Annotation of cis-regulatory elements in adult zebrafish and comparison with embryonic cis-regulatory elements.
Cis-regulatory elements (CREs) regulate the differential expression of developmental genes, which are crucial for determining cell fate and guiding the formation of various tissues and organs. Despite significant progress in the functional annotation of the zebrafish genome, the scarcity of integrated genomic resources limits our understanding of how the dynamics of functional elements drive organ morphogenesis and maintain adult physiological functions. Building upon the zebrafish genomic resources contributed by the DANIO-CODE consortium, we aimed to expand existing developmental resources to integrated resources spanning from embryonic stages to adulthood by incorporating published genomic data obtained from eleven adult zebrafish tissues. We re-annotated the adult CREs using published data of chromatin feature and integrated them into the DANIO-CODE repository, generating an integrative atlas of functional elements with publicly accessible track hub. We identified co-option and functional changes in CREs between embryos and adults, suggesting that candidate adult CREs represent a widespread reutilization of embryonic elements with a considerable shift in regulatory functions. We generated sets of curated promoters for adult brain, heart, intestine, liver, skin, testis tissues by introducing the transcription start sites mapped by CAGE-seq to provide more reliable active promoters. This study provides integrated transcriptional regulatory repertoire from embryos to adults, which will offer mechanistic insights into the underlying growth mechanisms of zebrafish and provide useful resources to study the impact of dynamic CREs on tissue differentiation or potential adult tissue regeneration.