Integrated annotation and analysis of genomic features reveal new functional elements in the developing zebrafish and other models

For the March 2025 Talk of the Monthly Meeting of the #animal-genomics special interest group it is a pleasure to announce Damir Baranasic from MRC, London Institute of Medical Sciences, UK who will introduce the DANIO-CODE project an international collaborative effort that aimed to annotate the functional elements of the zebrafish genome. Zebrafish, a widely used model for studying vertebrate development and human disease, has lacked a comprehensive functional annotation akin to other model organisms. This has limited researchers’ ability to interpret genomic data and design experiments with precision. To address this gap, we established the international DANIO-CODE consortium and developed a central repository (https://danio-code.zfin.org) that integrates 1,802 genomic datasets—both newly generated and reanalysed—to systematically annotate zebrafish developmental regulatory elements. Through this initiative, we constructed the first developmental atlas of zebrafish cis-regulatory elements (CREs), functionally categorised via chromatin-based genome segmentation and visualised using dimensionality reduction of epigenetic profiles. These efforts revealed novel classes of functional elements and uncovered substantial heterogeneity in regulatory profiles across the zebrafish developmental time course. We distinguished two major enhancer classes—early and late—based on chromatin and conservation signatures. We also extended the regulatory annotation to adult zebrafish tissues, discovering that many adult CREs represent repurposed embryonic elements with altered functional roles. Building upon these results, we also contributed to the AQUA-FAANG consortium, participating in the functional annotation of commercially important fish species to define cis-regulatory landscapes in common carp, Atlantic salmon, and rainbow trout using the same standardised methodology and principles developed in DANIO-CODE. Additionally, we produced and analysed new CAGE datasets across diverse vertebrate species, which cover all major evolutionary clades, to annotate promoters and systematically characterise conserved and lineage-specific transcriptional features. Together, these efforts illuminate the regulatory genome in model and non-model vertebrates, facilitating applications in evolutionary biology, aquaculture, and functional genomics. Our integrated annotation framework significantly enhanced the utility of model animal research and served as a foundation for broader cross-species regulatory genomics.