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Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig
Sylvain Foissac
1
Sarah Djebali
1
Kylie Munyard
2
Nathalie Vialaneix
3
Andrea Rau
4
Kévin Muret
5
Diane Esquerré
1
Matthias Zytnicki
3
Thomas Derrien
6
Philippe Bardou
1
Fany Blanc
4
Cédric Cabau
1
Elisa Crisci
4
Sophie Dhorne-Pollet
4
Françoise Drouet
7
Ignacio González
3
Adeline Goubil
4
Sonia Lacroix-Lamandé
7
Fabrice Laurent
7
Sylvain Marthey
4
Maria Marti-Marimon
1
Raphaëlle Momal-Leisenring
4
Florence Mompart
1
Pascale Quéré
7
David Robelin
1
Magali San Cristobal
1
Gwenola Tosser-Klopp
1
Silvia Vincent-Naulleau
8
Stéphane Fabre
1
Marie-Helene Pinard - van der Laan
4
Christophe Klopp
3
Michele Tixier-Boichard
4
Hervé Acloque
4, 1
Sandrine Lagarrigue
5
Elisabetta Giuffra
4
8
iRCM
Sylvain Foissac 1
Author IdHAL : sylvainfoissac ORCID : https://orcid.org/0000-0002-2631-5356
Sarah Djebali 1
Author
Kylie Munyard 2
Author
Nathalie Vialaneix 3
Author IdHAL : nathalie-vialaneix ORCID : https://orcid.org/0000-0003-1156-0639
Andrea Rau 4
Author IdHAL : andrea-rau ORCID : https://orcid.org/0000-0001-6469-488X
Kévin Muret 5
Author
Diane Esquerré 1
Author
Matthias Zytnicki 3
Author
Thomas Derrien 6
Author IdHAL : derrien-thomas ORCID : https://orcid.org/0000-0002-8211-5789
Philippe Bardou 1
Author IdHAL : philippe-bardou ORCID : https://orcid.org/0000-0002-0004-0251
Fany Blanc 4
Author IdHAL : fany-blanc
Cédric Cabau 1
Author Employer institution : Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement IdHAL : cedric-cabau ORCID : https://orcid.org/0000-0001-8560-4003
Elisa Crisci 4
Author
Sophie Dhorne-Pollet 4
Author IdHAL : sophie-pollet ORCID : https://orcid.org/0000-0002-6722-0003
Françoise Drouet 7
Author
Ignacio González 3
Author
Adeline Goubil 4
Author
Sonia Lacroix-Lamandé 7
Author IdHAL : sonia-lamande ORCID : https://orcid.org/0000-0002-7865-4587
Fabrice Laurent 7
Author IdHAL : falaurent ResearcherId : http://www.researcherid.com/rid/AAC-2266-2019 ORCID : https://orcid.org/0000-0002-9687-7952
Sylvain Marthey 4
Author
Maria Marti-Marimon 1
Author
Raphaëlle Momal-Leisenring 4
Author IdHAL : raphaelle-momal ORCID : https://orcid.org/0000-0002-1550-4530
Florence Mompart 1
Author
Pascale Quéré 7
Author
David Robelin 1
Author IdHAL : david-robelin IdRef : https://www.idref.fr/095136576 ISNI : http://isni.org/isni/0000000358341417
Magali San Cristobal 1
Author
Gwenola Tosser-Klopp 1
Author IdHAL : gwenola-tosser ORCID : https://orcid.org/0000-0003-0550-4673
Silvia Vincent-Naulleau 8
Author
Stéphane Fabre 1
Author IdHAL : stephane-fabre ORCID : https://orcid.org/0000-0001-7350-9500
Marie-Helene Pinard - van der Laan 4
Author IdHAL : marie-helene-pinard-van-der-laan ORCID : https://orcid.org/0000-0003-4992-8726
Christophe Klopp 3
Author IdHAL : 0000-0001-7126-5477 ORCID : https://orcid.org/0000-0001-7126-5477
Michele Tixier-Boichard 4
Author IdHAL : michele-tixier-boichard ORCID : https://orcid.org/0000-0001-5944-7884
Hervé Acloque 4, 1
Author IdHAL : herve-acloque ORCID : https://orcid.org/0000-0003-4761-1055
Sandrine Lagarrigue 5
Author Employer institution : AGROCAMPUS OUEST
Elisabetta Giuffra 4
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
Curtin University [Perth] (GPO Box U1987, Perth WA 6845 - Australia)
- PATREC - Planning and Transport Research Centre (University of western Australia - Australia)
3
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)
4
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)
5
PEGASE - Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (16, le Clos 35590 Saint-Gilles - France)
- INRA - Institut National de la Recherche Agronomique : UMR1348 (France)
- AGROCAMPUS OUEST (Institut Supérieur des Sciences Agronomiques, Agroalimentaires, Horticoles et du Paysage - 65, rue de St Brieuc - CS 84215 - 35042 Rennes cedex - France)
6
IGDR - Institut de Génétique et Développement de Rennes (Faculté de Médecine - CS 34317 2 Av du Professeur Léon Bernard 35043 Rennes Cedex - France)
- UR1 - Université de Rennes 1 (2 rue du Thabor - CS 46510 - 35065 Rennes cedex - France)
- UNIV-RENNES - Université de Rennes (France)
- CNRS - Centre National de la Recherche Scientifique : UMR6290 (France)
- Biosit : Biologie - Santé - Innovation Technologique - Structure Fédérative de Recherche en Biologie et Santé de Rennes (Université Rennes 1 - Campus Santé Villejean - 2, avenue Professeur Léon Bernard 35043 Rennes cedex - France)
7
UMR ISP - Infectiologie et Santé Publique (INRA 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)
8
iRCM (France)
- CEA - Commissariat à l'énergie atomique et aux énergies alternatives (Centre de Saclay Centre de Grenoble Centre de Cadarache etc - France)
Abstract : 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.
Document type :
Preprints, Working Papers, ...
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https://hal.inrae.fr/hal-02791029
Contributor : Migration Prodinra <>
Submitted on : Friday, June 5, 2020 - 7:08:09 AM
Last modification on : Thursday, May 6, 2021 - 2:21:16 PM
Contributor : Migration Prodinra <>
Submitted on : Friday, June 5, 2020 - 7:08:09 AM
Last modification on : Thursday, May 6, 2021 - 2:21:16 PM
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Foissac_Preprint_2018_1.pdf
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Distributed under a Creative Commons Attribution 4.0 International License
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- HAL Id : hal-02791029, version 1
- DOI : 10.1101/316091
- PRODINRA : 441070
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INRAE | INRA | INSMI | AGROCAMPUS-OUEST | UNAM | IGDR | UNIV-RENNES1 | CEA | BIOSIT | UR1-UFR-SVE | AGROPARISTECH | AGROCAMPUS-OUEST-UMR-PEGASE | UNIV-RENNES | UNIV-TOURS | CNRS | GS-BIOSPHERA
Citation
Sylvain Foissac, Sarah Djebali, Kylie Munyard, Nathalie Vialaneix, Andrea Rau, et al.. Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig. 2018. ⟨hal-02791029⟩
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