Integrative annotation of genomic features reveal functional elements and epigenetic landscapes in the developing zebrafish
Despite being a popular model for embryonic development and diseases, zebrafish have lacked systematic functional annotation programmes seen in other animal models. To address this, we formed the international DANIO-CODE consortium and created the first central repository to store and process zebrafish functional genomic data. Our Data Coordination Center (https://danio-code.zfin.org) combines a total of 1802 sets of unpublished and reanalysed published genomics data, with which we improve existing annotations and show its usefulness in experimental design. We define over 140,000 cis-regulatory elements and decribe novel classes with distinct features depending on time and space of activity. We delineate the difference between regulatory elements active during zygotic genome activation and those active during organogenesis, identifying new aspects of their relatedness. Finally, we match regulatory elements between zebrafish and mouse and predict functional relationships between them beyond sequence similarity, extending the utility of zebrafish developmental genomics to mammals.