Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig.

Foissac, S.; Djebali, S.; Munyard, K.; Villa-Vialaneix, N.; Rau, A.; Muret, K.; Esquerre, D.; Zytnicki, M.; Derrien, T.; Bardou, P.; Blanc, F.; Cabau, C.; Crisci, E.; Dhorne-Pollet, S.; Drouet, F.; Gonzales, I.; Goubil, A.; Lacroix-Lamande, S.; Laurent, F.; Marthey, S.; Marti-Marimon, M.; Momal-Leisenring, R.; Mompart, F.; Quere, P.; Robelin, D.; San Cristobal, M.; Tosser-Klopp, G.; Vincent-Naulleau, S.; Fabre, S.; Pinard-Van der Laan, M.-H.; Klopp, C.; Tixier-Boichard, M.; Acloque, H.; Lagarrigue, S.; Giuffra, E.

doi:10.1101/316091

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bioRxiv · 10.1101/316091

Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig.

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Abstract

BackgroundFunctional 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 (http://www.fragencode.org) aimed to profile the landscape of transcription (RNA-seq), chromatin accessibility (ATAC-seq) and conformation (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).\n\nResultsRNA-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.\n\nConclusionsWe 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 pressure shaping genome organization from birds to mammals. Overall, these results emphasize the value of FAANG for research on domesticated animals and reinforces the importance of future meta-analyses of the reference datasets being generated by this community on different species.

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Foissac, S., Djebali, S., Munyard, K., Villa-Vialaneix, N., Rau, A., Muret, K., Esquerre, D., Zytnicki, M., Derrien, T., Bardou, P., Blanc, F., Cabau, C., Crisci, E., Dhorne-Pollet, S., Drouet, F., Gonzales, I., Goubil, A., Lacroix-Lamande, S., Laurent, F., Marthey, S., Marti-Marimon, M., Momal-Leisenring, R., Mompart, F., Quere, P., Robelin, D., San Cristobal, M., Tosser-Klopp, G., Vincent-Naulleau, S., Fabre, S., Pinard-Van der Laan, M.-H., Klopp, C., Tixier-Boichard, M., Acloque, H., Lagarrigue, S., Giuffra, E.. 2018-05-11. Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig.. https://doi.org/10.1101/316091

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