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    • Transcriptome and chromatin structure annotation of liver, CD4+ and CD8+ T cells from four livestock species

    bioRxiv (Cold Spring Harbor Laboratory)（2019）

    GenPhySE

    Cited 14|Views37
    Abstract
    Background 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 () 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). 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 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. * DE : Differentially Expressed FAANG : Functional Annotation of Animal Genomes lncRNA : long non-coding RNA mRNA : messenger RNA PE : Paired-End polyA : polyAdenylation RT-PCR : Reverse Transcriptase Polymerase Chain Reaction TAD : Topological Associating Domain TF : Transcription Factor TFBS : Transcription Factor Biding Site TPM : Transcript Per Million TSS : Transcription Start Site TTS : Transcription Termination Site
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