Breakthrough Zebrafish Genome Database Now Available

Researchers now completed the largest zebrafish genome atlas to date, opening up new avenues for biomedical research. Zebrafish, while they are a popular model organism for research due to their transparent embryo growth and unusual regenerative properties, have lacked a systematic and functional annotation database similar to other model animals.

The international DANIO-CODE consortium was founded to address this issue, and it has created a centralized repository to store and analyze zebrafish developmental genomic data. This research published in Nature Genetics pinpointed over 140,000 cis-regulatory elements throughout zebrafish’s development, traced development-related chromatin features, and improved genetic understanding between zebrafish and mammals (mice).

“Now, with our new catalogue, we move one step closer to having a fully realised 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,” said author Ferenc Mueller, Professor of Developmental Genetics at the University of Birmingham.

Related article: Massive Human CRISPR-Based Genotype-Phenotype Map Is Now Complete

Zebrafish Are Ideal for Disease Research

Zebrafish in genomic studies have led to the discovery of chromatin signatures, promoters usages of DNA codes, regulatory patterns of DNA methylation, and post-transcriptional messenger RNA regulation. Single-cell analysis of zebrafish pioneered the usages for spatially resolving lineage-specific transcriptomes accrued during development.

The DANIO-CODE alliance was established at Imperial College London in December 2014, after members of the zebrafish genomics research community and previous contributors to ENCODE and FANTOM genome annotation projects identified new aims, this latest study is accessible at https://danio-code.zfin.org/. 

366 datasets were generated by consortium members to fill existing knowledge gaps and to aid functional annotation and functional element characterization, these include 15 CAGE-seq, 18 ChIP–seq, 11 ATAC-seq, 2 Hi-C, and 320 4C-seq datasets. The team said the resulting datasets represent a holistic annotation of the zebrafish genome during normal embryonic development, addressing urgent demands of numerous research depending on zebrafish’s embryonic and larval stages.

They also mapped transcription activities in 16 developmental stages, resulting in 16,303 genes and 4,070 novel promoters. To supplement the promoterome with cis-regulatory sites, researchers curated 581 regulatory motifs representing 814 zebrafish transcription factors (TFs) and predicted binding sites for these motifs across every promoter. The utility of these functional annotations extends well beyond zebrafish development, this research will expand and complement the existing ongoing mapping efforts in mammals as well.

Author

Fujie Tham