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Profiling the landscape of transcription, chromatin accessibility and chromosome conformation of cattle, pig, chicken and goat genomes [FAANG pilot project]

Foissac, Sylvain and Djebali Quelen, Sarah and Acloque, Hervé and Bardou, Philippe and Blanc, Fany and Cabau, Cédric and Derrien, Thomas and Drouet, Françoise and Esquerré, Diane and Fabre, Stéphane and Gaspin, Christine and GONZALEZ, Ignacio and Goubil, Adeline and Klopp, Christophe and Laurent, Fabrice and Marthey, Sylvain and Marti Marimon, Maria Eugenia and Mompart, Florence and Munyard, Kylie and Muret, Kévin and Pollet, Sophie and Quéré, Pascale and Rau, Andrea and Robelin, David and San Cristobal, Magali and Tixier-Boichard, Michele and Tosser, Gwenola and Villa-Vialaneix, Nathalie and Vincent-Naulleau, Silvia and Zytnicki, Matthias and Pinard - Van Der Laan, Marie-Helene and Lagarrigue, Sandrine and Giuffra, Elisabetta Profiling the landscape of transcription, chromatin accessibility and chromosome conformation of cattle, pig, chicken and goat genomes [FAANG pilot project]. (2017) In: 36th International Society for Animal Genetics Conference, 17 July 2017 - 21 July 2017 (Dublin, Ireland). (Unpublished)

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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.

Item Type:Conference or Workshop Item (Other)
ProdINRA Id:403710
Audience (conference):International conference without published proceedings
Uncontrolled Keywords:
Institution:French research institutions > Institut National de la Recherche Agronomique - INRA (FRANCE)
Université de Toulouse > Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE)
Laboratory name:
Funders:
FR-AgENCODE
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Deposited On:31 Mar 2020 08:53

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