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Multi-species annotation of transcriptome and chromatin structure in domesticated animals

Sylvain Foissac 1, * Sarah Djebali 1 Kylie Munyard 2 Nathalie Vialaneix 3 Andrea Rau 4 Kévin Muret 5 Diane Esquerre 1, 6 Matthias Zytnicki 3 Thomas Derrien 7, 8 Philippe Bardou 1 Fany Blanc 4 Cédric Cabau 1 Elisa Crisci 4 Sophie Dhorne-Pollet 4 Françoise Drouet 9 Thomas Faraut Ignacio González 3 Adeline Goubil 4 Sonia Lacroix-Lamandé 9 Fabrice Laurent 9 Sylvain Marthey 4 Maria Marti-Marimon 1 Raphaëlle Momal-Leisenring 4 Florence Mompart 1 Pascale Quéré 9 David Robelin 1 Magali San Cristobal 1 Gwenola Tosser-Klopp 1 Silvia Vincent-Naulleau 10, 11 Stéphane Fabre 1 Marie-Hélène Pinard-van Der Laan 4 Christophe C. Klopp 3 Michèle Tixier-Boichard 4 Hervé Acloque 4, 1 Sandrine Lagarrigue 5 Elisabetta Giuffra 4, * 
Abstract : Background: Comparative genomics studies are central in identifying the coding and non-coding elements associated with complex traits, and the functional annotation of genomes is a critical step to decipher the genotype-to-phenotype relationships in livestock animals. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aimed to create reference functional maps of domesticated animals by profiling the landscape of transcription (RNA-seq), chromatin accessibility (ATAC-seq) and conformation (Hi-C) in 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). Results: RNA-seq assays considerably extended the available catalog of annotated transcripts and identified differentially expressed genes with unknown function, including new syntenic lncRNAs. ATAC-seq highlighted an enrichment for transcription factor binding sites in differentially accessible regions of the chromatin. Comparative analyses revealed a core set of conserved regulatory regions across species. Topologically associating domains (TADs) and epigenetic A/B compartments annotated from Hi-C data were consistent with RNA-seq and ATAC-seq data. Multi-species comparisons showed that conserved TAD boundaries had stronger insulation properties than species-specific ones and that the genomic distribution of orthologous genes in A/B compartments was significantly conserved across species. Conclusions: We report the first multi-species and multi-assay genome annotation results obtained by a FAANG project. Beyond the generation of reference annotations and the confirmation of previous findings on model animals, the integrative analysis of data from multiple assays and species sheds a new light on the multi-scale selective (Continued on next page)
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Sylvain Foissac, Sarah Djebali, Kylie Munyard, Nathalie Vialaneix, Andrea Rau, et al.. Multi-species annotation of transcriptome and chromatin structure in domesticated animals. BMC Biology, BioMed Central, 2019, 17 (1), 25 p. ⟨10.1186/s12915-019-0726-5⟩. ⟨hal-02437599⟩

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