From Cells to Sight: A Systematic Review of Functional Genomics in Zebrafish Ocular Development and Disease Models

This project provides a systematic, critical synthesis of zebrafish ( Danio rerio ) ocular functional genomics, with a particular emphasis on single-cell, spatial, and perturbation-based approaches that resolve gene function at cellular and tissue resolution. Zebrafish have become a central vertebrate model for eye research due to their conserved ocular architecture, optical transparency, regenerative capacity, and amenability to high-throughput genetics. In parallel, recent advances in single-cell and spatial genomics have transformed our ability to map cell states, regulatory programs, and lineage trajectories in both development and disease. However, the rapid expansion of these datasets has outpaced efforts to integrate findings, evaluate methodological rigor, and assess translational relevance to human ocular disorders. The primary purpose of this project is to systematically review, curate, and critically evaluate zebrafish ocular functional genomics studies published through July 2025, following PRISMA 2020 guidelines and a prospectively registered protocol. By integrating data across tissues, developmental stages, perturbation types, and disease contexts, this work aims to clarify what has been robustly established, where inconsistencies or biases persist, and how zebrafish-based discoveries can more effectively inform human eye biology and disease mechanisms. Scope and Scientific Rationale The review encompasses all major ocular compartments, including the retina, retinal pigment epithelium (RPE), lens, cornea, anterior segment, optic nerve, and whole-eye profiling. It captures studies spanning embryonic development, adult homeostasis, regeneration, and pathological contexts such as inherited retinal degeneration, glaucoma-like models, cataract, refractive error, metabolic stress, and toxicant exposure. Eligible studies include single-cell and single-nucleus RNA sequencing, chromatin accessibility and multiome assays, spatial transcriptomics, CRISPR-based perturb-seq screens, enhancer and regulatory assays (CUT&Tag, CUT&RUN, MPRA), and lineage-tracing approaches. A central rationale of the project is that zebrafish functional genomics occupies a unique translational niche. Teleost-specific gene duplications provide opportunities to dissect paralog-specific functions, while conserved cell types and transcriptional programs—particularly in photoreceptors and Müller glia—enable meaningful cross-species comparisons with mammalian and human datasets. Increasingly, zebrafish models are used to functionally interpret human disease-associated variants, yet the extent to which these insights are validated in mammalian systems remains unclear. This project directly addresses that gap. Expected Outcomes and Deliverables 1. A curated, authoritative resource summarizing zebrafish ocular single-cell and functional genomics studies, including standardized descriptors of tissues, cell types, perturbations, and disease relevance. 2. Identification of conserved and robust transcriptional and regulatory programs, highlighting areas of strong convergence across studies as well as unresolved discrepancies. 3. A critical assessment of translational validity, documenting how frequently zebrafish-derived hypotheses are tested in mammalian models and where gaps remain. 4. Evaluation of methodological quality and reproducibility, including data availability, analytical transparency, and common sources of bias. 5. A forward-looking roadmap that prioritizes emerging strategies—such as spatial perturb-seq, enhancer editing, and systematic allele knock-ins—to accelerate causal inference and therapeutic discovery in ocular disease research. Broader Impact By consolidating fragmented literature into a unified, critical framework, this project will serve as a reference point for researchers in vision science, genomics, and translational biology. It aims to guide experimental design, promote reproducible and open science practices, and strengthen the role of zebrafish as a bridge between molecular perturbation, cell-state resolution, and clinically relevant ocular disease mechanisms. Ultimately, the work is intended to accelerate the translation of functional genomics insights into diagnostic and therapeutic advances for blinding eye diseases.