As IIMCB, we are proud to be part of the international DANIO-CODE consortium led by Profs. Ferenc Muller (University of Birmingham, UK), Boris Lenhard (Imperial College London, UK), and Carsten Daub (Karolinska Institute, Sweden).
The DANIO-CODE is a community effort which aims to annotate the functional elements in the genome of the zebrafish (Danio rerio), a well-established model organism for studying development of diseases.
The consortium was formed to create a centralized resource for zebrafish functional genomics dataset across the community. The DANIO-CODE repository contains more than 1800 published and unpublished datasets which has been re-analyzed using standard pipelines in order to improve the current annotation of the zebrafish genome. The first study of the consortia was published in Nature Genetics at the beginning of July, in which Maciej Łapiński and Cecilia Winata from the IIMCB’s Laboratory of Zebrafish Developmental Genomics were listed as co-authors. Their dataset on early embryonic zebrafish transcriptome contributed to the analyses which reported the identification of over 140,000 cis-regulatory elements with their spatiotemporal activity across development. The study also characterized the dynamic chromatin landscape which contributed to regulating the activity of these regulatory elements in various developmental processes. This regulatory landscape was compared to that of the mouse, which revealed conserved functional relationship and principles of gene regulation across evolution.
The DANIO-CODE study represents a breakthrough for biomedical sciences for a number of reasons. Firstly, the rich annotation resource will significantly increase the utility of the zebrafish – the second most utilized model organism after the mouse – for studying various aspects of human biology and disease. Secondly, the increased availability of zebrafish genomic data across various biological context will enable cross-comparison between systems, which will facilitate the interpretation of results obtained in zebrafish and further translate them into clinical applications in humans. Lastly, this study establishes the groundwork for further efforts in increasing the resolution of functional annotation of the zebrafish genome to progressively close the knowledge gap with mammalian model systems.