Transcriptome profiling of zebrafish optic fissure fusion

• Published in: Scientific reports Vol. 9; no. 1; p. 1541
• Main Authors: Richardson, R., Owen, N., Toms, M., Young, Rodrigo M., Tracey-White, D., Moosajee, M.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 07-02-2019; Nature Publishing Group
• Subjects: 38/32; 38/39; 38/91; 631/136; 631/337/2019; 64/116; 692/699/3161/3164; Animals; Antisense RNA; Blindness; Children; Cluster Analysis; Coloboma - genetics; Coloboma - metabolism; Coloboma - pathology; Danio rerio; Disease Models, Animal; DNA-Binding Proteins - antagonists & inhibitors; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; Embryo, Nonmammalian - metabolism; Fertilization; Gene expression; Gene Expression Profiling - methods; Humanities and Social Sciences; Hybridization; In Situ Hybridization, Fluorescence; Morphogenesis; Morpholinos - metabolism; multidisciplinary; Netrin-1; Netrin-1 - genetics; Netrin-1 - metabolism; Phenotypes; Principal Component Analysis; Retina; Retina - metabolism; Science; Science (multidisciplinary); Tissue analysis; Transcriptome; Zebrafish - genetics; Zebrafish - growth & development; Zebrafish - metabolism; Zebrafish Proteins - antagonists & inhibitors; Zebrafish Proteins - genetics; Zebrafish Proteins - metabolism
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-018-38379-5

Incomplete fusion of the optic fissure leads to ocular coloboma, a congenital eye defect that affects up to 7.5 per 10,000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before (32 hours post fertilisation, hpf), during (48 hpf) and after (56 hpf) optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT-PCR analysis and localisation investigated using
in situ
hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a (
ntn1a)
as highly differentially expressed across optic fissure fusion, with a resultant ocular coloboma phenotype following morpholino antisense translation-blocking knockdown and downstream disruption of
atoh7
expression. To support the identification of candidate genes in human studies, we have generated an online open-access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma.