1. Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research.
- Author
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Kern C, Wang Y, Xu X, Pan Z, Halstead M, Chanthavixay G, Saelao P, Waters S, Xiang R, Chamberlain A, Korf I, Delany ME, Cheng HH, Medrano JF, Van Eenennaam AL, Tuggle CK, Ernst C, Flicek P, Quon G, Ross P, and Zhou H more...
- Subjects
- Amino Acid Motifs, Animals, Animals, Domestic genetics, Chromatin Immunoprecipitation Sequencing, Enhancer Elements, Genetic genetics, Epigenesis, Genetic, Epigenomics, Genome-Wide Association Study, Mice, Organ Specificity genetics, Phylogeny, Polymorphism, Single Nucleotide, Transcription Factors genetics, Cattle genetics, Chickens genetics, Gene Expression Regulation genetics, Genome genetics, Regulatory Sequences, Nucleic Acid genetics, Swine genetics, Transcription Factors metabolism
- Abstract
Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. The Functional Annotation of Animal Genomes consortium was formed to collaboratively annotate the functional elements in animal genomes, starting with domesticated animals. Here we present an expansive collection of datasets from eight diverse tissues in three important agricultural species: chicken (Gallus gallus), pig (Sus scrofa), and cattle (Bos taurus). Comparative analysis of these datasets and those from the human and mouse Encyclopedia of DNA Elements projects reveal that a core set of regulatory elements are functionally conserved independent of divergence between species, and that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes are also conserved. These datasets represent a unique opportunity for the emerging field of comparative epigenomics, as well as the agricultural research community, including species that are globally important food resources. more...
- Published
- 2021
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