SRA

Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. Here we present a genome-wide annotation of regulatory elements in a non-mammalian vertebrate, chicken (Gallus gallus), as well as two important agricultural mammalian species: pig (Sus scrofa) and cattle (Bos taurus), with chicken and pig in particular being important to human biology and medicine. This report is the first to employ all core assays as defined by the Functional Annotation of Animal Genomes (FAANG) consortium, including information from a wide range of epigenomic assays for the same eight diverse tissues of three livestock species. Comparative analysis of these datasets and those from the human and mouse ENCODE projects revealed that although less than half of enhancers are positionally conserved between species, a core set of regulatory elements are functionally conserved independent of evolutionary distance. Further analysis suggested that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes were also conserved. Interestingly, the smaller chicken genome – relative to mammals – contains a reduced number of enhancers; however, each chicken enhancer targets more genes, on average, compared to their mammalian counterparts suggesting higher versatility. These datasets and corresponding analysis represent a unique opportunity for the emerging field of comparative epigenomics, as well as animal and human biology and medical research involving species that are globally important food resources. Overall design: H3K4me1 ChIP-seq in 8 tissues from 3 livestock species (2 adult male replicates per species)