Zebrafish regulatory genomic resources for disease modelling and regeneration

Abstract

In the past decades, the zebrafish has become a disease model with increasing popularity owing to its advantages that include fast development, easy genetic manipulation, simplicity for imaging, and sharing conserved disease-associated genes and pathways with those of human. In parallel, studies of disease mechanisms are increasingly focusing on non-coding mutations, which require genome annotation maps of regulatory elements, such as enhancers and promoters. In line with this, genomic resources for zebrafish research are expanding, producing a variety of genomic data that help in defining regulatory elements and their conservation between zebrafish and humans. Here, we discuss recent developments in generating functional annotation maps for regulatory elements of the zebrafish genome and how this can be applied to human diseases. We highlight community-driven developments, such as DANIO-CODE, in generating a centralised and standardised catalogue of zebrafish genomics data and functional annotations; consider the advantages and limitations of current annotation maps; and offer considerations for interpreting and integrating existing maps with comparative genomics tools. We also discuss the need for developing standardised genomics protocols and bioinformatic pipelines and provide suggestions for the development of analysis and visualisation tools that will integrate various multiomic bulk sequencing data together with fast-expanding data on single-cell methods, such as single-cell assay for transposase-accessible chromatin with sequencing. Such integration tools are essential to exploit the multiomic chromatin characterisation offered by bulk genomics together with the cell-type resolution offered by emerging single-cell methods. Together, these advances will build an expansive toolkit for interrogating the mechanisms of human disease in zebrafish.

Novel MIP gene mutation causes autosomal-dominant congenital cataract

“…To further verify how this novel MIP G29R mutation causes congenital cataract and whether it is a loss-of-function or a gain-of-function mutation, we constructed a human PCS2+MIP G29R plasmid, which was microinjected into zebrafish embryos to observe lens development (Figure 12). Zebrafish is functionally similar to humans and is genetically highly conserved [53][54][55] . The whole genome of zebrafish has been sequenced (http://zebrafish.org/home/guide.php), and its genome is approximately 87% homologous of the human genome [56][57] .…”