The most comprehensive atlas yet of genetic data on zebrafish has just been released by the multi-national DANIO-CODE consortium. The atlas will help researchers to better study a range of diseases, including cancer, heart disease, and neurodegeneration. It may also help more researchers replace mammal models in their studies.
“This extensive study consolidates all individual datasets into one framework allowing researchers across the world to address questions which could not be addressed by the individual studies,” said Carsten Daub, Associate Professor and Group Leader, Department of Biosciences and Nutrition and Science for Life Laboratory at Karolinska Institute, who led the data integration for this project.
Appearing in Nature Genetics this week, the paper details DNA elements involved in several embryonic stages of development, and improvements to an understanding of the genetic equivalence between zebrafish and mice. The data is available at the DANIO-CODE Data Coordination Center.
This new database adds to the growing number of public resources for omic-related research, including CHOP’s recently released database of cancer somatic mutations, the Breast Cancer Database System (BCDS), and the AlphaFold Protein Structure Database.
The DANIO-CODE consortium includes 27 laboratories, which worked together to catalogue published open-access datasets compensated with newly produced data. It comprises over 140,000 regions of DNA involved in regulating gene expression in zebrafish, which are the second most-used animal model for medical and life sciences research.
The atlas draws on 1,802 samples with millions of data points each and provides the broadest picture of candidate DNA regions for transgenic breeding and genetic research into development and diseases.
The more than 140,000 cis-regulatory elements play roles throughout development, and include classes with distinct features dependent on their activity in time and space. The group mapped topology and chromatin features between regulatory elements active during zygotic genome activation and organogenesis.
In addition, the researchers matched regulatory elements and epigenomic landscapes between the zebrafish and mouse and predicted functional relationships between these models beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.
Zebrafish’s Advantages
Ferenc Mueller, Professor of Developmental Genetics at the University of Birmingham who led this consortium, said, “The cataloguing of genetic information for zebrafish is a significant breakthrough that could underpin some of the most exciting medical and life sciences developments for years to come.”
He added that, “Zebrafish are an incredibly beneficial model for researchers. They are ideal candidates for studying various diseases and disorders because they grow transparently as embryos and have unusual regenerative properties. These properties have already given researchers insights into the human condition.
These fish are also convenient for genetic manipulation, there are wide-ranging genetics resources available (for example, Zebrafish Information Network; ZFIN), and there is high conservation of disease genes and mechanisms between humans and them.
Mueller said, “Now, with our new catalogue, we move one step closer to having a fully realized map from which to overlay with the human genome. This kind of activity will allow researchers around the world to pursue at pace novel treatments, drugs, and a better understanding of the human and animal disease.”
He added, about the consortium, “Professor Boris Lenhard from Imperial College London and Professor Carsten Daub from Karolinska Institute have been instrumental in coordinating over 50 researchers worldwide. The resulting atlas/map is a testament to how a bottom-up initiative for collaborating across borders can achieve impact for the benefit of our research community. The catalogue created by the DANIO-CODE consortium is open access to ensure that researchers can utilize the genetic information for their future studies.”
