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INRA
24, chemin de Borde Rouge –Auzeville – CS52627
31326 Castanet Tolosan CEDEX - France

Dernière mise à jour : Mai 2018

Menu Logo Principal AgroParisTech Université Paris-Saclay

INRA GABI Unit

GABI : Génétique Animale et Biologie IntégrativeUnité Mixte de Recherche INRA - AgroParisTech

Launching of the FR-AgENCODE project

Launching of the FR-AgENCODE project
The aim of the FR-AgENCODE project is to improve the functional annotation of the genomes of farm animals by producing and analyzing high-throughput sequencing data. This project is part of FAANG (Functional Annotation of ANimal Genomes, Andersson et al, Genome Biol, 2015, www.faang.org), implicating approximately fifty INRA employees (9 laboratories, 4 research centers and 4 research divisions) beginning with the functional anaysis of the genomes of four species (pigs, chickens, goats, catttle).

Context and stakes

Identifying the functional elements of farm animal genomes is a crucial step for the association of genotype and phenotype and in order to exploit genetic variability. Within this context and that of an international project comparable to ENCODE in humans (FAANG: wwww.faang.org), the INRA launched the pilot project FR-AgENCODE aimed at producing and analyzing high-throughput molecular data in order to better characterize genomes important for agronomy. Thus, the project includes sample analysis (hepatic and immune cells) collected from animals of different species (pigs, chickens, goats, catttle) by RNA-seq experiments and the characterization of the structure of chromatin (Hi-C, ATAC-seq). This project, financed within the framework of the SelGen metaprogram and built around international partnerships, will allow positioning INRA at the center of the FAANG consortium, contributing to a fundamental scientific production. 

Results

The project began at the beginning of 2015 and has provided the following:

- the sampling and storing in a bio-bank (CRB-Anim) of the tissues collected from four animal species (pigs, chickens, goats, catttle). 
- the development of new high-throughput molecular phenotyping techniques: the study of the 3D conformation of chromatin (Hi-C) and its accessibility (ATAC-seq), analysis of long and short transcripts (RNA-seq on a Hiseq3000 sequencer).
- the development of bioinformatic analysis pipelines from the data produced.
- the recruiting of an Agreenskills post-doctoral bioinoformatics scientist from the ENCODE project (S. Djebali, from the CRG Barcelona).
- the on site participation of a guest scientist (K. Munyard, University of Curtin, Australia).

- INRA's implication in the FAANG international initiative may be translated by the presence of four INRA "White paper" authors and the implication of our agents in the different committees of the consortium.

- An ANR grant (MRSEI) for the preparation of a European infrastructure project within the framework of FAANG. 

Perspectives

On the short term, the different tools developed and analysis pipelines done in 2015 will allow us to characterize the genomic activity of different samples (hepatic tissues and immune cells) taken from four different species. This includes the identification of long coding transcripts for proteins, short and long non-coding transcripts, 3D conformation of chromatin and its accessibility. The results will help define a multi-species map of the functional elements in livestock. Particular attention will be paid to the standardization of protocoles so that we may obtain such results. At the long term, these studies will be applied to other tissues and other functional elements of the genomes (histone and DNA methylation markers, regulating factor fixation, etc), with all being associated with genome polymorphisms. These studies will be performed in partnership with members of the FAANG international consortium with which we are members.

Valorisation

White paper : Andersson et al, Genome Biol, 2015 16:57, www.faang.org
GO-FAANG workshop – 7-8 oct 2015, Washington, USA :
- The Functional Annotation of ANimal Genomes (FAANG) initiative (presentation par E. Giuffra)
- Sampling tissues for FAANG, the example of cattle and chickens in France (Tixier-Boichard et al.), poster.
- Long non coding RNA repertoire in chicken liver and adipose tissue (Muret et al.), poster.

References

Andersson et al, 2015, "Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project", Genome Biology, 16:57