Ensembl’s regulatory annotation for human, mouse, livestock, and aquaculture species

Abstract Ensembl has long provided cis-regulatory annotation for human and mouse to support biomedical research, but comparable resources have been lacking for livestock and aquaculture species. In collaboration with Functional Annotation of Animal Genomes (FAANG) projects, we have redesigned and extended Ensembl’s regulatory build to provide consistent annotation across ten key species. The new build (http://regulation.ensembl.org) identifies promoters, enhancers, unclassified open chromatin regions, and, in some species, CTCF binding sites. We demonstrate its value and highlight limitations with the β-globin locus in human and the Myh7 locus in mouse, and illustrate how it reveals tissue-specific regulatory features using pig as an example.