chromosome conformation of cattle, pig, chicken and goat genomes [FAANG pilot project]
Sylvain Foissac
1, *
Sarah Djebali Quelen
1
Hervé Acloque
1
Philippe Bardou
1
Fany Blanc
2
Cédric Cabau
1
Thomas Derrien
2
Françoise Drouet
3
Diane Esquerre
4
Stéphane Fabre
1
Christine Gaspin
5
Ignacio Gonzalez
5
Adeline Goubil
2
Christophe Klopp
5
Fabrice Laurent
3
Sylvain Marthey
2
Maria Marti-Marimon
1
Florence Mompart
1
Kylie Munyard
1
Kévin Muret
6
Sophie Pollet
2
Pascale Quéré
3
Andrea Rau
2
David Robelin
1
Magali San Cristobal
4
Michele Tixier-Boichard
2
Gwenola Tosser-Klopp
1
Nathalie Villa-Vialaneix
5
Silvia Vincent-Naulleau
2
Matthias Zytnicki
5
Marie-Helene Pinard - van der Laan
2
Sandrine Lagarrigue
6
Elisabetta Giuffra
2
*
Corresponding author
Sylvain Foissac 1
Correspondent author
Sarah Djebali Quelen 1
Author
Hervé Acloque 1
Author IdHAL : herve-acloque ORCID : https://orcid.org/0000-0003-4761-1055
Philippe Bardou 1
Author IdHAL : philippe-bardou ORCID : https://orcid.org/0000-0002-0004-0251
Fany Blanc 2
Author
Cédric Cabau 1
Author IdHAL : cedric-cabau ORCID : https://orcid.org/0000-0001-8560-4003
Thomas Derrien 2
Author IdHAL : derrien-thomas ORCID : https://orcid.org/0000-0002-8211-5789
Françoise Drouet 3
Author
Diane Esquerre 4
Author
Stéphane Fabre 1
Author IdHAL : stephane-fabre ORCID : https://orcid.org/0000-0001-7350-9500
Christine Gaspin 5
Author IdHAL : 0000-0003-0304-5186 ORCID : https://orcid.org/0000-0003-0304-5186
Ignacio Gonzalez 5
Author
Adeline Goubil 2
Author
Christophe Klopp 5
Author IdHAL : 0000-0001-7126-5477 ORCID : https://orcid.org/0000-0001-7126-5477
Fabrice Laurent 3
Author
Sylvain Marthey 2
Author
Magali San Cristobal 4
Author
Michele Tixier-Boichard 2
Author
Gwenola Tosser-Klopp 1
Author IdHAL : gwenola-tosser ORCID : https://orcid.org/0000-0003-0550-4673
Nathalie Villa-Vialaneix 5
Author IdHAL : nathalie-vialaneix ORCID : https://orcid.org/0000-0003-1156-0639
Silvia Vincent-Naulleau 2
Author
Matthias Zytnicki 5
Author
Marie-Helene Pinard - van der Laan 2
Author
Sandrine Lagarrigue 6
Author Employer institution : AGROCAMPUS OUEST
Elisabetta Giuffra 2
Author IdHAL : elisabetta-giuffra ORCID : https://orcid.org/0000-0001-9568-2056
1
GenPhySE - Génétique Physiologie et Systèmes d'Elevage (INRA Auzeville -
24, chemin de Borde-Rouge -
Auzeville Tolosane
31326 Castanet Tolosan
- France)
- ENVT - Ecole Nationale Vétérinaire de Toulouse (23 chemin des Capelles
31076 Toulouse
Cedex - France)
- Toulouse INP - Institut National Polytechnique (Toulouse) (France)
- Université Fédérale Toulouse Midi-Pyrénées (41 Allée Jules Guesde, 31000 Toulouse - France)
- Toulouse INP - Institut National Polytechnique (Toulouse) (France)
- INRA - Institut National de la Recherche Agronomique : UMR1388 (France)
- École nationale supérieure agronomique de Toulouse [ENSAT] (France)
2
GABI - Génétique Animale et Biologie Intégrative (Domaine de Vilvert F-78252 Jouy-en-Josas - France)
- INRA - Institut National de la Recherche Agronomique : UMR1313 (France)
- AgroParisTech (16 rue Claude Bernard F-75231 Paris Cedex 05 - France)
3
UMR ISP - Infectiologie et Santé Publique (37380 Nouzilly - France)
- INRA - Institut National de la Recherche Agronomique : UMR1282 (France)
- Université de Tours (60 rue du Plat d'Étain, 37020 Tours cedex 1 - France)
4
DYNAFOR - Dynamiques Forestières dans l'Espace Rural (France)
- INRA - Institut National de la Recherche Agronomique : UR1201 (France)
- École nationale supérieure agronomique de Toulouse [ENSAT] (France)
- Toulouse INP - Institut National Polytechnique (Toulouse) (France)
- Université Fédérale Toulouse Midi-Pyrénées (41 Allée Jules Guesde, 31000 Toulouse - France)
5
MIAT INRA - Unité de Mathématiques et Informatique Appliquées de Toulouse (Chemin de Borde Rouge, 31320 Castanet Tolosan - France)
- INRA - Institut National de la Recherche Agronomique : UR875 (France)
6
PEGASE - Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (Domaine de la Prise 35590 Saint-Gilles - France)
- AGROCAMPUS OUEST (Institut Supérieur des Sciences Agronomiques, Agroalimentaires, Horticoles et du Paysage - 65, rue de St Brieuc - CS 84215 - 35042 Rennes cedex - France)
- INRA - Institut National de la Recherche Agronomique : UMR1348 (France)
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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Poster communications
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https://hal.archives-ouvertes.fr/hal-01608449
Contributor : Archive Ouverte Prodinra <>
Submitted on : Tuesday, June 2, 2020 - 2:51:36 PM
Last modification on : Friday, February 26, 2021 - 11:00:03 AM
Long-term archiving on: : Wednesday, December 2, 2020 - 2:39:28 PM
Contributor : Archive Ouverte Prodinra <>
Submitted on : Tuesday, June 2, 2020 - 2:51:36 PM
Last modification on : Friday, February 26, 2021 - 11:00:03 AM
Long-term archiving on: : Wednesday, December 2, 2020 - 2:39:28 PM
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- PRODINRA : 403710
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Sylvain Foissac, Sarah Djebali Quelen, Hervé Acloque, Philippe Bardou, Fany Blanc, et al.. Profiling the landscape of transcription, chromatin accessibility and chromosome conformation of cattle, pig, chicken and goat genomes [FAANG pilot project]. 36th International Society for Animal Genetics Conference, Jul 2017, Dublin, Ireland. 2017, ISAG 2017 - Genomes to Phenomes - Abstract Book. ⟨hal-01608449⟩
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